Conditions: Dysentery, Bacillary
Keywords: Challenge Efficacy Shigellosis Vaccination
Allocation: RANDOMIZED | Intervention model: PARALLEL
Enrollment: 71
Healthy volunteers: yes

Brief summary:
The purpose of this study is to evaluate the efficacy, safety and immunogenicity of the GSK3536852A vaccine, which was designed to protect against shigellosis caused by Shigella sonnei (S. sonnei) and is using the new Generalized Modules for Membrane Antigens (GMMA) platform technology developed by GlaxoSmithKline (GSK) Vaccines Institute for Global Health (GVGH).

The study vaccine could be the stepping stone for the development of a multivalent broadly protective Shigella vaccine for vaccination of impoverished communities where shigellosis is endemic. However, a standalone monovalent vaccine against S. sonnei could be used to protect travelers against diarrheal shigellosis, as the vast majority of travelers' shigellosis is caused by S. sonnei, and even to protect infants in endemic regions where shigellosis is primarily caused by S. sonnei.

The GSK3536852A vaccine has been tested in two Phase I dose escalation studies in Europe to assess its safety and immunogenicity via three routes of administration: intramuscular (IM), intranasal (IN) and intradermal (ID). The results from the first study (dose escalation with IM vaccination) have shown that the vaccine has an acceptable safety profile and is well-tolerated up to a dose of 100 micrograms (µg). The results from the second study (dose escalation with ID, IN and IM vaccination) showed that GSK3536852A vaccine is well-tolerated also when administered by the ID and IN routes of vaccination. However, immunogenicity data have shown that GSK3536852A vaccine administered by the ID and IN routes is not as immunogenic as GSK3536852A vaccine administered by the IM route. Therefore, it has been decided to proceed with the clinical development program of this vaccine only using the IM vaccination route. In terms of dosage, the regimen tested in Phase I studies (three doses given one month apart) did not show any significant benefit from the third dose in terms of immunogenicity, therefore a two dose schedule was selected for next studies.

A Phase IIa study, conducted in endemic regions of Africa (i.e., Kenya), has been completed and confirmed the acceptable safety profile and immunogenicity of GSK3536852A vaccine.

Performing this vaccine-human challenge study may give the opportunity to establish evidence of clinical protection induced by the candidate S. sonnei vaccine (GSK3536852A vaccine) at an early development stage.

Detailed description:
The original study protocol has been amended due to requests from the Food and Drug Administration (FDA), requests from the funder of the study, Bill \& Melinda Gates Foundation (BMGF), to add an additional interim analysis for immunogenicity data that will accelerate the release of key results to help the planning of other studies, and to further align the protocol to other GSK studies and to the challenge model established at the Cincinnati Children's Hospital Medical Centre.

Arms:
arm 1: Male or female subjects between, and including, 18 and 50 years of age at the time of the first vaccination, received 2 doses of the S. sonnei study vaccine at Day 1 and Day 29 respectively, by intramuscular injection into the upper deltoid region of the non-dominant arm. At 28 days after the second dose (Day 57), subjects received the challenge dose of S. sonnei 53G strain, orally. arm 2: Male or female subjects between, and including, 18 and 50 years of age at the time of the first vaccination, received 2 doses of the placebo at Day 1 and Day 29 respectively, by intramuscular injection into the upper deltoid region of the non-dominant arm. At 28 days after the second dose (Day 57), subjects received the challenge dose of S. sonnei 53G strain, orally.

Interventions: intervention 1: S.sonnei vaccine intervention 2: Placebo intervention 3: S. sonnei 53G challenge strain
Intervention descriptions: intervention 1: Subjects receiving 2 doses of the study vaccine by intramuscular route, 28 days apart (at Day 1 and Day 29). intervention 2: Subjects receiving 2 doses of placebo by intramuscular route, 28 days apart (at Day 1 and Day 29). intervention 3: Subjects receiving the challenge dose of S. sonnei 53G strain, orally, at Day 57.

Protocol document:
Prot_000.pdf: 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
1
Clinical Study Protocol
Sponsor:
GlaxoSmithKline Biologicals SA
Rue de l’Institut 89,
1330, Rixensart, Belgium
Primary Study vaccine and 
number
!
GlaxoSmithKline (GSK) Vaccines Institute for 
Global Health (GVGH) Shigella sonnei GMMA 
vaccine (GVGH S. sonnei 1790GAHB vaccine), 
property of GSK Biologicals.
Other Study products
!
GAHB-Placebo (control and diluent in the bedside
mixing).
!
Shigella sonnei 53G (challenge strain developed 
by the Walter Reed Army Institute of Research 
[WRAIR], Silver Spring, Maryland, USA)
referred to as the challenge agent.
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003
[H03_03TP])
Investigational New Drug 
(IND) number
IND18163
Date of protocol
Final: 12 December 2017
Date of protocol amendment Amendment 1 Final: 08 February 2018
Amendment 2 Final: 22 June 2019
Amendment 3 Final: 07 September 2019
Amendment 4 Final: 19 February 2019
Amendment 5 Final: 15 April 2019
Amendment 6 Final: 23 July 2019
Title
Efficacy, safety and immunogenicity of GVGH 
Shigella sonnei vaccine (1790GAHB) in a human 
challenge study of healthy non-immune adults.
Detailed Title
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population.
Coordinating authors
, 
, Scientific Writers
(XPE Pharma & Science for GSK Biologicals)

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
1
23-JUL-2019
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
2
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Investigational New Drug 
(IND) number
IND18163
Detailed Title
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population.
Contributing authors
!
, GVGH Head of 
Clinical Development and Regulatory Affairs 
!
, Project Physician
!
, 
, 
Biostatisticians
!
, GVGH Clinical Research 
Associate
!
, GVGH Head of Clinical 
Operations
!
, Clinical Laboratory Sciences 
Read-out Team Leader
!
, 
, 
, 
Clinical Laboratory Sciences Study Managers
!
, 
, GVGH 
Serology Representatives (Scientific Technical 
Leaders)
!
, 
, Safety 
Physician, Safety Evaluation and Risk 
Management team
!
, Safety Scientist, Safety 
Evaluation and Risk Management team
!
, Oversight Data Manager
!
, GVGH Head of Regulatory 
Affairs
!
, Global Patent Affairs Manager
GSK Biologicals’ Protocol DS for Legacy Novartis programs v 1.0
©2017-2019 GlaxoSmithKline group of companies or its licensor.

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
2
23-JUL-2019
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
3
Protocol Amendment 6 Sponsor Signatory Approval
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003
[H03_03TP])
Investigational New Drug 
(IND) number
IND18163
Date of protocol amendment
Amendment 6 Final: 23 July 2019
Detailed Title 
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population
Sponsor signatory
Audino Pietro Mario Podda,
GVGH Head of Clinical Development and 
Regulatory Affairs
Signature
Date
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
3
23-JUL-2019
- ----------------Checksum----------------!Ver.!Created On -  - 
5889c076f178fb77b7f8644dc83edbbe4030715b 2.0 7/26/2019 10:04:04 AM -  - 
----------------------------------------------------------------------------
For internal use only
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
4
Protocol Amendment 6 Rationale
Amendment number:
Amendment 6
Rationale/background for changes:

To add an additional interim analysis for immunogenicity data, which will allow a
faster interpretation of study results and planning of subsequent follow-up studies.

To correct an error in the definitions of dysentery and more severe shigellosis, and
align these definitions to other CHIM studies; oral temperature ≥ 38.0°C (fever) is
added to the definitions.

To correct an error in the primary completion date of the study.

To clarify the different applicable case definitions of dysentery in the study.

To provide clarification in the study design by showing the inpatient stay in the
study design figure as per the Schedule of Activities table.

To specify the allowed time interval window for the blood draw that occurs during
the inpatient stay.

To specify the assay used for the α4β7 plasmablast analysis as measuring both
positive and negative cells by ELISA, and not using flow cytometry.

To change the assay used for HLA-B27 testing from PCR to qualitative flow
cytometry.
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
4
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
5
Protocol Amendment 6 Investigator Agreement
I agree:

To conduct the study in compliance with this protocol, any future protocol 
amendments or protocol administrative changes, with the terms of the clinical trial 
agreement and with any other study conduct procedures and/or study conduct 
documents provided by GlaxoSmithKline (GSK) Biologicals.

To assume responsibility for the proper conduct of the study at this site.

That I am aware of, and will comply with, ‘Good Clinical Practice’ (GCP) and all 
applicable regulatory requirements.

To ensure that all persons assisting me with the study are adequately informed about 
the GSK Biologicals’ study vaccine/placebo and challenge agent and other study-
related duties and functions as described in the protocol and that bedside mixing at 
the study site will be performed according to GSK Biologicals instructions only by 
trained site staff with appropriate qualification required by local regulations.

To acquire the reference ranges for laboratory tests performed locally and, if required 
by local regulations, obtain the laboratory’s current certification or Quality 
Assurance procedure manual.

To ensure that no clinical samples (including serum samples) are retained onsite or 
elsewhere without the approval of GSK Biologicals and the express written informed 
consent of the subject.

To perform no other biological assays on the clinical samples except those described 
in the protocol or its amendment(s).

To co-operate with a representative of GSK Biologicals in the monitoring process of 
the study and in resolution of queries about the data.

That I have been informed that certain regulatory authorities require the sponsor to 
obtain and supply, as necessary, details about the investigator’s ownership interest in 
the sponsor or the investigational vaccine, and more generally about his/her financial 
ties with the sponsor. GSK Biologicals will use and disclose the information solely 
for the purpose of complying with regulatory requirements.
Hence I:

Agree to supply GSK Biologicals with any necessary information regarding 
ownership interest and financial ties (including those of my spouse and dependent 
children).

Agree to promptly update this information if any relevant changes occur during the 
course of the study and for one year following completion of the study.

Agree that GSK Biologicals may disclose any information it has about such 
ownership interests and financial ties to regulatory authorities.

Agree to provide GSK Biologicals with an updated Curriculum Vitae and other 
documents required by regulatory agencies for this study.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
5
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
6
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003
[H03_03TP])
IND number
IND18163
Date of protocol amendment
Amendment 6 Final: 23 July 2019
Detailed Title
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population
Investigator name
Signature
Date
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
6
23-JUL-2019
- ----------------Checksum----------------!Ver.!Created On -  - 
5889c076f178fb77b7f8644dc83edbbe4030715b 2.0 7/26/2019 10:04:04 AM -  - 
----------------------------------------------------------------------------
For internal use only
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
7
Sponsor Information
1.
Sponsor
GlaxoSmithKline Biologicals
Rue de l’Institut 89,
1330 Rixensart, Belgium
2.
Sponsor Medical Expert for the Study
Refer to the local study contact information document.
3.
Sponsor Study Monitor
Refer to the local study contact information document.
4.
Sponsor Study Contact for Reporting of a Serious Adverse Event
GSK Biologicals Central Back-up Study Contact for Reporting SAEs: refer to protocol 
Section 9.4.2.
5.
GSK Biologicals’ Central Safety Physician On-Call Contact information for 
Emergency Unblinding
GSK Biologicals Central Safety Physician and Back-up Phone contact: refer to
protocol Section 9.8.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
7
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
8
SYNOPSIS
Detailed Title
A phase IIb, randomized, placebo-controlled, single center, 
observer-blind, human-challenge study to evaluate the 
efficacy, safety and immunogenicity of 2 vaccinations with 
GVGH Shigella sonnei vaccine (1790GAHB) administered by 
intramuscular route in healthy non-immune adult population.
Indication
The targeted indication of the vaccine is the prevention of 
moderate to severe diarrheal disease caused by Shigella 
sonnei (S. sonnei).
Rationale for the 
study and study 
design

Rationale for the study
GSK Vaccines Institute for Global Health (GVGH) has 
developed a vaccine against S. sonnei (1790GAHB vaccine) 
using the new Generalized Modules for Membrane Antigens 
(GMMA) platform technology.
The study vaccine could be the stepping stone for the 
development of a multivalent broadly protective Shigella 
vaccine for vaccination of impoverished communities where 
shigellosis is endemic. However, a standalone monovalent 
vaccine against S. sonnei could be used to protect travelers
against diarrheal shigellosis, as the vast majority of travelers’
shigellosis is caused by S. sonnei, and even to protect infants 
in endemic regions where shigellosis is primarily caused by 
S. sonnei.
The 1790GAHB vaccine has been tested in two Phase I dose 
escalation studies in Europe to assess its safety and 
immunogenicity via three routes of administration: 
intramuscular (IM), intranasal (IN) and intradermal (ID). The 
results from the first study (dose escalation with IM 
vaccination) have shown that the vaccine has an acceptable 
safety profile and is well-tolerated up to a dose of 100 µg. 
Additionally, the serologic assessment showed that one dose 
of 1.5/25 µg OAg/protein of 1790GAHB vaccine elicits 
serum immunoglobulin G (IgG) anti-S sonnei
lipopolysaccharide (LPS) levels ≥ 121 enzyme-linked 
immunosorbent assay (ELISA) units/mL (EU/mL) (i.e., 
median antibody titer in a panel of 87 Israeli convalescent 
subjects after natural infection by S. sonnei). The results from 
the second study (dose escalation with ID, IN and IM 
vaccination) showed that 1790GAHB vaccine is well-
tolerated also when administered by the ID and IN routes of 
vaccination. However, immunogenicity data have shown that 
1790GAHB vaccine administered by the ID and IN routes is 
not as immunogenic as 1790GAHB vaccine administered by 
the IM route.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
8
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
9
Therefore, it has been decided to proceed with the clinical 
development program of this vaccine only using the IM 
vaccination route. In terms of dosage, the regimen tested in 
Phase I studies (three doses given one month apart) did not 
show any significant benefit from the third dose in terms of 
immunogenicity, therefore a two dose schedule was selected 
for next studies. A Phase IIa study, conducted in endemic 
regions of Africa (i.e., Kenya), has just been completed and 
confirmed the acceptable safety profile and immunogenicity 
of 1790GAHB vaccine.
Performing a vaccine-human challenge study may give the 
opportunity to establish evidence of clinical protection 
induced by the candidate S. sonnei vaccine (1790GAHB 
vaccine) at an early development stage.

Rationale for the study design
A human challenge model of S. sonnei disease for vaccine 
testing was established in Thailand [Bodhidatta, 2012] and 
showed an attack rate (AR) of 75% in non-immune adult 
volunteers receiving a challenge dose of 1680 colony forming 
units (CFU) of S. sonnei strain 53G. Clinical and laboratory 
endpoints of infection and disease, namely diarrhea, 
dysentery, fever and shedding of S. sonnei in stools were used 
to calculate the AR and thus to establish the optimal infective 
dose. In a subsequent study though [Pitisuttithum, 2016], the 
AR in the control group, using this model, was much less than 
previously published.
Given this variability, before starting a vaccine-challenge 
study, the proposed human challenge model of S. sonnei to be 
used has been appropriately developed and the challenge dose 
and AR reliably established by the Cincinnati Children’s 
Hospital Medical Center (CCHMC) (Ohio, United States of 
America). The current GSK vaccine-human challenge study 
will be conducted at CCHMC and will use the developed 
challenge model. Volunteers will be treated after development 
of symptoms of shigellosis.

Rationale for the use of placebo
As currently there is no widely available vaccine against 
shigellosis, the efficacy and safety of the 1790GAHB vaccine 
will be evaluated against a placebo. The placebo is used to 
better describe the safety profile of the S. sonnei vaccine as 
well as its efficacy in terms of clinical protection against 
shigellosis caused by S. sonnei.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
9
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
10
Objectives
Primary

To demonstrate the efficacy of two vaccinations with 
25 µg of 1790GAHB vaccine in healthy adults compared 
to placebo (reduction of shigellosis according to the 
protocol primary case definition, i.e. Shedding of S. 
sonnei 53G accompanied by moderate or severe diarrhea, 
OR shedding with an oral temperature of 38.5°C after 
challenge with S. sonnei strain 53G).
Criterion:
Vaccine efficacy (VE) of 1790GAHB vaccine will be 
shown if the lower limit (LL) of the 90% confidence 
interval (CI) of VE will be above zero.
Secondary
Efficacy

To determine the efficacy of the 1790GAHB vaccine 
compared to placebo against:

Shigellosis as defined by the Controlled Human 
Infection Model (CHIM) expert working group on 
case definition.*

Shigellosis, as defined by: severe diarrhea OR 
moderate diarrhea with fever or with one or more 
moderate constitutional/enteric symptoms OR 
dysentery [[ ≥2 loose stools with gross blood 
(hemoccult positive) in 24 hours] AND [≥1 
reportable constitutional/enteric symptom]].

More severe shigellosis, as defined by: severe or
moderate diarrhea with fever or with one or more 
severe constitutional/enteric symptoms OR dysentery 
[[≥2 loose stools with gross blood (hemoccult 
positive) in 24 hours] AND [oral temperature ≥ 
38.0°C OR ≥1 severe constitutional/enteric 
symptom]]. (Amended: 23 July 2019)

Shedding of S. sonnei strain 53G.

Severe diarrhea.

More severe diarrhea.

Dysentery.

Weight of all grade 3-5 stools.

Total number of all grade 3-5 stools.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
10
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
11

Confirmed S. sonnei 53G shedding AND moderate 
or severe diarrhea OR dysentery OR presence of oral 
temperature 38.5°C OR presence of one or more 
severe intestinal symptoms (abdominal pain, 
cramping, nausea, vomiting, gas, and anorexia).

Disease not fulfilling the protocol primary case 
definition for shigellosis associated or not with mild 
to moderate symptoms including: passing loose stool 
(not meeting the protocol definition of moderate or 
severe diarrhea), abdominal pain, abdominal cramps, 
gas, anorexia, nausea, headache, myalgia, malaise,
arthralgia, fever, vomiting and IV fluid 
administration.

Time to onset of shigellosis according to the primary 
case definition after challenge.
*According to the working group, the participant must fulfil 
any one of the three following possible endpoints to qualify as 
having reached the CHIM case definition for this objective:
1.
Severe diarrhea defined as [6 loose stools in 24 hours] 
OR [˃800 grams loose stools in 24 hours] 
2.
Moderate diarrhea defined as [4-5 loose stools in 24 
hours OR 400-800 grams loose stools in 24 hours] AND 
[oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of 
vomiting in 24 hours] 
3.
Dysentery defined as [2 loose stools with gross blood 
(hemoccult positive) in 24 hours] AND [oral temperature 
38.0oC OR 1 moderate constitutional/enteric symptom 
OR 2 episodes of vomiting in 24 hours].
Safety

To assess the safety and reactogenicity of the 1790GAHB 
vaccine in terms of solicited adverse events, unsolicited 
adverse events, serious adverse events (SAEs), adverse 
events of special interest (AESI) and laboratory 
parameters.

To assess safety after challenge in terms of SAEs, 
unsolicited adverse events, AESI, and laboratory 
parameters.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
11
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
12
Immunogenicity

To evaluate the IgG ELISA immunogenicity profile of 
the 1790GAHB vaccine at 7 days and 28 days after the 
first and second vaccination (IgG ELISA coated with 
OAg containing LPS).

To evaluate the immunogenicity profile of the 
1790GAHB vaccine at pre-challenge and at 7 and 28 days 
after challenge (IgG ELISA coated with OAg containing 
LPS).

Number and percentage of seroresponders for anti-S. 
sonnei LPS at 28 days after first and second vaccination.

To assess anti- S.sonnei LPS concentration ≥ 121 EU/ml 
at 28 days after first and second vaccination. 
Tertiary
The following tertiary objectives, which are part of the study 
exploratory objectives may be evaluated in addition to the 
primary and secondary objectives and will complement 
assessment of the vaccine immunogenicity profile:

Evaluate S. sonnei specific secretory immunoglobulin A
(sIgA) in stool at Day 1 and 7 days after first and second 
vaccination and 7 days after challenge (Day 64).

Evaluate S. Sonnei LPS IgG-specific α4β7+/-
plasmablast response at Day 1 and 7 days after first and 
second vaccination and 7 days after challenge (Day 64).
(Amended: 23 July 2019)

Evaluate serum bactericidal activity against S. sonnei at 
Day 1 and 28 days after first and second vaccination.

Evaluate correlation between serum anti-S. sonnei LPS 
IgG level, serum bactericidal activity titer, shigellosis, 
shedding, mild, moderate, severe or more severe diarrhea, 
and dysentery after challenge.

Evaluate glycosylation of fragment crystallisable (Fc) 
portion of IgG antibodies at Day 1 and 28 days after 
second vaccination and association with clinical 
protection and/or serological endpoints.

Evaluate inflammatory response from stools collected 
before challenge at Visit 5 (Day 57) and daily, post 
challenge, during inpatient stay (Day 57 to Day 64).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
12
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
13

Evaluate gene expression signatures at Day 1 and 7 days 
after first and second vaccination and 7 days after 
challenge (Day 64).

Investigate gut microbiome at Day 1 and 28 days after 
second vaccination and its potential association with 
protection and immune response.
Study design

Experimental design: Phase IIb, observer-blind, 
randomized, placebo-controlled, mono-centric study with 
two parallel groups.

Duration of the study:

Epoch 001: Starting at Screening Visit (Day -45 to 
Day -1) and ending before Visit 1 (Day 1).

Epoch 002: Starting the day of randomization and 
first vaccination (Visit 1) and ending before the 
receipt of the challenge agent, 28 days after second 
vaccination (Visit 5).

Epoch 003: Starting with the receipt of the challenge 
agent at 28 days after second vaccination (Visit 5) 
and ending 6 months after challenge (Visit 8).

Primary completion date (PCD): Visit 5 (Day 64).
(Amended: 23 July 2019)

End of Study (EoS): Last testing results released of 
samples collected for primary and secondary objectives at 
Visit 8.

Study groups:
Synopsis Table 1
Study groups and epochs foreseen in the study
Study 
groups
Number of 
subjects
Age (Min - Max)
Epochs
Epoch 001
Epoch 002
Epoch 003
Screening
1st and 2nd vaccination
Challenge
S. sonnei
36
18 years – 50 years
x
x
x
Placebo
36
18 years – 50 years
x
x
x
Synopsis Table 2
Study groups and treatment foreseen in the study
Treatment name
Vaccine/placebo/
challenge agent name
Study Groups
S. sonnei
Placebo
S. sonnei
1790GAHB
x
Placebo
GAHB-Placebo
x
Challenge
S. sonnei 53G strain
x
x
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
13
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
14

Control: Placebo control with GAHB-Placebo with the 
same composition as the vaccine except the active 
ingredient. GAHB-Placebo will also be used as diluent 
for bedside mixing of the vaccine.

Vaccination schedule: Subjects will receive 2 doses of 
either the study vaccine or placebo 28 days apart. At 28 
days after the second dose, all subjects will receive the 
challenge dose.

Treatment allocation: Following the screening period 
before the first vaccination (Day -45 to Day -1), 
subjects will be randomized in a 1:1 ratio to receive 
either the study vaccine or the placebo.

Blinding: The study will be observer-blind.
Synopsis Table 3
Blinding of study epochs
Study Epochs
Blinding
Screening (Epoch 001)
N/A
1st and 2nd vaccination (Epoch 002)
observer-blind
Challenge (Epoch 003)
observer-blind

Sampling schedule:

5 mL for hematology: Screening Visit, Visit 2, 
Visit 3, Visit 4, Visit 5 and Visit 8. 
Additionally, hematology is repeated weekly 
until resolution if neutropenia occurs.

5 mL for biochemical analysis: Screening 
Visit.

10 mL for hepatitis B, hepatitis C and HIV: 
Screening Visit.

10 mL for HLA-B27 testing: Screening Visit.

5 mL for local anti S. sonnei LPS IgG 
Screening-ELISA: Screening Visit.

Urine sample for urinalysis: Screening Visit 
and Visit 5.

Urine sample for pregnancy test for women of 
childbearing potential: Screening Visit, Visit 1, 
Visit 3, Visit 5 and Visit 8.

20 mL for immunological tests (antibody 
response) at Visit 1, Visit 2, Visit 3, Visit 4, 
Visit 5, 7 days after Visit 5 (Day 64), Visit 6,
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
14
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
15

For serum bactericidal activity tests at Visit 1, 
Visit 3 and Visit 5

And for Fc glycosylation test on leftover serum 
samples collected at Visit 1 and Visit 5.

50 mL of peripheral venous blood for α4β7+/-
plasmablast analysis by ELISA and RNA 
extraction from peripheral blood mononuclear 
cells (PBMC) for gene expression profiling: 
Visit 1, Visit 2, Visit 4 and 7 days after Visit 5 
(Day 64). (Amended: 23 July 2019)

Stool sample for inflammatory response before 
challenge at Visit 5 (Day 57) and daily, post 
challenge, during inpatient stay (Day 57 to Day 
64).

Stool sample: for microbiome testing at Visit 1 
and Visit 5, for S. sonnei specific sIgA at Visit 
1, Visit 2, Visit 4 and 7 days after challenge 
(Day 64) and stool analysis, culture and qPCR 
daily during inpatient stay (from Visit 5 to 7 
days after challenge [Day 57 to Day 64] or 
prolonged until 2 consecutive negative stool 
samples if subject still shedding).

Type of study: self-contained.

Data collection: Standardized electronic Case 
Report Form (eCRF).

Safety monitoring:
An Independent Data Monitoring Committee 
(IDMC) will be established to monitor the safety of 
subjects throughout the study. The IDMC will 
review unblinded data, to assess safety signals and 
make recommendations to the Sponsor concerning 
continuation, termination, or other modifications of 
the study based on the observed adverse effects. 
The membership and roles of the IDMC will be 
outlined in the IDMC charter.
The safety review team (SRT) will monitor the 
safety of subjects throughout the study. The SRT 
will review blinded data, assess safety signals and 
make recommendations to the IDMC and to the 
Sponsor concerning continuation, termination, or 
other modifications of the study based on the 
observed adverse effects.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
15
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
16
A dedicated Safety Management Plan will be 
prepared to ensure appropriate safety reporting 
responsibilities and roles are defined.
Case definitions
Stools will be graded as follows: Grade 1: firm formed; 
Grade 2: soft formed; Grade 3: viscous opaque liquid or 
semi-liquid which assumes the shape of the bowl; Grade 
4: watery opaque liquid; Grade 5: clear watery or 
mucoid liquid.
Diarrhea
For the purpose of this study, diarrhea is defined as:

Moderate diarrhea: 4 to 5 loose or watery (Grade 3 
to 5) stools or 400 to 800 grams of Grade 3 to 5 
stools within 24 hours.

Severe diarrhea: 6 or more loose or watery (Grade 3 
to 5) stools or > 800 grams of Grades 3 to 5 stools 
within 24 hours or required medical intervention. In
case of severe diarrhea, medical intervention is 
defined as intravenous (IV) fluids administration or 
anticipation of antibiotic treatment before the 5th
day after challenge.

More severe diarrhea: 10 or more loose or watery
(Grade 3 to 5) stools or 1000 grams of Grade 3 to 
5 stools within 24 hours.
Dysentery (Amended: 23 July 2019)
For the purpose of the endpoint “Rate of shigellosis as 
defined by the CHIM expert working group occurring 
within a period starting with challenge visit and 
lasting until the end of the inpatient stay, in all 
subjects”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult 
positive) in 24 hours AND [oral temperature 
≥38.0oC OR ≥1 moderate constitutional/enteric 
symptom OR ≥2 episodes of vomiting in 24 hours]. 
In this case constitutional/enteric symptom are the 
following: nausea, abdominal pain, abdominal 
cramping, myalgia, arthralgia, malaise.
For the purpose of the endpoint “Rate of shigellosis, 
as defined by: severe diarrhea OR moderate diarrhea 
with fever or with one or more moderate 
constitutional/enteric symptoms OR dysentery”, 
dysentery is defined as follows:
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
16
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
17

At least 2 loose stools with gross blood (hemoccult 
positive) in 24 hours AND [≥1 reportable 
constitutional/enteric symptom]. In this case 
constitutional/enteric symptom are the following: 
headache, fatigue, arthralgia, malaise, myalgia, 
chills, nausea, abdominal cramping, abdominal 
pain, gas, anorexia, vomiting.
For the purpose of the endpoint “Rate of more severe 
shigellosis as defined by: severe or moderate diarrhea 
with fever or with one or more severe 
constitutional/enteric symptom OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature ≥38.0oC OR ≥1 severe 
constitutional/enteric symptom]].”, dysentery is 
defined as follows:

At least 2 loose stools with gross blood (hemoccult 
positive) in 24 hours] AND [oral temperature 
≥38.0oC OR ≥1 severe constitutional/enteric 
symptom]. In this case constitutional/enteric 
symptom are the following: headache, fatigue, 
arthralgia, malaise, myalgia, chills, nausea, 
abdominal cramping, abdominal pain, gas, 
anorexia, vomiting.
For the purpose of the endpoints “Dysentery” and 
“Confirmed S. sonnei 53G shedding AND moderate or 
severe diarrhea OR dysentery OR presence of oral 
temperature ≥ 38.5°C OR presence of one or more 
severe intestinal symptoms (abdominal pain, 
cramping, nausea, vomiting, gas, and anorexia)”, 
dysentery is defined as follows:
A Grade 3, 4, or 5 stool with gross blood on at least 2 
occasions within 24 hours and presence of 
constitutional/enteric symptoms. In this case, 
constitutional/enteric symptoms consist of headache, 
fatigue, arthralgia, malaise, myalgia, chills, nausea, 
abdominal cramping, abdominal pain, gas, anorexia, 
vomiting, and fever.
[Amended: 23 July 2019)
Shigellosis
For the primary and secondary objectives in the 
challenge phase of the study, the protocol primary case 
definition for shigellosis is:
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
17
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
18

Shedding of S. sonnei 53G accompanied by 
moderate or severe diarrhea OR shedding with an 
oral temperature of 38.5°C. 
For the secondary objectives in the challenge phase of 
the study, 2 definitions of shigellosis are used:
1.
CHIM working group case definition for shigellosis 
as defined by any one of the three following 
possible endpoints:

Severe diarrhea defined as [6 loose stools in 
24 hours] OR [˃800 grams loose stools in 24 
hours]

Moderate diarrhea defined as [4-5 loose stools 
in 24 hours OR 400-800 grams loose stools in 
24 hours] AND [oral temperature 38.0oC OR 
1 moderate constitutional/enteric symptom 
OR 2 episodes of vomiting in 24 hours]  

Dysentery defined as [2 loose stools with 
gross blood (hemoccult positive) in 24 hours] 
AND [oral temperature 38.0°C OR 1 
moderate constitutional/enteric symptom OR 
2 episodes of vomiting in 24 hours].
2.
Shigellosis as defined by any one of the three 
following possible endpoints:

Severe diarrhea defined as [≥6 loose stools in 
24 hours OR ˃800 grams loose stools in 24 
hours]

Moderate diarrhea defined as [4-5 loose stools 
in 24 hours OR 400-800 grams loose stools in 
24 hours] AND [oral temperature ≥38.0oC OR 
≥1 moderate constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with 
gross blood (hemoccult positive) in 24 hours] 
AND [≥1 reportable constitutional/enteric 
symptom].
For the secondary objectives in the challenge phase of 
the study, more severe shigellosis is defined by any one 
of the two following possible endpoints:

Moderate OR severe diarrhea [≥4 loose stools 
in 24 hours OR ≥400 grams loose stools in 24 
hours] AND [oral temperature ≥38.0oC OR ≥1 
severe constitutional/enteric symptom].
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
18
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
19

Dysentery defined as [≥2 loose stools with 
gross blood (hemoccult positive) in 24 hours] 
AND [oral temperature ≥38.0oC OR ≥1 severe 
constitutional/enteric symptom]. (Amended: 23
July 2019)
Number of subjects
Target enrolment is approximately 72 subjects (36 per 
treatment group).
Endpoints
Primary
Efficacy
VE will be evaluated with:

Rate of shigellosis (fulfilling the protocol primary 
case definition) occurring within a period starting 
with the challenge visit and lasting up to the end of 
the inpatient stay, in all subjects.
Secondary
Efficacy
VE, in subjects receiving the 1790GAHB vaccine vs. 
placebo, will be also measured during inpatient stay 
(Day 57 to Day 64) against:

Rate of shigellosis as defined by the CHIM 
working group case definition for shigellosis) 
occurring within a period starting with challenge 
visit and lasting until the end of the inpatient stay, 
in all subjects. (Amended: 23 July 2019)

Rate of shigellosis, as defined by: severe diarrhea 
OR moderate diarrhea with fever or with one or 
more moderate constitutional/enteric symptom OR 
dysentery [[≥2 loose stools with gross blood 
(hemoccult positive) in 24 hours] AND [≥1 
reportable constitutional/enteric symptom]].

Rate of more severe shigellosis as defined by: 
severe or moderate diarrhea with fever or with one 
or more severe constitutional/enteric symptom OR 
dysentery [[≥2 loose stools with gross blood 
(hemoccult positive) in 24 hours] AND [oral 
temperature ≥ 38.0°C OR ≥1 severe 
constitutional/enteric symptom]]. (Amended: 23
July 2019)
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
19
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
20

Shedding of S. sonnei strain 53G. 
Shedding of S. sonnei strain 53G is defined as 
positivity of at least one stool sample either by 
culture or qPCR or both.

Severe diarrhea.

More severe diarrhea.

Dysentery.

Weight of all grade 3-5 stools.

Total number of all grade 3-5 stools.

Confirmed S. sonnei 53G shedding AND moderate 
or severe diarrhea OR dysentery OR presence of 
oral temperature 38.5°C OR presence of one or 
more severe intestinal symptoms (abdominal pain, 
cramping, nausea, vomiting, gas, and anorexia)

Disease not fulfilling the protocol primary case 
definition for shigellosis associated or not with mild 
to moderate symptoms including: passing loose 
stool (not meeting the protocol definition of 
moderate or severe diarrhea), abdominal pain, 
abdominal cramps, gas, anorexia, nausea, headache, 
myalgia, malaise, arthralgia, fever, vomiting and IV 
fluid administration.

Time to onset of shigellosis after challenge, 
according to the protocol primary case definition.
Safety
Solicited adverse events

Occurrence of each solicited local and systemic 
adverse event within 7 days after each vaccination.
Unsolicited adverse events

Occurrence of unsolicited AEs within 28 days after 
vaccination and after challenge, according to 
Medical Dictionary for Regulatory Activities 
(MedDRA) classification.
Serious adverse events

Occurrence of all SAEs and related SAEs from Day
1 to study end.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
20
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
21
Adverse events of special interest

Occurrence of AESI (i.e., symptomatic 
neutropenia) from Day 1 to study end.
Laboratory parameters

Out of laboratory reference range and/or clinically 
significant value (according to local ranges) for 
hematology at 7 days after first and second 
vaccination and at last study visit (Visit 8).
Immunogenicity
The measures of immunogenicity, against the LPS of 
S. sonnei, will include:

IgG geometric mean concentrations (GMCs) pre-
vaccination (Day 1), 7 and 28 days after first and 
second vaccination by antibody concentration at 
baseline (i.e., above vs. below the assay detection 
limit), as determined by anti-S. sonnei LPS IgG 
ELISA.

IgG GMC pre-challenge (Day 57), 7 and 28 days 
after challenge (Day 64 and Day 85) as determined 
by anti-S. sonnei LPS IgG ELISA.

Number and percentage of subjects achieving a post 
vaccination anti- S. Sonnei LPS concentration ≥ 121 
EU/ml at 28 days after first and second vaccination.

Number and percentage of seroresponders* for anti-
S. sonnei LPS at 28 days after first and second 
vaccination.
*Seroresponse is aimed to define a significant 
increase in anti S. sonnei LPS IgG concentration in 
post-vaccination samples and relies on the 
definition already used in a previous phase II study 
in Kenyan population. For the purpose of this study 
seroresponse is defined as:

If the baseline value is greater than 50 EU/mL 
then an increase of at least 50% in the post-
vaccination sample as compared to baseline.

If the baseline value is less or equal to 
50 EU/mL then an increase of at least 
25 EU/mL in the post-vaccination sample as 
compared to baseline.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
21
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
22
Note: Threshold values/increases given in the definition 
of seroresponse might be subject to change during the 
course of the study (e.g., in case of optimization 
/qualification/validation of the anti S. sonnei LPS IgG
ELISA).
Tertiary

Specific anti-S. sonnei LPS sIgA antibody 
concentration in stool samples at Day 1, 7 days 
after first and second vaccination and 7 days after 
challenge (Day 64).

Frequency of S. sonnei LPS specific IgG α4β7+/-
antibody secreting cells per 10^6 PBMC 
plasmablast at Day 1 and 7 days after first and 
second vaccination and 7 days after challenge 
(Day 8, Day 36 and Day 64). (Amended: 23 July
2019)

Glycosylation profiles of IgG antibodies at Day 1 
and 28 days after second vaccination (Visit 5; Day 
57).

Number and percentage of subjects that show 
correlation between serum anti-S. sonnei LPS IgG 
concentration, serum bactericidal activity titer, 
shigellosis, shedding, moderate to severe diarrhea 
(MSD), dysentery and mild diarrhea after 
challenge.

Concentration of stool markers of intestinal 
inflammation (e.g. calprotectin and 
myeloperoxidase) before oral challenge with S. 
sonnei, 53G at Visit 5 (Day 57) and daily during the 
inpatient stay after challenge administration (Day 
57 to Day 64).

The number of differential expressed genes 7 days 
after first and second vaccination and 7 days after 
challenge by comparing the relative abundance of 
mRNA sequences compared to Day 1 (pre-
vaccination baseline).

Diversity and frequency of microbiome components
(taxa and/or genes according to technology) at 
Day 1 prior to vaccination and 28 days after second 
vaccination (Visit 5; Day 57).
Exploratory analysis for hypotheses generation will 
include the evaluation of the association of the 
microbiome components with efficacy and 
immunogenicity described above.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
22
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
23
TABLE OF CONTENTS
PAGE
SPONSOR INFORMATION ............................................................................................7
SYNOPSIS......................................................................................................................8
LIST OF ABBREVIATIONS (AMENDED: 23 JULY 2019)..............................................31
GLOSSARY OF TERMS ...............................................................................................34
TRADEMARKS .............................................................................................................39
1.
INTRODUCTION....................................................................................................40
1.1.
Background ................................................................................................40
1.2.
Rationale for the study and study design ....................................................40
1.2.1.
Rationale for the study.................................................................40
1.2.2.
Rationale for the study design......................................................41
1.2.3.
Rationale for the use of placebo ..................................................41
1.3.
Benefit:Risk assessment.............................................................................42
1.3.1.
Risk assessment..........................................................................42
1.3.2.
Benefit assessment .....................................................................44
1.3.3.
Overall benefit: Risk conclusion...................................................44
2.
OBJECTIVES.........................................................................................................45
2.1.
Primary objective ........................................................................................45
2.2.
Secondary objectives..................................................................................45
2.3.
Tertiary objectives.......................................................................................47
3.
STUDY DESIGN OVERVIEW ................................................................................47
3.1.
Vaccination Phase......................................................................................48
3.2.
Challenge Phase ........................................................................................49
4.
CASE DEFINITIONS..............................................................................................54
4.1.
Diarrhea......................................................................................................54
4.2.
Dysentery (Amended: 23 July 2019)...........................................................55
4.3.
Shigellosis ..................................................................................................56
5.
STUDY COHORT...................................................................................................57
5.1.
Number of subjects/center ..........................................................................57
5.2.
Inclusion criteria..........................................................................................57
5.3.
Exclusion criteria.........................................................................................58
6.
CONDUCT OF THE STUDY ..................................................................................60
6.1.
Regulatory and ethical considerations, including the informed 
consent process..........................................................................................60
6.2.
Subject identification and randomization.....................................................61
6.2.1.
Subject identification....................................................................61
6.2.2.
Randomization of treatment.........................................................61
6.2.2.1.
Randomization of supplies..........................................61
6.2.2.2.
Treatment allocation to the subject.............................61
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
23
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
24
6.2.2.2.1.
Study group and treatment 
number allocation ...................................61
6.2.3.
Allocation of subjects to assay subsets........................................62
6.3.
Method of blinding ......................................................................................62
6.4.
General study aspects ................................................................................63
6.4.1.
Independent data monitoring committee ......................................63
6.5.
Outline of study procedures ........................................................................64
6.6.
Detailed description of study procedures ....................................................67
6.6.1.
Informed consent.........................................................................67
6.6.2.
Check inclusion and exclusion criteria .........................................67
6.6.3.
Collect demographic data ............................................................67
6.6.4.
Medical history.............................................................................68
6.6.5.
Physical examination / history directed physical 
examination .................................................................................68
6.6.6.
Pregnancy test.............................................................................68
6.6.7.
Check contraindications to vaccination ........................................68
6.6.8.
Assess pre-vaccination body temperature ...................................69
6.6.9.
Study group and treatment number allocation..............................69
6.6.10.
Sampling......................................................................................69
6.6.10.1.
Blood sampling for safety or immune response 
assessments ..............................................................69
6.6.10.2.
Urine sampling ...........................................................69
6.6.10.3.
Stool sampling............................................................69
6.6.11.
Study vaccine/placebo administration..........................................70
6.6.12.
Challenge administration and inpatient stay.................................70
6.6.13.
Check and record concomitant medication/vaccination and 
intercurrent medical conditions ....................................................70
6.6.14.
Recording of AEs, SAEs, pregnancies and AESIs .......................70
6.6.14.1.
Subject Diary..............................................................71
6.6.14.2.
Post-vaccination reminders ........................................71
6.6.14.2.1.
Subject Diary reminder calls ...................71
6.6.15.
Study conclusion..........................................................................71
6.7.
Biological sample handling and analysis.....................................................72
6.7.1.
Use of specified study materials ..................................................73
6.7.2.
Biological samples.......................................................................73
6.7.3.
Laboratory assays .......................................................................73
6.7.4.
Biological samples evaluation......................................................77
6.7.4.1.
Immunological read-outs ............................................77
6.7.4.2.
Hematology/blood chemistry ......................................78
6.7.5.
Immunological correlates of protection.........................................78
7.
STUDY VACCINE/PRODUCTS AND ADMINISTRATION......................................79
7.1.
Description of study vaccine/placebo and challenge agent .........................79
7.2.
Storage and handling of study vaccine/placebo and challenge agent .........79
7.3.
Dosage and administration of study vaccine/placebo and challenge 
agent ..........................................................................................................80
7.3.1.
Vaccine/placebo preparation........................................................80
7.3.2.
Preparation of challenge agent ....................................................80
7.3.3.
Vaccine/placebo dosage and administration................................80
7.3.4.
Challenge agent dosage and administration ................................81
7.4.
Replacement of unusable vaccine/placebo doses and challenge 
agent ..........................................................................................................82
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
24
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
25
7.5.
Contraindications to subsequent vaccination or challenge..........................82
7.6.
Concomitant medications/products and concomitant vaccinations..............83
7.6.1.
Recording of concomitant medications/products and 
concomitant vaccinations.............................................................83
7.6.2.
Concomitant medications/products/vaccines that may lead 
to the elimination of a subject from per-protocol analyses............83
7.7.
Intercurrent medical conditions that may lead to elimination of a 
subject from per-protocol analyses .............................................................84
8.
HEALTH ECONOMICS ..........................................................................................84
9.
SAFETY.................................................................................................................85
9.1.
Safety definitions ........................................................................................85
9.1.1.
Definition of an adverse event......................................................85
9.1.2.
Definition of a serious adverse event ...........................................86
9.1.3.
Solicited adverse events..............................................................87
9.1.3.1.
Solicited local Adverse events ....................................87
9.1.3.2.
Solicited systemic Adverse events..............................87
9.1.3.3.
Solicited events after challenge phase........................88
9.1.4.
Unsolicited Adverse Events .........................................................88
9.1.5.
Clinical laboratory parameters and other abnormal 
assessments qualifying as adverse events or serious 
adverse events ............................................................................89
9.1.6.
Adverse events of special interest................................................89
9.2.
Events or outcomes not qualifying as adverse events or serious 
adverse events ...........................................................................................91
9.2.1.
Pregnancy ...................................................................................91
9.3.
Detecting and recording adverse events, serious adverse events 
and pregnancies .........................................................................................92
9.3.1.
Time period for detecting and recording adverse events, 
serious adverse events and pregnancies.....................................92
9.3.2.
Post-study adverse events and serious adverse events...............94
9.3.3.
Evaluation of adverse events and serious adverse events...........94
9.3.3.1.
Active questioning to detect adverse events 
and serious adverse events........................................94
9.3.3.2.
Assessment of adverse events...................................94
9.3.3.2.1.
Assessment of intensity..........................94
9.3.3.2.2.
Assessment of causality .........................97
9.3.3.3.
Assessment of outcomes............................................98
9.3.3.4.
Medically attended visits.............................................98
9.4.
Reporting of serious adverse events, pregnancies, and other events .........98
9.4.1.
Prompt reporting of serious adverse events, pregnancies, 
and other events to GSK Biologicals............................................98
9.4.2.
Contact information for reporting serious adverse events, 
pregnancies and AESIs ...............................................................99
9.4.3.
Completion and transmission of SAE reports to GSK 
Biologicals ...................................................................................99
9.4.3.1.
Back-up system in case the electronic 
reporting system does not work..................................99
9.4.4.
Completion and transmission of pregnancy reports to GSK 
Biologicals .................................................................................100
9.4.5.
Reporting of AESIs to GSK Biologicals ......................................100
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
25
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
26
9.4.6.
Updating of SAE, pregnancy, and AESI information after 
removal of write access to the subject’s eCRF...........................101
9.4.7.
Regulatory reporting requirements for serious adverse 
events........................................................................................101
9.5.
Follow-up of adverse events, serious adverse events, and 
pregnancies..............................................................................................101
9.5.1.
Follow-up of adverse events and serious adverse events..........101
9.5.1.1.
Follow-up during the study........................................101
9.5.1.2.
Follow-up after the subject is discharged from 
the study...................................................................102
9.5.2.
Follow-up of pregnancies...........................................................102
9.6.
Treatment of adverse events ....................................................................102
9.7.
Unblinding.................................................................................................102
9.8.
Emergency unblinding ..............................................................................103
9.9.
Subject card..............................................................................................103
9.10.
Holding rule and safety monitoring............................................................104
9.10.1.
Holding rule ...............................................................................104
9.10.2.
Safety monitoring.......................................................................104
10. SUBJECT COMPLETION AND WITHDRAWAL...................................................104
10.1.
Subject completion ...................................................................................104
10.2.
Subject withdrawal....................................................................................104
10.2.1.
Subject withdrawal from the study .............................................104
10.2.2.
Subject withdrawal from study vaccine/placebo or 
challenge agent .........................................................................105
11. STATISTICAL METHODS....................................................................................106
11.1.
Primary endpoint.......................................................................................106
11.2.
Secondary endpoints ................................................................................106
11.3.
Tertiary endpoints.....................................................................................108
11.4.
Determination of sample size....................................................................109
11.5.
Analysis sets.............................................................................................109
11.5.1.
All Enrolled Set ..........................................................................109
11.5.2.
All Exposed Set .........................................................................109
11.5.3.
Safety set...................................................................................109
11.5.3.1.
Solicited Safety Set (solicited local and 
systemic adverse events and other solicited 
adverse events)........................................................109
11.5.3.2.
Unsolicited Safety Set (unsolicited adverse 
events) .....................................................................110
11.5.3.3.
Overall safety set......................................................110
11.5.4.
Full analysis set (FAS) efficacy/Immunogenicity set...................110
11.5.4.1.
Full analysis set efficacy...........................................110
11.5.4.2.
Full analysis set Immunogenicity ..............................110
11.5.5.
Per-protocol (PP) set for efficacy/Immunogenicity set................110
11.5.6.
Other analysis sets ....................................................................111
11.5.7.
Sub-groups................................................................................111
11.6.
Derived and transformed data...................................................................111
11.7.
Analysis of demographics.........................................................................112
11.8.
Analysis of efficacy ...................................................................................112
11.9.
Analysis of immunogenicity.......................................................................112
11.10. Analysis of safety......................................................................................113
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
26
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
27
11.11. Interpretation of analyses..........................................................................114
11.12. Conduct of analyses .................................................................................114
11.12.1. Sequence of analyses................................................................114
11.12.2. Statistical considerations for interim analyses............................114
12. ADMINISTRATIVE MATTERS .............................................................................115
12.1.
Electronic case report form instructions ....................................................115
12.2.
Subject Diary ............................................................................................115
12.3.
Study monitoring by GSK biologicals ........................................................116
12.4.
Record retention .......................................................................................117
12.5.
Quality assurance.....................................................................................117
12.6.
Posting of information on publicly available clinical trial registers and 
publication policy ......................................................................................117
12.7.
Provision of study results to investigators .................................................118
12.8.
Data sharing .............................................................................................118
12.9.
Pharmacogenomics..................................................................................118
13. COUNTRY SPECIFIC REQUIREMENTS.............................................................118
14. REFERENCES.....................................................................................................119
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
27
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
28
LIST OF TABLES
PAGE
Table 1
Study groups and epochs foreseen in the study.....................................52
Table 2
Study groups and treatment foreseen in the study .................................52
Table 3
Blinding of study epochs ........................................................................53
Table 4
List of study procedures .........................................................................64
Table 5
Intervals between study visits (Amended: 23 July 2019) ........................67
Table 6
Biological samples .................................................................................73
Table 7
Immunity (Antibody determination).........................................................74
Table 8
Cell-Mediated Immunity (CMI) (Amended: 23 July 2019) .......................74
Table 9
Excretion of Challenge agent .................................................................74
Table 10
Hematology, Serum Chemistry, Virology, HLA-B27 test, Urine 
and Stool tests (Amended: 23 July 2019)...............................................75
Table 11
Immunological read-outs........................................................................77
Table 12
Hematology/Blood Chemistry read-outs.................................................78
Table 13
Study vaccine/placebo and challenge agent...........................................79
Table 14
Dosage and administration.....................................................................81
Table 15
Solicited local adverse events ................................................................87
Table 16
Solicited systemic adverse events..........................................................87
Table 17
List of potential AESI to be followed during the study .............................89
Table 18
Evaluation of symptomatic neutropenia..................................................90
Table 19
Reporting periods for collecting safety information .................................93
Table 20
Intensity scales for solicited symptoms...................................................95
Table 21
Timeframes for submitting serious adverse event, pregnancy and 
other events reports to GSK Biologicals .................................................99
Table 22
GSK Biologicals’ laboratories ...............................................................122
Table 23
Outsourced laboratories.......................................................................122
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
28
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
29
LIST OF FIGURES
PAGE
Figure 1
Study design (Amended: 23 July 2019)..................................................51
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
29
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
30
LIST OF APPENDICES
PAGE
Appendix A
LABORATORY ASSAYS .....................................................................120
Appendix B
CLINICAL LABORATORIES ................................................................122
Appendix C
AMENDMENTS AND ADMINISTRATIVE CHANGES TO THE 
PROTOCOL.........................................................................................123
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
30
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
31
LIST OF ABBREVIATIONS (Amended: 23 July 2019)
AE:
Adverse Event
AESI:
Adverse Event of Special Interest
AR:
Attack Rate
CCHMC:
Cincinnati Children’s Hospital Medical Center (USA)
CDC:
Centers for Disease Control and Prevention
CFU:
Colony Forming Units
CHIM:
Controlled Human Infection Model
CI:
Confidence Interval
CMI:
Cell-Mediated Immunity
DNA:
Deoxyribonucleic acid
eCRF:
electronic Case Report Form
ELISA:
Enzyme-linked immunosorbent assay
EoS:
End of Study
EU:
ELISA unit
FAS:
Full Analysis Set
Fc:
Fragment crystallisable
FDA:
Food and Drug Administration, United States of America
GCP:
Good Clinical Practice
GMC:
Geometric Mean Concentration
GMMA:
Generalized Modules for Membrane Antigens
GMR:
Geometric Mean Ratio
GSK:
GlaxoSmithKline
GVGH:
GSK Vaccines Institute for Global Health
HCG:
Human Chorionic Gonadotropin
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
31
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
32
HIV:
Human Immunodeficiency Virus
HLA:
Human Leukocyte Antigen
IB:
Investigator Brochure
ICF:
Informed Consent Form
ICH:
International Council for Harmonisation
ID:
Intradermal
IDMC:
Independent Data Monitoring Committee
IEC:
Independent Ethics Committee
IgG:
Immunoglobulin G
IM:
Intramuscular
IMP:
Investigational Medicinal Product
IN:
Intranasal
IRB:
Institutional Review Board
LL:
Lower Limit
LPS:
Lipopolysaccharide
LSLV:
Last Subject Last Visit
MACDP:
Metropolitan Atlanta Congenital Defects Program
MedDRA:
Medical Dictionary for Regulatory Activities
MSD:
Moderate to Severe Diarrhea
OAg:
O antigen
PBMC:
Peripheral Blood Mononuclear Cells
PCD:
Primary Completion Date
PPS:
Per-Protocol Set
qPCR:
quantitative Polymerase Chain Reaction
S. sonnei:
Shigella sonnei
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
32
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
33
SAE:
Serious Adverse Event
SBA:
Serum Bactericidal Assay
SBIR:
Source DataBase for Internet Randomization
SDB:
Source Document Verification
sIgA:
Secretory Immunoglobulin A
SPM:
Study Procedures Manual
TMP-SMX:
Trimethoprim-sulfamethoxazole
TSA:
Trypticase soy agar
VE:
Vaccine Efficacy
WRAIR:
Walter Reed Army Institute of Research
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
33
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
34
GLOSSARY OF TERMS
Adequate contraception:
Adequate contraception is defined as a contraceptive 
method with failure rate of less than 1% per year when 
used consistently and correctly and when applicable, in 
accordance with the product label for example:

Abstinence from penile-vaginal intercourse, when 
this is their preferred and usual lifestyle,

Combined estrogen and progesterone oral 
contraceptives,

Injectable progestogen,

implants of etonogestrel or levonorgestrel,

Contraceptive vaginal ring,

Percutaneous contraceptive patches,

Intrauterine device or intrauterine system,

Male partner sterilization prior to the female 
subject’s entry into the study, and this male is the 
sole partner for that subject,
The information on the male sterility can come from 
the site personnel’s review of the subject’s medical 
records; or interview with the subject on her medical 
history.

Male condom combined with a vaginal spermicide 
(foam, gel, film, cream or suppository), and/or 
progesterone alone oral contraceptive.
Adequate contraception does not apply to subjects of 
childbearing potential with same sex partners, or for 
subjects who are and will continue to be abstinent from 
penile-vaginal intercourse on a long term and persistent 
basis, when this is their preferred and usual lifestyle.
Adverse event:
Any untoward medical occurrence in a patient or clinical 
investigation subject, temporally associated with the use 
of a medicinal product, whether or not considered related 
to the medicinal product.
An adverse event (AE) can therefore be any unfavorable
and unintended sign (including an abnormal laboratory 
finding), symptom, or disease (new or exacerbated) 
temporally associated with the use of a medicinal product. 
For marketed medicinal products, this also includes 
failure to produce expected benefits (i.e. lack of efficacy), 
abuse or misuse.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
34
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
35
Adverse Event of Special 
Interest: 
Adverse events of special interest (AESIs): are predefined 
(serious or non-serious) adverse events of scientific and 
medical concern specific to the product or program, for 
which ongoing monitoring and rapid communication by 
the investigator to the sponsor can be appropriate, 
because such an event might warrant further investigation 
in order to characterize and understand it.
Blinding:
A procedure in which one or more parties to the trial are 
kept unaware of the treatment assignment in order to 
reduce the risk of biased study outcomes. The level of 
blinding is maintained throughout the conduct of the trial, 
and only when the data are cleaned to an acceptable level 
of quality will appropriate personnel be unblinded or 
when required in case of a serious adverse event. In an 
observer-blind study, the subject and the site and sponsor 
personnel involved in the clinical evaluation of the 
subjects are blinded while other study personnel may be 
aware of the treatment assignment (see Section 6.2.3 for 
details on observer-blinded studies).
Eligible:
Qualified for enrolment into the study based upon strict 
adherence to inclusion/exclusion criteria.
End of Study:
(Synonym of End of Trial)
For studies without collection of human biologicals 
samples or imaging data EoS is the last subject last visit 
(LSLV).
For studies with collection of Human Biologicals 
Samples or imaging data, EoS is defined as the date of the 
last testing/reading released of the Human Biological 
Samples or imaging data, related to primary and 
secondary endpoints. EoS must be achieved no later than 
8 months after LSLV.
Epoch:
An epoch is a set of consecutive timepoints or a single 
timepoint from a single protocol. Epochs are defined to 
support a main purpose which is either to draw 
conclusions on subject participation or to draw a 
complete conclusion to define or precise the targeted 
label of the product. Supporting means that data collected 
at the timepoints included in an epoch must be sufficient 
to fulfil the purpose of the epoch.
Typical examples of epochs are screening, primary 
vaccinations, boosters, yearly immunogenicity follow-
ups, and surveillance periods for efficacy or safety.
eTrack:
GSK’s tracking tool for clinical trials.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
35
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
36
Immunological correlate 
of protection:
The defined immune response above which there is a high 
likelihood of protection in the absence of any host factors 
that might increase susceptibility to the infectious agent.
Investigational vaccine:
(Synonym of 
Investigational Medicinal 
Product)
A pharmaceutical form of an active ingredient being 
tested in a clinical trial, including a product with a 
marketing authorization when used in a way different 
from the approved form, or when used for an unapproved 
indication, or when used to gain further information about 
an approved use.
Menarche:
Menarche is the onset of menses for the first time in a 
young female and is preceded by several changes 
associated with puberty including breast development and 
pubic hair growth. Menarche usually occurs within 1-2 
years of breast development, thelarche. However, a young 
female can become pregnant before her first menses. 
Thus, a conservative definition of non-childbearing 
potential in a pre-menarcheal female is a young female 
who has not yet entered puberty as evidenced by lack of 
breast development (palpable glandular breast tissue).
Menopause:
Menopause is the age associated with complete cessation 
of menstrual cycles, menses, and implies the loss of 
reproductive potential by ovarian failure. A practical 
definition accepts menopause after 1 year without menses 
with an appropriate clinical profile at the appropriate age 
e.g. > 45 years.
Pharmacogenomics:
The International Council for Harmonisation (ICH) E15 
Guidance for Industry defines pharmacogenomics as 
Study of variation of DNA and RNA characteristics as 
related to drug or treatment response. Pharmacogenetics, 
which is a subset of pharmacogenomics, is “the study of 
variations in DNA sequence as related to drug response.” 
Pharmacogenomic biomarkers include germline (host) 
DNA and RNA as well as somatic changes (e.g., 
mutations) that occur in cells or tissues. 
Pharmacogenomic biomarkers are not limited to human 
samples but include samples from viruses and infectious 
agents as well as animal samples. The term 
pharmacogenomic experiment includes both the 
generation of new genetic or genomic (DNA and/or 
RNA) data with subsequent analysis as well as the 
analysis of existing genetic or genomic data to understand 
drug or treatment response (pharmacokinetics, safety, 
efficacy or effectiveness, mode of action). Proteomic and 
metabolomic biomarker research are not 
pharmacogenomics.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
36
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
37
Primary completion 
date:
The date that the final subject was examined or received 
an intervention for the purpose of final collection of data 
for all primary outcomes, whether the clinical trial was 
concluded according to the pre-specified protocol or was 
terminated.
Protocol amendment:
The International Council for Harmonisation (ICH) 
defines a protocol amendment as: ‘A written description 
of a change(s) to or formal clarification of a protocol.’ 
GSK Biologicals further details this to include a change 
to an approved protocol that affects the safety of subjects, 
scope of the investigation, study design, or scientific 
integrity of the study.
Randomization:
Process of random attribution of treatment/schedule to 
subjects in order to reduce bias of selection.
Self-contained study:
Study with objectives not linked to the data of another 
study.
Site Monitor:
An individual assigned by the sponsor who is responsible 
for assuring proper conduct of clinical studies at one or 
more investigational sites.
Solicited adverse event:
AEs to be recorded as endpoints in the clinical study. The 
presence/occurrence/intensity of these events is actively 
solicited from the subject or an observer during a 
specified post-vaccination follow-up period.
Study vaccine/product:
Any investigational vaccine/product being tested and/or 
any authorized use of a vaccine/ product /placebo as a 
reference or administered concomitantly, in a clinical trial 
that evaluates the use of an investigational 
vaccine/product.
Subject:
Term used throughout the protocol to denote an 
individual who has been contacted in order to participate 
or participates in the clinical study, either as a recipient of 
the vaccine or as a control.
Subject number:
A unique number identifying a subject, assigned to each 
subject consenting to participate in the study.
Subset:
(Synonym of Immuno-
subset)
Selection of blood samples among all blood sample 
collected at given timepoint(s) for testing by specific 
assay.
Treatment:
Term used throughout the clinical study to denote a set of 
investigational product(s) or marketed product(s) or 
placebo intended to be administered to a subject.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
37
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
38
Treatment number:
A unique number identifying a treatment to a subject, 
according to treatment allocation.
Unsolicited adverse 
event:
Any AE reported in addition to those solicited during the 
clinical study. Also any ‘solicited’ symptom with onset 
outside the specified period of follow-up for solicited 
symptoms will be reported as an unsolicited adverse 
event.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
38
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
39
TRADEMARKS
The following trademarks are used in the present protocol.
Note: In the body of the protocol (including the synopsis), the names of the 
vaccines/products and/or medications will be written without the superscript symbol ™ 
or ® and in italics.
Trademarks not owned by the GSK
group of companies
Generic description
Alhydrogel (Brenntag Nordic A/S [Brenntag 
Biosector A/S])
Aluminium Hydroxide, Hydrated, for 
Adsorption (Alhydrogel 2% - Ph.Eur.)
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
39
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
40
1.
INTRODUCTION
1.1.
Background
Shigellosis is a major public health problem around the world; it is one of the leading 
causes of diarrheal disease in low and middle income countries and is estimated to cause 
an all age mortality of 164 300 deaths every year [GBD, 2015]. The majority of these 
cases occur in children less than 5 years of age living in middle and low income 
countries. Currently, there are no vaccines licensed for use in these populations (except 
for China) and available interventions are under threat from the increasing rates of 
antibiotic resistance of Shigella sonnei (S. sonnei) around the world. Natural infection 
generates a serotype specific protective immune response against the O antigen (OAg) of 
the bacterial lipopolysaccharide (LPS). Previously, S. sonnei and Shigella flexneri type 2a 
were selected for a prototype OAg conjugate vaccine that produced a protective efficacy 
of 70% in children three years of age and older. However, there was no noted efficacy in 
children younger than three years of age, thus necessitating new approaches to vaccine 
development. Additionally, it is likely that a multivalent OAg vaccine will be required in 
order to achieve broad protection against the 4-6 serotypes causing the largest burden of 
disease in young children living in sub-Saharan Africa and South Asia.
Please refer to the current Investigator Brochure for information regarding the pre-
clinical and clinical studies with the 1790GAHB vaccine and the epidemiological 
information.
1.2.
Rationale for the study and study design
1.2.1.
Rationale for the study
GlaxoSmithKline (GSK) Vaccines Institute for Global Health (GVGH) has developed a 
vaccine against S. sonnei (1790GAHB vaccine) using the new Generalized Modules for 
Membrane Antigens (GMMA) platform technology that in future could be also used to 
develop vaccines against other gram negative pathogens. 
The study vaccine could be the stepping stone for the development of a multivalent 
broadly protective Shigella vaccine for vaccination of impoverished communities where 
shigellosis is endemic. However, a standalone monovalent vaccine against S. sonnei
could be used to protect travelers against diarrheal shigellosis, as the vast majority of 
travelers’ shigellosis is caused by S. sonnei, and even to protect infants in endemic 
regions where shigellosis is primarily caused by S. sonnei.
The 1790GAHB vaccine has been tested in two Phase I dose escalation studies in Europe 
to assess its safety and immunogenicity via three routes of administration: intramuscular 
(IM), intranasal (IN) and intradermal (ID). The results from the first study (dose 
escalation with IM vaccination) have shown that the vaccine has an acceptable safety 
profile and is well-tolerated up to a dose of 100 µg. Additionally, the serologic 
assessment showed that one dose of ≥ 1.5/25 µg OAg/protein of 1790GAHB vaccine 
elicits serum immunoglobulin G (IgG) anti-S sonnei LPS levels ≥ 121 enzyme-linked 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
40
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
41
immunosorbent assay (ELISA) units/mL (EU/mL) (i.e., median antibody titer in a panel 
of 87 Israeli convalescent subjects after natural infection by S. sonnei). The results from 
the second study (dose escalation with ID, IN and IM vaccination) showed that 
1790GAHB vaccine is well-tolerated also when administered by the ID and IN routes of 
vaccination. However, immunogenicity data have shown that 1790GAHB vaccine 
administered by the ID and IN routes is not as immunogenic as 1790GAHB vaccine
administered by the IM route. Therefore, it has been decided to proceed with the clinical 
development program of this vaccine only using the IM vaccination route. In terms of 
dosage, the regimen tested in Phase I studies (three doses given one month apart) did not 
show any significant benefit from the third dose in terms of immunogenicity, therefore a 
two dose schedule was selected for next studies.
A Phase IIa study, conducted in endemic regions of Africa (i.e., Kenya), has just been 
completed and confirmed the acceptable safety profile and immunogenicity of 
1790GAHB vaccine.
Performing a vaccine-human challenge study may give the opportunity to establish 
evidence of clinical protection induced by the candidate S. sonnei vaccine (1790GAHB 
vaccine) at an early development stage.
1.2.2.
Rationale for the study design
A human challenge model of S. sonnei disease for vaccine testing was established in 
Thailand [Bodhidatta, 2012] and showed an attack rate (AR) of 75% in non-immune 
adult volunteers receiving a challenge dose of 1680 colony forming units (CFU) of S. 
sonnei strain 53G. Clinical and laboratory endpoints of infection and disease, namely 
diarrhea, dysentery, fever and shedding of S. sonnei in stools were used to calculate the 
AR and thus to establish the optimal infective dose. In a subsequent study though 
[Pitisuttithum, 2016], the AR in the control group, using this model, was much less than 
previously published.
Given this variability, before starting a vaccine-challenge study, the proposed human 
challenge model of S. sonnei to be used has been appropriately developed and the 
challenge dose and AR reliably established by the Cincinnati Children’s Hospital 
Medical Center (CCHMC) (Ohio, United States of America). The current GSK vaccine-
human challenge study will be conducted at CCHMC and will use the developed 
challenge model. Volunteers will be treated after development of symptoms of 
shigellosis.
1.2.3.
Rationale for the use of placebo
As currently there is no widely available vaccine against shigellosis, the efficacy and 
safety of the 1790GAHB vaccine will be evaluated against a placebo. The placebo is used 
to better describe the safety profile of the S. sonnei vaccine as well as its efficacy in terms 
of clinical protection against shigellosis caused by S. sonnei.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
41
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
42
1.3.
Benefit:Risk assessment
Please refer to the current Investigator Brochure for the summary of potential risks and 
benefits of the 1790GAHB vaccine.
The following section outlines the risk assessment and mitigation strategy for this study 
protocol:
1.3.1.
Risk assessment
Important Potential/Identified 
Risk
Data/Rationale for Risk
Mitigation Strategy
Investigational vaccine: 1790GAHB vaccine
Symptomatic Neutropenia
Eight cases of Grade 2 or Grade 3 
neutropenia were reported from 
Phase 1 clinical trials 
(asymptomatic).
All cases occurred in the first 20 
days after administration of first 
vaccine dose, and reversed after 
discontinuation.
Literature review of reports of 
neutropenia in association with 
vaccination indicates factors noted 
to be associated with neutropenia 
(including ethnicity, and low 
baseline counts) with the majority 
of cases detected within 2 weeks 
of the vaccination. None of the 
reported cases was clinically 
symptomatic.
Five cases of asymptomatic 
neutropenia (Grade 1 and 2) have 
been reported at Day 7 after 
receipt of the first dose in 5 
subjects.
One of the 5 subjects had an 
additional Grade1 neutropenia 
episode at Day 28, and another 
one had two additional episodes, 
one of which was Grade 3 (940 
cells/mL) at 7 days after the 
second dose and the second was
Grade 2 (1,410 cells/mL) at 28 
days after second vaccination. All 
cases were resolved before last 
study visit.
Exclusion criteria for this clinical study
include:

Subjects with a low baseline 
neutrophil count below 1800 
cells/µL (LLN).

Previous history of Benign Ethnic 
Neutropenia, or drug related 
Neutropenia.

Concomitant treatment with 
neutropenic agents.
Monitoring for this clinical study to 
include:

Baseline neutrophil counts.

Full blood counts with differential 
measured at 7 days post each 
scheduled vaccination.

Assessment of clinical impact of 
neutropenia.
Subjects will be closely monitored 
during the entire study and have 
hematology repeated every 7 days 
when neutropenia is identified until 
resolution. If a case of neutropenia does 
not resolve based on most recent 
available laboratory results, before the 
second vaccination, or challenge agent 
administration, the subject will not be re-
vaccinated or administered the 
challenge agent.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
42
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
43
Important Potential/Identified 
Risk
Data/Rationale for Risk
Mitigation Strategy
Study Procedures
Risks related to blood sample 
collection
When blood samples are taken 
from a vein, there is a risk of 
bruising at the site. There is a rare 
possibility of bleeding, fainting and 
infection or of nerve injury 
soreness.
Safe sampling procedures will be 
applied by appropriately trained and 
qualified staff to minimize distress and 
sampling errors.
The potential risk of feeling faint, or 
experiencing mild local pain, bruising, 
irritation or redness at the site where 
blood was taken, is mentioned in the 
informed consent form. The amount of 
blood to be taken for sampling will not 
be harmful to the subject’s health.
Risk related to rectal swabs
Rectal swabs may cause 
discomfort for patients and in case 
of special conditions (e.g. 
hemorrhoids, and rectal polyps) 
bleeding might happen.
Rectal swabs are only collected when it 
is not possible to obtain a stool sample. 
Study staff will instruct the subjects on 
how to do the rectal swab.
Other (challenge phase)
Severe and invasive diarrhea after 
challenge
Illness caused by Shigella ranges 
from mild (watery diarrhea being 
the main symptom) to severe 
illness (fever and abdominal 
cramping with frequent small 
volume blood streaked stools 
containing mucus), dehydration 
and even shock.
Perianal soreness, which is a skin 
irritation on your buttocks as a 
result of diarrhea, is possible.
Administration of an effective antibiotic 
will significantly reduce, or eliminate, 
symptoms within 24 hours of initiation. 
In addition, all challenged subjects will 
receive an effective antibiotic on the 5th
day after challenge or earlier as 
required and intensive care unit is 
available to provide appropriate care in 
case of emergency.
If perianal soreness occurs, it can be 
treated with topical lotion.
Risk of bacteremia after challenge
Bacteremia can occur with any 
invasive bacterial infection not 
appropriately contained with 
adequate antibacterial therapy.
The S. sonnei 53G challenge strain used 
in the challenge phase is known to be 
susceptible to multiple antimicrobial 
agents including Trimethoprim-
Sulfamethoxazole (TMP-SMX) and 
quinolones which will be used in this 
study. To ensure there is no spread of 
shigella in the environment, subject will 
be discharged only following two 
negative Shigella cultures in stools.
Reiter’s syndrome
A post-dysenteric reactive arthritis, 
with ocular and/or urethral 
inflammation, which has an onset 
typically 1 to 3 weeks after the 
onset of diarrhea, has been 
reported to occur in patients with 
shigellosis.
Data suggest that the risk of reactive 
arthritis following shigellosis may be 
higher in persons carrying the human 
leukocyte antigen (HLA)-B27, thus the 
exclusion of subjects with a positive 
HLA-B27 test at screening.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
43
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
44
Important Potential/Identified 
Risk
Data/Rationale for Risk
Mitigation Strategy
Other (challenge phase)
Risk related to antibacterial 
therapy
There are documented side effects 
with the use of antibiotics.
However, ciprofloxacin, the antibiotic 
given to all subjects on the 5th day after 
challenge, is generally well-tolerated. 
The most frequently reported drug 
related events for all indications of 
ciprofloxacin therapy have been 
nausea, diarrhea, abnormal liver 
function tests, vomiting, and rash which 
are all mild to moderate in most cases.
The most common symptoms that 
happen after taking TMP-SMX are 
nausea, vomiting, loss of appetite, skin 
rash and itching.
All subjects will be monitored closely 
and given adequate care when the need 
arises.
1.3.2.
Benefit assessment
There may not be a direct medical benefit to the subject as a result of taking part in this 
study. However, the study vaccine may provide protection against S. sonnei bacteria as 
well as the administered challenge agent.
The subject, by participating in this study may help provide data about the tolerability of 
the experimental vaccine and about its ability to stimulate the immune system to produce 
antibodies against S. sonnei and provide clinical protection.
1.3.3.
Overall benefit: Risk conclusion
Based on the clinical experience with 1790GAHB vaccine, tested in clinical studies, it is 
expected that 1790GAHB vaccine will also have an acceptable safety profile in future 
clinical studies and will be associated with clinically acceptable local and systemic 
reactions. In previous studies, the vaccine has shown good immunogenicity. If 
immunogenicity will correlate to clinical protection in this proposed study, the vaccine 
will help protect the subjects who received it from shigellosis caused by S. sonnei.
However, a similar benefit is not anticipated for subjects who will receive placebo. 
Overall, all subjects may help in the characterization of the vaccines’ immunogenicity 
and ability to provide protection. Administration of the challenge agent causes discomfort 
and illness that ranges from mild (watery diarrhea being the main symptom) to severe 
(fever and abdominal cramping with frequent small volume blood streaked stools 
containing mucus) diarrhea. However, the S. sonnei 53G challenge strain used in the 
challenge phase is known to be susceptible to multiple antimicrobial agents including 
TMP-SMX and quinolones which will be used in this study and will be given to all 
challenged subjects 5 days after administration of the challenge agent (day 62) or earlier 
if medically needed. Additionally, should any allergic reaction occur after challenge 
administration, an intensive care unit with medications is available at the study site in 
order to treat the possible anaphylactic/allergic reactions.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
44
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
45
2.
OBJECTIVES
2.1.
Primary objective

To demonstrate the efficacy of two vaccinations with 25 µg of 1790GAHB vaccine 
in healthy adults compared to placebo (reduction of shigellosis according to the 
protocol primary case definition, i.e. Shedding of S. sonnei 53G accompanied by 
moderate or severe diarrhea, OR shedding with an oral temperature of ≥38.5°C after 
challenge with S. sonnei strain 53G).
Criterion:
Vaccine efficacy (VE) of 1790GAHB vaccine will be shown if the lower limit (LL) of 
the 90% confidence interval (CI) of VE will be above zero.
Refer to Section 4 for the protocol primary case definition of shigellosis and to Section 
11.1 for the definition of the primary endpoint.
2.2.
Secondary objectives
Efficacy

To determine the efficacy of the 1790GAHB vaccine compared to placebo against:

Shigellosis as defined by the CHIM expert working group on case definition.* 

Shigellosis, as defined by: severe diarrhea OR moderate diarrhea with fever or 
with one or more moderate constitutional/enteric symptoms OR dysentery [[ ≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 
reportable constitutional/enteric symptom]].

More severe shigellosis, as defined by: severe or moderate diarrhea with fever or 
with one or more severe constitutional/enteric symptoms OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [oral 
temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]].
(Amended: 23 July 2019)

Shedding of S. sonnei strain 53G.

Severe diarrhea.

More severe diarrhea.

Dysentery.

Weight of all grade 3-5 stools.

Total number of all grade 3-5 stools.

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR 
dysentery OR presence of oral temperature ≥38.5°C OR presence of one or 
more severe intestinal symptoms (abdominal pain, cramping, nausea, vomiting, 
gas, and anorexia).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
45
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
46

Disease not fulfilling the protocol primary case definition for shigellosis 
associated or not with mild to moderate symptoms including: passing loose stool 
(not meeting the protocol definition of moderate or severe diarrhea), abdominal 
pain, abdominal cramps, gas, anorexia, nausea, headache, myalgia, malaise, 
arthralgia, fever, vomiting and IV fluid administration.

Time to onset of shigellosis after challenge, according to the primary case 
definition.
*According to the working group, the participant must fulfil any one of the three 
following possible endpoints to qualify as having reached the CHIM case definition for 
this objective:
1.
Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose stools 
in 24 hours]
2.
Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams loose 
stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours]
3.
Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature 38.0oC OR 1 moderate constitutional/enteric 
symptom OR 2 episodes of vomiting in 24 hours].
Safety

To assess the safety and reactogenicity of the 1790GAHB vaccine in terms of 
solicited adverse events, unsolicited adverse events, serious adverse events (SAEs), 
adverse events of special interest (AESI) and laboratory parameters.

To assess safety after challenge in terms of SAEs, unsolicited adverse events, AESI, 
and laboratory parameters.
Immunogenicity

To evaluate the IgG ELISA immunogenicity profile of the 1790GAHB vaccine at 7 
days and 28 days after the first and second vaccination (IgG ELISA coated with OAg 
containing LPS).

To evaluate the immunogenicity profile of the 1790GAHB vaccine at pre-challenge 
and at 7 and 28 days after challenge (IgG ELISA coated with OAg containing LPS).

Number and percentage of seroresponders for anti-S. sonnei LPS at 28 days after 
first and second vaccination.

To assess anti- S.sonnei LPS concentration ≥ 121 EU/ml at 28 days after first and 
second vaccination.
Refer to Section 11.2 for the definition of the secondary endpoints.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
46
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
47
2.3.
Tertiary objectives
The following tertiary objectives which are part of the study exploratory objectives may 
be evaluated in addition to the primary and secondary objectives and will complement 
assessment of the vaccine immunogenicity profile:

Evaluate S. sonnei specific secretory immunoglobulin A (sIgA) in stool at Day 1 and 
7 days after first and second vaccination and 7 days after challenge (Day 64).

Evaluate S. Sonnei LPS IgG-specific α4β7+/- plasmablast response at Day 1 and 7 
days after first and second vaccination and 7 days after challenge (Day 64).
(Amended: 23 July 2019)

Evaluate serum bactericidal activity against S. sonnei at Day 1 and 28 days after first 
and second vaccination.

Evaluate correlation between serum anti-S. sonnei LPS IgG level, serum bactericidal 
activity titer, shigellosis, shedding, mild, moderate, severe or more severe diarrhea, 
and dysentery after challenge.

Evaluate glycosylation of fragment crystallisable (Fc) portion of IgG antibodies at 
Day 1 and 28 days after second vaccination and association with clinical protection 
and/or serological endpoints.

Evaluate inflammatory response from stools collected before challenge at Visit 5 
(Day 57) and daily, post challenge, during inpatient stay (Day 57 to Day 64).

Evaluate gene expression signatures at Day 1 and 7 days after first and second 
vaccination and 7 days after challenge (Day 64).

Investigate gut microbiome at Day 1 and 28 days after second vaccination and its 
potential association with protection and immune response.
These last two tertiary objectives involve pharmacogenomics testing. Refer to the 
glossary of terms for the definition of Pharmacogenomics.
Refer to Section 11.3 for the definition of the tertiary endpoints and to Section 11.12.1 for 
the reporting of tertiary endpoint results.
3.
STUDY DESIGN OVERVIEW
This study will evaluate the efficacy, safety and immunogenicity of the 1790GAHB 
vaccine administered via IM route to adults (18-50 years of age at enrolment). The 
objectives will be assessed through the conduct of the study in two phases: a vaccination 
phase with 1790GAHB vaccine or placebo followed by a challenge phase with S. sonnei 
strain 53G.
The total of 72 subjects will be divided in 4 cohorts of 18 subjects each (for logistical 
reasons due to bed capacity at the study site). The vaccination and challenge will be done 
in overlapping cohorts and randomization will ensure there is the same number of 
vaccines and controls in each cohort. However, if for any reason, a cohort does not reach 
the planned 18 subjects, additional subjects can be added in the next cohorts. The 
maximum number of subjects must not be more than 20 (maximum number of beds in the 
clinic) in each cohort.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
47
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
48
3.1.
Vaccination Phase
During the screening period before the first vaccination (Day -45 to Day -1), subjects 
providing informed consent will have their medical history recorded and be screened for 
general health status.
Female subjects with childbearing potential must use acceptable birth control measures 
(defined as hormonal [e.g., oral, injection, transdermal patch, implant, cervical ring], 
barrier [e.g., condom with spermicide or diaphragm with spermicide], intrauterine device, 
or be in a monogamous relationship with a partner who has been vasectomized for 6 
months or more prior to the subject’s study entry) during the entire study participation.
Refer to the glossary of terms for the definition of adequate contraception.
At the end of the screening, subjects will be evaluated for eligibility. Only subjects who 
meet all inclusion criteria and none of the exclusion criteria will be eligible for 
enrolment. Following informed consent and confirmation of eligibility according to the 
inclusion and exclusion criteria, subjects will be randomized in a 1:1 ratio to receive 
either the study vaccine or the placebo. Subjects will receive two vaccinations, 28 days 
apart.
Subjects will be observed at the site for at least 30 minutes after each vaccination. All 
subjects will have their vital signs (temperature, heart rate, sitting blood pressure) taken
before vaccination and at the end of the observation period to ensure they are stable 
before they go home. Subjects will be provided with a diary card and will be trained on 
how to fill it in. Subjects will be reminded before they go home of the importance of 
filling the diary card and a phone call will be performed by the site staff to the subjects at 
2 and 6 days following each vaccination to remind them that the diary card should be 
completed (no update on the status of the subject’s health will be solicited during these 
phone calls, as they are not intended for safety data collection) and of the clinical visit at 
7 days after each vaccination. The diary card will be used to collect all solicited and 
unsolicited AEs, and medications for the first 7 days after each vaccination starting 6 
hours after the administration of the vaccine/placebo. At 7 days following each 
vaccination and until 28 days after vaccination, only unsolicited AEs, solicited adverse 
reactions that continue at the 7th day, and related medications will be collected during 
visits at the study site. Any AE reported in the diary card beyond the 7th day will be 
followed up accordingly and the frequency of the follow-up will depend on its nature.
Prior to each vaccination, subjects will be assessed through their medical history since the 
last visit and physical examination to check if continued participation in the study is in 
their best interest and that there are no contraindications for vaccination (e.g. fever or 
acute illness on the day of vaccination). Subjects will also be evaluated for continued 
eligibility with regard to the inclusion and exclusion criteria. Vaccination will only take 
place after the subjects’ medical history, clinical examination and evaluation of inclusion 
and exclusion criteria confirm his/her continuous eligibility. Investigator judgment will 
also apply to evaluate subjects’ continued eligibility in the study. Subjects will be 
encouraged to visit the study clinic or call the study staff if they have fever or are unwell 
between planned visits. This, depending on the nature, may prompt an unscheduled visit 
by a study physician. Any Grade 3 or more reaction after vaccination may also prompt a 
review by a study physician at the study clinic.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
48
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
49
3.2.
Challenge Phase
Four weeks after completion of the two-dose vaccination schedule (approximately 28 
days after Visit 3) subjects will be admitted the day before the challenge date (Day 56) 
and will stay for 9 days in the inpatient unit. Biological sample collection could start for 
logistical reason at Day 56 (the day of admission before challenge). The day of challenge 
(Visit 5; Day 57), they will be administered a 1500 CFU challenge dose of S. sonnei 53G. 
Before receiving the challenge, all inclusion and exclusion criteria and hematology will 
be assessed.
When assessing inclusion and exclusion criteria, the investigator will also inquire about
antibiotic treatment during the week prior to the challenge date. Any subject who had a 
course of antibiotic the week prior to challenge, will not receive the challenge agent.
Subjects will fast for 90 minutes prior to receiving the S. sonnei 53G challenge inoculum 
and an additional 90 minutes after challenge. All subjects in the same cohort will be 
challenged in the same day using the same inoculum, which will ensure the consistency 
of the dose used. Approximately 5 minutes before drinking the challenge suspension, the 
subject will drink a 120 mL solution of sodium bicarbonate to neutralize gastric acidity. 
A subject with fever or signs of acute illness will not receive the challenge agent and any 
subject who vomits following ingestion of the challenge agent will not be re-dosed. A 
note will be made in the subject source documents regarding the apparent amount of the 
vomitus (small, moderate or large). The subject will still continue in the study and 
undergo all study-related procedures. Care will be taken to ensure that a minimum 
amount of time, not to exceed 2 hours, is spent between the reconstitution of the 
challenge inoculum and the oral administration of the inoculum to the subject.
Two mL of the inoculum will be retained for pre- and post-challenge quantification of the 
dose. Aliquots of the retained inoculum will be streaked onto trypticase soy agar (TSA) 
plates and after incubation, average number of colonies on the TSA plates will be 
counted and CFU/mL will be calculated. Study staff will take all necessary precaution 
needed for handling of S. sonnei 53G and adhere to the CCHMC policy and procedures.
During the first 8 days in the inpatient unit (Day 57 to Day 64) following challenge,
subjects will be monitored daily for AEs, gastrointestinal or other systemic signs and 
symptoms. Subjects will be assessed for vital signs (including sitting blood pressure, 
temperature and pulse rate) according to local standards for inpatient care. Stool analysis 
will be carried out daily during the inpatient stay. All stools will be collected and visually 
assessed for consistency, blood or mucus. Stools that are loose or watery (grades 3-5) will 
be weighed, and if there is visible blood, a Hemoccult test will be performed to confirm 
presence of occult blood. Up to two stools with blood present by visual inspection in a 24 
hour period will be tested by Hemoccult. Study staff will record the information in the 
subject’s source document. If a subject is unable to produce a stool by midnight, a rectal 
swab will be obtained (up to 2 adequately collected swabs per day). Study staff will 
record the information in the subject’s source document. The first stool sample collected 
during a 24 hour period on the day after challenge agent administration (from 00:01 to 
24:00) will be analyzed by culture and quantitative polymerase chain reaction (qPCR) 
specific for S. sonnei 53G. The day before discharge (Day 64), two stool samples will be 
collected to confirm that the subject is no longer shedding. Instructions for appropriate 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
49
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
50
collection, transportation and storage of stool samples will be provided to the 
investigators. For diarrhea episodes to be considered as separate episodes, there should be 
at least a 6-hour interval between them (refer to Section 4 for details on stool grading).
On the 5th day after challenge (Day 62), subjects will receive as first-line treatment
500 mg of ciprofloxacin twice daily for 3 days. Subjects with contraindication to 
ciprofloxacin may receive as second-line treatment trimethoprim-sulfamethoxazole 
(160 mg/800 mg twice daily), amoxicillin (500 mg three times daily) for 5 days, or any 
antibiotic that is deemed suitable according to local guidelines and the investigator’s 
assessment can be used.
Subjects may be treated with antibiotics before the 5th day after challenge (Day 62) if:

They have diarrhea (any severity stool Grade 3 or higher) and two or more of the 
following symptoms: severe abdominal pain/cramps, severe nausea, severe 
headache, severe myalgia, severe arthralgia, gross blood in 2 stools, any fever 
(38.0ºC measured orally), or any vomiting.

They experience unexpectedly severe events such as hypotension (disproportionate 
to volume loss), renal dysfunction, or altered mental state (e.g. somnolence) at the 
discretion of the investigators.

A study physician determines early treatment is warranted for other reasons.
A subject receiving early antibiotic treatment will still remain on the unit until the 
planned day of discharge (the 9th day of inpatient stay: Day 65). On that day, if a subject 
is clinically well and has had at least 2 negative stool cultures, collected at least 6 hours 
apart, for S. sonnei, s/he will be discharged. A subject that, on the planned day of 
discharge, still had S. sonnei isolated from the Day 64 stools will be asked to remain in 
the unit until s/he is no longer shedding. A subject still shedding 48 hours after initiation 
of ciprofloxacin will be switched to a Septra DS (1 tablet twice a day for five days). If a 
subject is still positive 48 hours after the second-line antibiotic is administered, a culture 
and antibiotic sensitivity test will be obtained and therapy initiated based on sensitivity
results. If a subject has two consecutive negative stool samples and is eligible to be 
discharged from the inpatient stay but did not finish his treatment course, s/he can be 
given the remaining doses to complete at home.
Following discharge, subjects will return at 28 days (Visit 6), 56 days (Visit 7) and 6 
months (Visit 8) after challenge for outpatient clinical assessment. During these visits, 
clinical assessment will be done to assess their general health status and find out about 
the occurrence of AESI, any AE and SAE. 
Subjects will be advised at the time of their discharge to contact the study staff/doctor if 
they feel unwell. The subjects will be followed up until 6 months after the challenge. At 
the last study visit, at 6 months after challenge, the subject will be reviewed for the 
occurrence of any AESI and the site staff will ensure all AEs are resolved.
Through the entire study, all subjects will be advised to report to the study facility 
whenever they are sick. Standard patient care, according to local guidelines will be 
provided for all illnesses in both the outpatient and inpatient facilities. Additional 
investigations may be conducted if the investigator considers them necessary to better 
evaluate the subject’s condition. An overview of the study design is given in Figure 1.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
50
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
51
Figure 1
Study design (Amended: 23 July 2019)
*Refer to Section 3.2 for details of procedures during the inpatient stay (Amended: 23 July 2019)
Scr: Screening
N: Number of subjects
B: Blood sampling
S: Stool sampling
U: Urine sampling
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
51
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
52
Protocol waivers or exemptions are not allowed unless necessary for the management of 
immediate safety concerns. Therefore, adherence to the study design requirements, 
including those specified in the outline of study procedures (Section 6.4.1), are essential 
and required for study conduct.

Experimental design: Phase IIB, observer-blind, randomized, placebo control, 
mono-centric study with two parallel groups (S. sonnei group and placebo group).

Duration of the study: Each subject will be followed up for approximately 6 months 
after challenge with the pathogenic S. sonnei strain 53G, with a total study duration 
of approximately 32 weeks (i.e., 8 months) for each study subject.

Epoch 001: Starting at Screening Visit (Day -45 to Day -1) and ending before 
Visit 1 (Day 1).

Epoch 002: Starting the day of randomization and first vaccination (Visit 1) and 
ending before the receipt of the challenge agent, 28 days after second 
vaccination (Visit 5).

Epoch 003: Starting with the receipt of the challenge agent at 28 days after 
second vaccination (Visit 5) and ending 6 months after challenge (Visit 8).

Primary completion date (PCD): End of inpatient stay (Visit 5, Day 64).
(Amended: 23 July 2019)
Refer to glossary of terms for the definition of PCD.

End of Study (EoS): Last testing results released of samples collected for primary 
and secondary objectives at Visit 8.
Refer to glossary of terms for the definition of EoS.

Study groups:
Table 1
Study groups and epochs foreseen in the study
Study 
groups
Number of 
subjects
Age (Min - Max)
Epochs
Epoch 001
Epoch 002
Epoch 003
Screening
1st and 2nd vaccination
Challenge
S. sonnei
36
18 years – 50 years
x
x
x
Placebo
36
18 years – 50 years
x
x
x
Table 2
Study groups and treatment foreseen in the study
Treatment name
Vaccine/ placebo/
challenge agent name
Study Groups
S. sonnei
Placebo
S. sonnei
1790GAHB
x
Placebo
GAHB-Placebo
x
Challenge
S. sonnei 53G strain
x
x

Control: Placebo control with GAHB-Placebo with the same composition as the 
vaccine except the active ingredient. GAHB-Placebo will also be used as diluent for 
bedside mixing of the vaccine.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
52
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
53

Vaccination schedule: Subjects will receive 2 doses of either the study vaccine or 
placebo 28 days apart. At 28 days after the second dose, all subjects will receive the 
challenge dose.

Treatment allocation: Following the screening period before the first vaccination 
(Day -45 to Day -1), subjects will be randomized in a 1:1 ratio to receive either the 
study vaccine or the placebo.

Blinding: The study will be observer-blind.
Table 3
Blinding of study epochs
Study Epochs
Blinding
Screening (Epoch 001)
N/A
1st and 2nd vaccination (Epoch 002)
observer-blind
Challenge (Epoch 003)
observer-blind

Sampling schedule:

5 mL for hematology: Screening Visit, Visit 2, Visit 3, Visit 4, Visit 5 and 
Visit 8. Additionally, hematology is repeated weekly until resolution if 
neutropenia occurs.

5 mL for biochemical analysis: Screening Visit.

10 mL for hepatitis B, hepatitis C and HIV: Screening Visit.

10 mL for HLA-B27 testing: Screening Visit.

5 mL for local anti S. sonnei LPS IgG Screening-ELISA: Screening Visit.

Urine sample for urinalysis: Screening Visit and Visit 5.

Urine sample for pregnancy test for women of childbearing potential: Screening 
Visit, Visit 1, Visit 3, Visit 5 and Visit 8.

20 mL for immunological tests (antibody response) at Visit 1, Visit 2, Visit 3, 
Visit 4, Visit 5, 7 days after Visit 5 (Day 64), Visit 6,

For serum bactericidal activity tests at Visit 1, Visit 3 and Visit 5

And for Fc glycosylation test on leftover serum samples collected at Visit 1 and 
Visit 5.

50 mL of peripheral venous blood for α4β7+/- plasmablast analysis by ELISA
and RNA extraction from PBMCs for gene expression profiling: Visit 1, Visit 2, 
Visit 4 and 7 days after Visit 5 (Day 64). (Amended: 23 July 2019)

Stool sample for inflammatory response before challenge at Visit 5 (Day 57) and 
daily, post challenge, during inpatient stay (Day 57 to Day 64).

Stool sample: for microbiome testing at Visit 1 and Visit 5, for S. sonnei specific
sIgA at Visit 1, Visit 2, Visit 4 and 7 days after challenge (Day 64) and stool 
analysis, culture and qPCR daily during inpatient stay (from Visit 5 to 7 days 
after challenge [Day 57 to Day 64] or prolonged until 2 consecutive negative 
stool samples if subject still shedding).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
53
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
54

Type of study: self-contained.

Data collection: Standardized electronic Case Report Form (eCRF).

Safety monitoring: An Independent Data Monitoring Committee (IDMC) will be 
established to monitor the safety of subjects throughout the study. The IDMC will 
review unblinded data, to assess safety signals and make recommendations to the 
Sponsor concerning continuation, termination, or other modifications of the study 
based on the observed adverse effects. The membership and roles of the IDMC will 
be outlined in the IDMC charter.
The safety review team (SRT) will monitor the safety of subjects throughout the 
study. The SRT will review blinded data, assess safety signals and make 
recommendations to the IDMC and Sponsor concerning continuation, termination, or 
other modifications of the study based on the observed adverse effects.
A dedicated Safety Management Plan will be prepared to ensure appropriate safety 
reporting responsibilities and roles are defined.
Refer to Section 9.10 for detailed description of holding rule and safety monitoring.
4.
CASE DEFINITIONS
Stools will be graded as follows:

Grade 1: firm formed;

Grade 2: soft formed;

Grade 3: viscous opaque liquid or semi-liquid which assumes the shape of the bowl;

Grade 4: watery opaque liquid;

Grade 5: clear watery or mucoid liquid.
4.1.
Diarrhea
For the purpose of this study, diarrhea is defined as:

Moderate diarrhea: 4 to 5 loose or watery (Grade 3 to 5) stools or 400 to 800 grams 
of Grade 3 to 5 stools within 24 hours.

Severe diarrhea: 6 or more loose or watery (Grade 3 to 5) stools or > 800 grams of 
Grades 3 to 5 stools within 24 hours or required medical intervention. In case of 
severe diarrhea, medical intervention is defined as intravenous (IV) fluids 
administration or anticipation of antibiotic treatment before the 5th day after 
challenge.

More severe diarrhea: 10 or more loose or watery (Grade 3 to 5) stools or 1000 
grams of Grade 3 to 5 stools within 24 hours.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
54
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
55
4.2.
Dysentery (Amended: 23 July 2019)
For the purpose of the endpoint “Rate of shigellosis as defined by the CHIM expert 
working group occurring within a period starting with challenge visit and lasting until 
the end of the inpatient stay, in all subjects”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [oral 
temperature ≥38.0oC OR ≥1 moderate constitutional/enteric symptom OR ≥2 
episodes of vomiting in 24 hours]. In this case constitutional/enteric symptom are 
the following: nausea, abdominal pain, abdominal cramping, myalgia, arthralgia, 
malaise.
For the purpose of the endpoint “Rate of shigellosis, as defined by: severe diarrhea OR 
moderate diarrhea with fever or with one or more moderate constitutional/enteric 
symptoms OR dysentery”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [≥1 
reportable constitutional/enteric symptom]. In this case constitutional/enteric 
symptom are the following: headache, fatigue, arthralgia, malaise, myalgia, chills, 
nausea, abdominal cramping, abdominal pain, gas, anorexia, vomiting.
For the purpose of the endpoint “Rate of more severe shigellosis as defined by: severe 
or moderate diarrhea with fever or with one or more severe constitutional/enteric 
symptom OR dysentery [[≥2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric 
symptom]].”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours] AND 
[oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]. In this 
case constitutional/enteric symptom are the following: headache, fatigue, 
arthralgia, malaise, myalgia, chills, nausea, abdominal cramping, abdominal pain, 
gas, anorexia, vomiting.
For the purpose of the endpoints “Dysentery” and “Confirmed S. sonnei 53G shedding 
AND moderate or severe diarrhea OR dysentery OR presence of oral temperature ≥ 
38.5°C OR presence of one or more severe intestinal symptoms (abdominal pain, 
cramping, nausea, vomiting, gas, and anorexia)”, dysentery is defined as follows:

A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours 
and presence of constitutional/enteric symptoms. In this case, 
constitutional/enteric symptoms consist of headache, fatigue, arthralgia, malaise, 
myalgia, chills, nausea, abdominal cramping, abdominal pain, gas, anorexia, 
vomiting, and fever.
(Amended: 23 July 2019)
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
55
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
56
4.3.
Shigellosis
For the primary and secondary objectives in the challenge phase of the study, the protocol
primary case definition for shigellosis is:

Shedding of S. sonnei 53G accompanied by moderate or severe diarrhea OR 
shedding with an oral temperature of 38.5°C).
For the secondary objectives in the challenge phase of the study, 2 definitions of 
shigellosis are used:
1.
CHIM working group case definition for shigellosis as defined by any one of the 
three following possible endpoints:

Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose 
stools in 24 hours]

Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours]  

Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [oral temperature 38.0°C OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours].
2.
Shigellosis as defined by any one of the three following possible endpoints:

Severe diarrhea defined as [≥6 loose stools in 24 hours OR ˃800 grams loose 
stools in 24 hours]

Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 moderate 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [≥1 reportable constitutional/enteric symptom].
For the secondary objectives in the challenge phase of the study, more severe shigellosis 
is defined by any one of the two following possible endpoints: 

Moderate OR severe diarrhea [≥4 loose stools in 24 hours OR ≥400 grams loose 
stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 severe 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric 
symptom]. (Amended: 23 July 2019)
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
56
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
57
5.
STUDY COHORT
5.1.
Number of subjects/center
Target enrolment is up to 72 eligible subjects (36 per treatment group). Refer to Sections 
5.2 and 5.3 for eligibility criteria and to Section 11.4 for the determination of sample size.
Enrolment will take place in 4 overlapping cohorts of 18 subjects each to accommodate 
for the availability of beds required for the challenge phase of the study at the clinical site 
(see also Section 11.12.1). However, if for any reason, a cohort does not reach the 
planned 18 subjects, additional subjects can be added in the next cohorts. The maximum 
number of subjects must not be more than 20 (maximum number of beds in the clinic) in 
each cohort. The vaccination and challenge will be done per cohort.
5.2.
Inclusion criteria
Deviations from inclusion criteria are not allowed because they can potentially jeopardize 
the scientific integrity, regulatory acceptability of the study or subject safety. Therefore, 
adherence to the criteria as specified in the protocol is essential.
All subjects must satisfy ALL the following criteria at study entry:

Subjects who, in the opinion of the investigator, can and will comply with the 
requirements of the protocol (e.g. completion of the diary cards, return for follow-up 
visits).

Written informed consent obtained from the subject prior to performing any study 
specific procedure.

Individuals who, after the nature of the study has been explained to them, have 
shown adequate comprehension of the study procedures and knowledge of study.

A male or female between, and including, 18 and 50 years of age at the time of the 
first vaccination.

Healthy subjects as established by medical history and clinical examination before 
entering into the study.

Seronegative for HIV, hepatitis B and C.

Female subjects of non-childbearing potential may be enrolled in the study.

Non-childbearing potential is defined as pre-menarche, current bilateral tubal 
ligation or occlusion, hysterectomy, bilateral ovariectomy or post-menopause. 
Please refer to the glossary of terms for the definition of menarche and menopause.

Female subjects of childbearing potential may be enrolled in the study, if the subject:

Has practiced adequate contraception for 30 days prior to vaccination, and

Has a negative pregnancy test on the day of vaccination, and

Has agreed to continue adequate contraception during the entire study period.
Please refer to the glossary of terms for the definition of adequate contraception.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
57
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
58
5.3.
Exclusion criteria
Deviations from exclusion criteria are not allowed because they can potentially 
jeopardize the scientific integrity, regulatory acceptability of the study or subject safety. 
Therefore, adherence to the criteria as specified in the protocol is essential.
The following criteria should be checked at the time of study entry and at each 
vaccination and challenge administration visit. If ANY exclusion criterion applies, the
subject must not be included in the study:

Received an investigational or non-registered medicinal product within 30 days (Day 
-29 to Day 1) prior to informed consent, or planned use during the study period.

Any behavioral or cognitive impairment or psychiatric disease that, in the opinion of 
the investigator, may interfere with the subject's ability to participate in the study.

History of any neurological disorders or seizures.

Any other clinical condition that, in the opinion of the investigator, might pose 
additional risk to the subject due to participation in the study.

HLA-B27 positive test at screening and/or with history of reactive arthritis.

Clinical conditions representing a contraindication to intramuscular vaccination and 
blood draws.

Chronic administration (defined as more than 14 days in total) of 
immunosuppressants or other immune-modifying drugs during the period starting six 
months prior to the first vaccine/placebo dose. For corticosteroids, this will mean 
prednisone 20 mg/day, or equivalent. Inhaled except for doses > 800 g/day and 
topical steroids are allowed.

Administration of long-acting immune-modifying drugs at any time during the study 
period (e.g. infliximab). Subjects may be on chronic or as needed medications if, in 
the opinion of the site principal investigator or appropriate sub-investigator, they 
pose no additional risk to subject safety or assessment of reactogenicity and 
immunogenicity and do not indicate a worsening of medical diagnosis or condition.

Known bleeding diathesis or any condition that may be associated with a prolonged 
bleeding time.

Concurrently participating in another clinical study, at any time during the study 
period, in which the subject has been or will be exposed to an investigational or a 
non-investigational vaccine/product (pharmaceutical product or device).

History of having participated in a previous Shigella challenge study.

Individuals who have a previously laboratory confirmed case of disease caused by S. 
sonnei or serology positive for local anti S. sonnei LPS IgG Screening-ELISA at 
screening.

History of any serious chronic or progressive disease according to judgment of the 
investigator (e.g., neoplasm, insulin dependent diabetes, cardiac, renal or hepatic 
disease).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
58
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
59

History of any malignancy or lymphoproliferative disorder.

Known to be part of study personnel or being a close family member to the personnel 
conducting this study.

History of anaphylactic reaction or allergy to vaccine/placebo or challenge agent
components or any other allergies deemed by the investigator to increase the risk of 
an AE if they were to participate in the study.

Known allergy to ciprofloxacin or the other antibiotics used for treatment as deemed 
by the investigator.

Individuals receiving a course of antibiotics within a week of the challenge will be 
ineligible to receive the challenge strain.

History of gastric acid hyper-secretory disorders (e.g., Zollinger-Ellison syndrome) 
as assessed and judged by the investigator or any other significant intestinal disorder.

Any confirmed or suspected immunosuppressive or immunodeficient condition, 
based on medical history and physical examination (no laboratory testing required).

Family history of congenital or hereditary immunodeficiency.

History of any reaction or hypersensitivity likely to be exacerbated by any 
component of the vaccine/placebo or challenge agent.

Acute disease and/or fever at the time of enrolment.

Fever is defined as temperature 38.0°C / 100.4°F. The preferred location for 
measuring temperature in this study will be the oral cavity.

Subjects with a minor illness (such as mild diarrhea, mild upper respiratory 
infection) without fever may, be enrolled at the discretion of the investigator. 
Note: enrolment may be postponed/delayed until such transient circumstances have 
terminated.

Acute or chronic, clinically significant pulmonary, cardiovascular, hepatic or renal 
functional abnormality, as determined by physical examination or laboratory 
screening tests. Chronic medical diagnoses or conditions should be stable for the last 
60 days. This includes no change in chronic prescription medication, dose, or 
frequency as a result of deterioration of the chronic medical diagnosis or condition in 
the 60 days prior to enrolment.

A clinically significant sign or symptoms of acute illness, significant anomalies in 
vital signs.

Known to handle food as part of work related activities.

Hepatomegaly, right upper quadrant abdominal pain or tenderness.

Received immunoglobulins or any blood products within 180 days prior to informed 
consent or planned administration during the study period.

Pregnant or lactating female.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
59
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
60

Female planning to become pregnant or planning to discontinue contraceptive 
precautions.

Females with history of stillbirth, neonatal loss, or previous infant with anomaly, 
except those who have had a planned termination of pregnancy, hysterectomy or 
bilateral tubal ligation.

History of chronic alcohol consumption and/or drug abuse. Chronic alcohol 
consumption is defined as: a prolonged period of frequent, heavy alcohol use; the 
inability to control drinking once it has begun; physical dependence manifested by 
withdrawal symptoms when the individual stops using alcohol; tolerance, or the need 
to use more and more alcohol to achieve the same effects; a variety of social and/or 
legal problems arising from alcohol use.

Known to have close household or professional contacts with people with 
immunosuppressive condition.

Documented HIV, hepatitis B and C positive subject.

Any condition which, in the opinion of the investigator, may pose an increased and 
unreasonable safety risk to the subject if they participated in the study.

Subjects with a baseline neutrophil count below 1800 cells/L (LLN) OR with 
clinically significant abnormalities in other laboratory values (CBC, CMP, UA), 
according to local reference ranges and investigator judgment.

Previous history of Benign Ethnic Neutropenia, or drug related Neutropenia.

Concomitant treatment with neutropenic agents.
6.
CONDUCT OF THE STUDY
6.1.
Regulatory and ethical considerations, including the 
informed consent process
The study will be conducted in accordance with all applicable regulatory requirements.
The study will be conducted in accordance with the ICH Guideline for GCP, all 
applicable subject privacy requirements and the guiding principles of the Declaration of 
Helsinki. 
GSK will obtain favorable opinion/approval to conduct the study from the appropriate 
regulatory agency, in accordance with applicable regulatory requirements, prior to a site 
initiating the study in that country.
Conduct of the study includes, but is not limited to, the following:

Institutional Review Board (IRB)/Independent Ethics Committee (IEC) review and 
favorable opinion/approval of study protocol and any subsequent amendments.

Subject informed consent.

Investigator reporting requirements as stated in the protocol.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
60
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
61
GSK will provide full details of the above procedures to the investigator, either verbally, 
in writing, or both.
Freely given and written informed consent must be obtained from each subject prior to 
participation in the study. 
GSK Biologicals will prepare a model Informed Consent Form (ICF) which will embody 
the ICH GCP and GSK Biologicals required elements. While it is strongly recommended 
that this model ICF is to be followed as closely as possible, the informed consent 
requirements given in this document are not intended to pre-empt any local regulations 
which require additional information to be disclosed for informed consent to be legally 
effective. Clinical judgment, local regulations and requirements should guide the final 
structure and content of the local version of the ICF.
The investigator has the final responsibility for the final presentation of the ICF, 
respecting the mandatory requirements of local regulations. The ICF generated by the 
investigator with the assistance of the sponsor’s representative must be acceptable to 
GSK Biologicals and be approved (along with the protocol, and any other necessary 
documentation) by the IRB/IEC.
6.2.
Subject identification and randomization
6.2.1.
Subject identification
Subject identification numbers will be assigned sequentially to the subjects who have 
consented to participate in the study, according to the range of subject identification 
numbers allocated to the study center.
6.2.2.
Randomization of treatment
6.2.2.1.
Randomization of supplies
The randomization of supplies for the Vaccination Phase (1790GAHB vaccine and 
placebo) within blocks will be performed by the study biostatistician or delegate. Entire 
blocks will be shipped to the study center. No randomization will be done for the 
challenge phase.
6.2.2.2.
Treatment allocation to the subject
The treatment numbers will be allocated by dose. Throughout the study, a single 
treatment number will identify each dose to be administered to each randomized subject.
6.2.2.2.1.
Study group and treatment number allocation
The target will be to enroll approximately 72 eligible subjects who will be randomly 
assigned to two study groups in a 1:1 ratio (approximately 36 subjects in each group).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
61
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
62
Subjects will be enrolled in 4 overlapping cohorts of 18 subjects each, for logistical 
reasons at the clinical site, therefore a 1:1 ratio should be maintained at the cohort level.
However, if for any reason, a cohort does not reach the planned 18 subjects, additional 
subjects can be added in the next cohorts. The maximum number of subjects must not be 
more than 20 (maximum number of beds in the clinic) in each cohort.
Allocation of the subject to a study group at the investigator site will be performed using 
the Source DataBase for Internet Randomization system (SBIR). The randomization 
algorithm might use a minimization procedure; more details are provided in the Statistical 
Analysis Plan.
After obtaining the signed and dated ICF from the subject and having checked the
eligibility of the subject, the site staff in charge of the vaccine/placebo administration will 
access SBIR. Upon providing the subject identification number, the randomization
system will determine the study group and will provide the treatment number to be used 
for each dose.
A randomization blocking scheme (1:1 ratio) will be used to ensure the balance between 
treatments is maintained, accounting also for the enrolment cohorts: same number of 
vaccine and control recipients in each cohort.
The number of each administered treatment must be recorded in the eCRF on the Vaccine 
Administration screen.
When SBIR is not available, please refer to the SBIR user guide or the Study Procedures 
Manual (SPM) for specific instructions.
6.2.3.
Allocation of subjects to assay subsets
Leftover serum samples collected at Day 1 and 28 days after second vaccination for the 
antibody response analysis will be used for the Fc glycosylation test (immunological tests 
mentioned in the tertiary objectives) that will be performed at Rockefeller University (see 
Appendix B).
6.3.
Method of blinding
Data will be collected in an observer-blind manner. By observer-blind, it is meant that 
during the course of the study, the vaccine/placebo recipient and those responsible for the 
evaluation of any study endpoint (e.g. safety, reactogenicity, immunogenicity and 
efficacy) will be unaware of which vaccine (study vaccine or placebo) was administered. 
To do so, vaccine/placebo preparation and administration will be done by authorized
medical personnel who will not participate in any of the study clinical evaluation assays.
The laboratories in charge of the laboratory testing will be blinded to the treatment, 
subject and visit number, and codes will be used to link the subject, visit and study
(without any link to the treatment attributed to the subject) to each sample.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
62
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
63
6.4.
General study aspects
Supplementary study conduct information not mandated to be present in this protocol is 
provided in the accompanying SPM. The SPM provides the investigator and the site 
personnel with administrative and detailed technical information that does not impact the 
safety of the subjects.
6.4.1.
Independent data monitoring committee
An IDMC will be established by GSK Biologicals for the purpose of monitoring the 
study and to provide independent, non-binding advice on safety and ethics. The IDMC 
will provide recommendations about stopping, continuing or modifying the study. Refer 
to Section 9.10 for a description of the holding rule and safety monitoring put in place for 
this study.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
63
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
64
6.5.
Outline of study procedures
Table 4
List of study procedures
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient 
stay
Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to
Day -1
Day 1
Day 3 and
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to
Day 65 8
Day 
85
Day 
113
Day 237 
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9
Inpatient 
stay
Post-challenge
Informed consent
●
Check inclusion/exclusion criteria
●
●
●
Collect demographic data
●
Measure/record height and weight
●
Medical history
●
History directed physical examination
O
O
O
O
O
O
Physical examination
●
●
●
●
Urine pregnancy test 1
●
●
●
●
●
Check contraindications to vaccination
O
O
O
Pre-vaccination/placebo/challenge agent 
administration body temperature
●
●
●
Vaccine/placebo/challenge agent administration
Study group and treatment number 
allocation
●
Recording of administered treatment 
number
●
●
Vaccine/placebo administration
●
●
Challenge with S. sonnei 53G
●
Laboratory assays
Blood sampling for antibody response 
(~20 mL)
●2, 3
●
●2
●
●2, 3
●4
●
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
64
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
65
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient 
stay
Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to
Day -1
Day 1
Day 3 and
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to
Day 65 8
Day 
85
Day 
113
Day 237 
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9
Inpatient 
stay
Post-challenge
Blood sampling for PBMC isolation 
(α4β7+/- plasmablasts response and 
transcriptomics) (~50 mL) (Amended: 23
July 2019)
●
●
●
●4
Blood sampling for hematology (5 mL) 5
●
●
●
●
●
●
Blood sampling for biochemical analysis 
(~5 mL)
●
Serology for virology: HIV, HBV, HCV 
(~10 mL)
●
Blood test for HLA-B27 and local anti S. 
sonnei LPS IgG (Screening-ELISA) (~15 
mL)
●
Urine sampling for urinalysis 6
●
●
Stool sample for sIgA
●
●
●
●4
Stool sample for microbiome testing7
●
●
Stool sample for inflammatory response
●
●
Stool assessment: weight, consistency, 
blood and S. sonnei by culture and qPCR
●
Safety assessment
Record any concomitant 
medications/vaccinations
●
●
●
●
●
●
●
●
●
●
Distribution of diary cards
O
O
Return of diary cards
●
●
Diary card transcription by investigator
●
●
Recording of solicited adverse events 
within 7 days post-vaccination
●
●
Recording of unsolicited adverse events 
within 28 days post-vaccination
●
●
●
●
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
65
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
66
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient 
stay
Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to
Day -1
Day 1
Day 3 and
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to
Day 65 8
Day 
85
Day 
113
Day 237 
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9
Inpatient 
stay
Post-challenge
Recording of solicited adverse events 
within 7 days post-challenge
●
Recording of unsolicited adverse events 
within 28 days post-challenge
●
●
Recording of AESI, SAEs and
pregnancies
●
●
●
●
●
●
●
●
●
●
Recording of SAEs related to study 
participation, or to a concurrent GSK 
medication/vaccine
●
●
●
●
●
●
●
●
●
●
Study Conclusion
●
V: Visit, D: Day, Vacc: Vaccination; HIV: Human Immunodeficiency Virus, HCV: Hepatitis C Virus, HBV: Hepatitis B Virus, ELISA: Enzyme-linked immunosorbent assay, AESI: 
Adverse Events of Specific Interest, SAEs: Serious Adverse Events.
● is used to indicate a study procedure that requires documentation in the individual eCRF.
O is used to indicate a study procedure that does not require documentation in the individual eCRF.
1Female subjects will be randomized and study vaccine/placebo or challenge agent may only be administered if the pregnancy test is negative.
2Serum bactericidal assay will be performed at these visits in addition to the S. sonnei LPS IgG antibody response.
3Fc glycosylation test on leftover serum samples will be performed at these visits in addition to the S. sonnei LPS IgG antibody response and serum bactericidal assay.
4Sampling to be done 7 days after challenge agent administration (i.e., Day 64).
5Additionally, hematology is repeated weekly until resolution if neutropenia occurs. On the day of vaccination/challenge, sampling will be done before vaccination/challenge.
6Urine dipstick to be done for all subjects and, in case of abnormal results, a urine culture is to be performed (urinalysis).
7Before vaccination/challenge (Day 1/Day 57 sample can be collected by the subject at most a week before and stored as described in the Investigator Manual and SPM.
8Sampling to be done daily during inpatient stay and if subject is still shedding 7 days post-challenge administration (Day 64). However, all subjects even if not shedding anymore will 
remain in the inpatient stay until 7 days post-challenge and will be discharged on Day 65.
9 Samples collection can be performed between Day 56 and Day 57.
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
66
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
67
Whenever possible, the investigator should arrange study visits within the interval 
described in Table 5.
Table 5
Intervals between study visits (Amended: 23 July 2019)
Interval
Optimal length of interval
Allowed interval
Screening visit Visit 1
-7 days
-45 days – -1 days
Visit 1 Phone Call
3 days
2 days - 6 days
Visit 1 Visit 2
7 days
7 days - 10 days
Visit 1 Visit 3
28 days
26 days - 33 days
Visit 3 Phone call
3 days
2 days - 6 days
Visit 3 Visit 4
7 days
7 days - 10 days
Visit 3 Visit 5
28 days
26 days - 33 days
Visit 5 Inpatient stay
9 days
9 days - as needed
Visit 5 Visit 5 post-challenge 
blood draw
(Amended: 23 July 2019)
7 days
(Amended: 23 July 2019)
7 days – 10 days
(Amended: 23 July 2019)
Visit 5 Visit 6
28 days
28 days - 35 days
Visit 5 Visit 7
56 days
49 days - 63 days
Visit 5 Visit 8
180 days
166 days - 194 days
6.6.
Detailed description of study procedures
6.6.1.
Informed consent
The signed informed consent of the subject must be obtained before study participation. 
Refer to Section 6.1 for the requirements on how to obtain informed consent.
6.6.2.
Check inclusion and exclusion criteria
Check all inclusion and exclusion criteria as described in Sections 5.2 and 5.3 before 
enrolment.
Subjects who meet all inclusion criteria and none of the exclusion criteria, with screening 
tests within normal values and women of childbearing potential with negative urine 
pregnancy test at Screening will be eligible for enrolment.
Continued participation of the subject in the study will also be checked against inclusion 
and exclusion criteria.
6.6.3.
Collect demographic data
Record demographic data such as year of birth, gender, geographic ancestry and 
anthropometric measurements (height and weight) in the subject’s eCRF.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
67
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
68
6.6.4.
Medical history
Obtain the subject’s medical history by interview and/or review of the subject’s medical 
records and record any pre-existing conditions or signs and/or symptoms present in a 
subject prior to the first study vaccination in the eCRF.
Relevant medical history can also include any medical history that contributes to the 
understanding of an adverse event that occurs during study participation, if it represents 
an exacerbation of an underlying disease/pre-existing problem.
6.6.5.
Physical examination / history directed physical examination
Perform a complete physical examination at Screening, at each vaccination visit and at 
the day of challenge (Day 57) and a symptom/history directed physical examination of 
the subject at each other visit of the vaccination and challenge phase.
The physical examination will be performed by the investigator and any outcome 
recorded in the subject source document. Physical examination includes assessment of 
oral body temperature and resting vital signs as appropriate, after at least 10 minutes of 
rest.
If the investigator determines that the subject’s health on the days of vaccination 
temporarily precludes vaccination, the visit will be rescheduled within the site planning 
as possible. As challenge is performed per cohort, any subject with fever the day of 
challenge will not receive the challenge dose.
Treatment of any abnormality observed during this examination has to be performed 
according to local medical practice outside this study or by referral to an appropriate 
health care provider.
6.6.6.
Pregnancy test
Female subjects of childbearing potential are to have a urine pregnancy test at Screening
visit, prior to study vaccine/placebo administration (any dose), prior to challenge and at 
last study visit (Visit 8). The study vaccine/placebo and challenge agent may only be 
administered if the pregnancy test is negative.
Note: Pregnancy test must be performed even if the subject is menstruating at the time of 
the study visit.
6.6.7.
Check contraindications to vaccination
Contraindications to vaccination must be checked at Screening visit and at the beginning 
of each vaccination visit. Refer to Section 7.5 for more details.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
68
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
69
6.6.8.
Assess pre-vaccination body temperature
The oral body temperature of each subject needs to be measured prior to any study 
vaccine/placebo or challenge agent administration. If the subject has fever (fever is 
defined as temperature 38.0°C/100.4°F) on the day of vaccination, the visit will be 
rescheduled within the allowed interval (see Table 5). If fever occurs at the day of 
challenge, the subject will not receive the challenge agent.
6.6.9.
Study group and treatment number allocation
Study group and treatment number allocation will be performed as described in Section 
6.2.2. The number of each administered treatment must be recorded in the eCRF.
6.6.10.
Sampling
Refer to the Module on Biospecimen Management in the Sponsor’s SPM for detailed 
instructions for the collection, handling and processing of the samples.
6.6.10.1.
Blood sampling for safety or immune response assessments
Blood samples will be taken during certain study visits as specified in Section 3 and 
Section 6.5. Refer to the SPM for details on samples handling, storage and shipment 
conditions.

An overall volume of 400 mL will be collected per subject during the entire study 
period (8 months).
6.6.10.2.
Urine sampling

A urine sample for urinalysis should be collected from all subjects at each predefined
timepoint, as per investigator’s judgment.

Urine samples for the pregnancy test will be collected from women of childbearing 
potential at each predefined timepoint (refer to Section 6.6.6).
6.6.10.3.
Stool sampling
For the microbiome analysis, subjects will take a stool sample at home/at the hospital 
using the sampling material and instructions provided as close as possible to the study
visit (preferably on the day of the visit). Immediately after stool sampling, participants 
will write down date and time of sampling and time since previous defecation and 
determine stool consistency using the Bristol Stool Score chart provided.
Aliquots of stool will be collected for fecal sIgA, inflammatory response, culture and 
qPCR, at each predefined timepoint (see Table 4). If, during the inpatient stay, no stools
are passed on a given day, up to two rectal swabs can be collected for culture and qPCR 
(see also Section 3.2). The aliquots for fecal sIgA and inflammatory markers should be 
frozen at -80°C as soon as possible at the clinical site.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
69
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
70
Refer to the SPM for more details on sample collection and storage conditions.
6.6.11.
Study vaccine/placebo administration

After completing all prerequisite procedures prior to vaccination, one dose of study 
vaccine or placebo will be administered IM preferably in the deltoid of the non-
dominant arm (refer to Section 7 for detailed description of the vaccine/placebo
administration procedure). If the investigator or delegate determines that the 
subject’s health on the day of administration temporarily precludes vaccine/placebo
administration, the visit will be rescheduled within the allowed interval for this visit 
(refer to Table 5).

The subjects will be observed closely for at least 30 minutes following the 
administration of the vaccine/placebo, with appropriate medical treatment readily 
available in case of anaphylaxis.
6.6.12.
Challenge administration and inpatient stay

After completing all prerequisite procedures prior to challenge, one challenge dose 
of S. sonnei 53G will be administered. If the investigator or delegate determines that 
the subject’s health on the day of administration precludes challenge administration, 
the challenge agent will not be administrated to the subject.

The subjects will be observed closely for the entire period of the inpatient stay 
(9 days, from Day 57 to Day 65) following the administration of the challenge, with 
appropriate medical treatment readily available in case of need.
Refer to Section 3.2 and SPM for more details related to the preparation and 
administration of the challenge agent and the collection of samples during the inpatient 
stay.
6.6.13.
Check and record concomitant medication/vaccination and 
intercurrent medical conditions
Concomitant medication/vaccination must be checked and recorded in the eCRF as 
described in Section 7.6.
Intercurrent medical conditions must be checked and recorded in the eCRF as described 
in Section 7.7.
6.6.14.
Recording of AEs, SAEs, pregnancies and AESIs

Refer to Section 9.3 for procedures for the investigator to record AEs, SAEs, 
pregnancies and AESIs. Refer to Section 9.4 for guidelines and how to report SAE, 
pregnancy and AESI reports to GSK Biologicals.

The subjects will be instructed to contact the investigator immediately should they
manifest any signs or symptoms they perceive as serious. 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
70
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
71
6.6.14.1.
Subject Diary
A Paper Diary (pDiary), hereafter referred to as Subject Diary, will be used in this study 
to capture solicited adverse events. The subject should be trained on how and when to 
complete each field of the Subject Diary.
Subject Diary training should be directed at the individual(s) who will perform the 
measurements of adverse events and who will enter the information into the Subject 
Diary. This individual may not be the subject, but if a person other than the subject enters 
information into the Subject Diary, this person’s identity must be documented in the 
Subject’s source records. Any individual that makes entries into the Subject Diary must 
receive training on completion of the Subject Diary at the time of the visit when Subject 
Diary is dispensed. This training must be documented in the subject’s source record.
The same individual should complete the Subject Diary throughout the course of the 
study.
The subject should be trained on how to self-measure local solicited adverse events and 
body temperature. 
The measurement of solicited local adverse events is to be performed using the ruler 
provided by the site.
Subjects will be instructed to measure and record the oral body temperature in the 
evening. Should additional temperature measurements be performed at other times of 
day, subjects will be instructed to record the highest temperature in the Subject Diary.
6.6.14.2.
Post-vaccination reminders
Reminder calls or alerts are not intended to be an interview for collection of safety data. 
If the subject wishes to describe safety information, this information should only be 
collected by a healthcare professional at the site, and the safety data described must be 
written down in the subject’s medical chart.
6.6.14.2.1. Subject Diary reminder calls
Subject Diary reminder calls will be performed on Day 3, Day 7, Day 31 and Day 35. 
The purpose of this call is to remind the subject about completion of the Subject Diary. 
The call follows the Subject Diary Reminder Telephone Call Script provided to the site. 
The subject should be reminded to contact the site via the telephone number provided in 
the informed consent to discuss medical questions.
6.6.15.
Study conclusion
The investigator will:

Review data collected to ensure accuracy and completeness.

Complete the Study Conclusion screen in the eCRF.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
71
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
72
6.7.
Biological sample handling and analysis
Please refer to the SPM and Investigator Manual for details on biospecimen management 
(handling, storage and shipment).
Samples stored at the clinical site or shipped to external laboratories will not be labelled 
with information that directly identifies the subject but will be coded with a unique 
sample identifier. Samples analyzed locally (e.g., safety lab samples) would have a label 
with the subject’s identifiers and medical record number.

Collected samples will be used for protocol-mandated research and purposes related 
to the improvement, development and quality assurance of the laboratory tests 
described in this protocol. This may include the management of the quality of these 
tests, the maintenance or improvement of these tests, the development of new test 
methods, as well as making sure that new tests are comparable to previous methods 
and work reliably.

It is also possible that future findings may make it desirable to use the samples 
acquired in this study for future research, not described in this protocol. Therefore, 
all subjects will be asked to give a specific consent to allow GSK or a contracted 
partner to use the samples for future research. Future research will be subject to the 
laws and regulations in the respective countries and will only be performed once an 
independent Ethics Committee or Review Board has approved this research.
Information on further investigations and their rationale can be obtained from GSK 
Biologicals.
Any sample testing will be done in line with the consent of the individual subject.
Refer also to the Investigator Agreement, where it is noted that the investigator cannot 
perform any other biological assays except those described in the protocol or its 
amendment(s). 
If additional testing is performed, the marker priority ranking given in Section 6.7.4 may 
be changed.
Collected samples will be stored for a maximum of 20 years (counting from when the last 
subject performed the last study visit), unless local rules, regulations or guidelines require 
different timeframes or different procedures, which will then be in line with the subject 
consent. These extra requirements need to be communicated formally to and discussed 
and agreed with GSK Biologicals.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
72
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
73
6.7.1.
Use of specified study materials
When materials are provided by GSK Biologicals, it is MANDATORY that all clinical 
samples (including serum samples) be collected and stored exclusively using those 
materials in the appropriate manner. The use of other materials could result in the 
exclusion of the subject from the per-protocol analysis (See Section 11.5.5 for the 
definition of analysis sets to be analyzed). The investigator must ensure that his/her 
personnel and the laboratory(ies) under his/her supervision comply with this requirement. 
However, when GSK Biologicals does not provide material for collecting and storing 
clinical samples, appropriate materials from the investigator’s site must be used. Refer to 
the Module on Clinical Trial Supplies in the SPM.
6.7.2.
Biological samples
Table 6
Biological samples
Sample type (analysis) (All subjects)
Quantity
Unit
Timepoint
Blood (hematology)
~ 5
ml
scheduled
Blood (biochemistry)
~ 5
ml
scheduled
Blood (hepatitis B, hepatitis C and HIV)
~ 10
ml
scheduled
Blood (HLA-B27)
~ 10
ml
scheduled
Blood (anti S. sonnei LPS IgG-Screening)*
~ 5
ml
scheduled
Blood (antibody response**, SBA and Fc glycosylation)
~ 20
ml
scheduled
Blood (PBMC) for α4β7+/- plasmablasts response and 
transcriptomics) (Amended: 23 July 2019)
~ 50
ml
scheduled
Urine (urinalysis)
scheduled
Stool*** (sIgA, microbiome, inflammatory markers, weight, 
consistency and blood assessment, culture and qPCR)
scheduled
*For local Screening-ELISA.
**Includes anti S. sonnei LPS IgG-ELISA
***During the challenge phase, if stool samples are unavailable, rectal swabs will be taken for culture and qPCR.
HIV: Human immunodeficiency virus
HLA: Human leukocyte antigen
ELISA: Enzyme-linked immunosorbent assay
IgG: Immunoglobulin G7
SBA: Serum bactericidal assay
Fc: Fragment crystallisable
sIgA: Secretory immunoglobulin A
qPCR: quantitative polymerase chain reaction
6.7.3.
Laboratory assays
Please refer to Appendix A for a detailed description of the assays performed in the 
study. Please refer to Appendix B for the address of the clinical laboratories used for 
sample analysis.
The assays to be performed in the study are summarized in the Table 7, Table 8, Table 9
and Table 10:
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
73
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
74
Table 7
Immunity (Antibody determination)
System
Component
Method
Kit/
Manufacturer
Unit2
Cut-off2
Laboratory3
Serum
(screening)
Anti-S. sonnei
LPS IgG
ELISA1
WRAIR
Endpoint 
titer
plate 
dependent
CCHMC
Serum
(except 
screening)
Anti-S. sonnei
LPS IgG
ELISA
In-house
EU/mL
plate 
dependent
GVGH4 or 
GVGH 
designated lab
Serum
Bactericidal 
antibodies
SBA
In-house
Dilution 
Factor 
(titer)
NA
GVGH4 or 
GVGH 
designated lab
Stool
Anti-S. sonnei
LPS sIgA
ELISA
WRAIR
EU/mL
10
CCHMC
Stool 
Anti-total sIgA 
ELISA
WRAIR 
mg/mL 
0.001 
CCHMC 
1 Local Screening-ELISA will be used for this testing.
2Assay cut-off and unit might be subject to change during the course of the study (e.g. in case of requalification, 
revalidation or standardization). In this case, this will be documented in the clinical report.
3Refer to Appendix B for the laboratory addresses.
4 GVGH laboratory refers to the GVGH-laboratories in Siena, Italy.
ELISA: enzyme-linked immunosorbent assay, NA: not applicable, EU: ELISA unit, LPS: lipopolysaccharide, IgA/G: 
immunoglobulin A/G, SBA: serum bactericidal Assay, WRAIR: Walter Reed Army Institute of Research (US), GVGH: 
GSK Vaccines Institute for Global Health, CCHMC: Cincinnati Children’s Hospital Medical Center; sIgA: secretory 
Immunnoglobulin A
Table 8
Cell-Mediated Immunity (CMI) (Amended: 23 July 2019)
System
Component
Method
Unit
Laboratory
PBMC
α4β7 positive 
plasmablast
(Amended: 23
July 2019)
ELISA
(Amended: 23
July 2019)
Anti- S. sonnei 
LPS specific Titer/ 
5x10^6 cells
(Amended: 23
July 2019)
WRAIR or GVGH designated lab
PBMC
(Amended: 
23 July
2019)
α4β7 negative 
plasmablast
(Amended: 23
July 2019)
ELISA
(Amended: 23
July 2019)
Anti- S. sonnei 
LPS specific Titer/ 
5x10^6 cells
(Amended: 23
July 2019)
WRAIR or GVGH designated lab
(Amended: 23 July 2019)
PBMC
Gene 
expression 
(transcriptomics) 
study
NextGen 
sequencing/ 
microarray
Sequencing or 
fluorescent 
intensity
GVGH* or GVGH designated lab
ELISA: Enzyme-Linked Immunosorbent Assay; PBMC: peripheral blood mononuclear cells, WRAIR: Walter Reed 
Army Institute of Research (US), GVGH: GSK Vaccines Institute for Global Health.
*GVGH laboratory refers to the GVGH-laboratories in Siena, Italy.
Table 9
Excretion of Challenge agent
System
Component Family
Method
Unit
Laboratory
Stool
S. sonnei 53G
culture
Not applicable
CCHMC
Stool
S. sonnei 53G
qPCR
RFU
WRAIR
qPCR: quantitative polymerase chain reaction, RFU: relative fluorescence units, CCHMC: Cincinnati Children’s 
Hospital Medical Center, WRAIR: Walter Reed Army Institute of Research (US).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
74
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
75
Table 10
Hematology, Serum Chemistry, Virology, HLA-B27 test, Urine and 
Stool tests (Amended: 23 July 2019)
System
Component
Method
Laboratory
EDTA Blood
Hematology
CBC
Study site
EDTA blood
Chemistry*
Renal and liver function test
Study site
Clotted Blood
Hep B, Hep C and HIV
TBD
Study site
EDTA Blood
HLA-B27
Qualitative flow cytometry (Amended: 23
July 2019)
Study site
Urine
Urinalysis
Urine dipstick (urine culture as appropriate)
Study site
Urine
Urine pregnancy test
HCG
Study site
Stool
Microbiome
16s ribosomal DNA amplicon sequencing 
and/or shotgun whole genome sequencing
GVGH** or GVGH
designated lab
Stool 
Inflammatory markers
ELISA 
WRAIR or GVGH 
designated lab
EDTA: Ethylene Diamine Tetra-Acetic Acid, CBC: Complete Blood Count, ELISA: Enzyme-Linked Immunosorbent 
Assay, Hep: Hepatitis, HIV: Human Immunodeficiency Virus, HLA: Human Leukocyte Antigen, HCG: beta-Human 
Chorionic Gonadotropin, GVGH: GSK Vaccines Institute for Global Health, WRAIR: Walter Reed Army Institute of 
Research (US).
*Chemistry performed only at screening unless required for subject management
**GVGH laboratory refers to the GVGH-laboratories in Siena, Italy
Note that hematology data post vaccination/challenge will be transferred from the study 
laboratory performing the testing into the clinical database as soon as possible to ensure 
that all necessary information are available for IDMC reviews. In addition, results will be 
communicated as soon as possible to the investigators via lab reports, hard copies, faxes 
or emails.
Microbiome analysis in stool will be done using 16s ribosomal deoxyribonucleic acid 
(DNA) amplicon sequencing and/or shotgun whole genome sequencing. These will use 
DNA sequencing to identify the bacteria and their genes present in the sample to explore 
associations to immunogenicity and challenge outcome. Shotgun sequencing might 
generate subject’s DNA sequence information; however, these sequences are filtered out 
and will not be analyzed. Depending on the results of the microbiome analysis, additional 
follow-up studies might include microbiome gene expression profiling (ribonucleic acid
sequencing or another method), culture and functional characterization of the bacteria in 
the sample in animal models.
Fecal markers of intestinal inflammation will be measured as a sensitive predictor for 
inflammatory activities in the gastrointestinal tract. This analysis will assess if 
concentrations of inflammatory markers such as calprotectin and myeloperoxidase will 
increase after oral challenge with S. sonnei 53G and will additionally investigate if the S. 
sonnei 1790GAHB vaccine can reduce or abrogate the inflammatory response in the 
intestine after oral challenge.
Gene expression will be studied using high-throughput technologies (including but not 
limited to RNAseq or microarrays) measuring the relative abundance of RNA molecules 
in PBMCs harvested at several timepoints following vaccination and challenge. 
Computational analysis will subsequently identify pathways and biological themes 
associated with vaccination and acute disease and transcriptional patterns may be related 
to metadata including humoral and cellular responses to vaccination.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
75
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
76
Additional exploratory testing on the vaccine and/or on the disease under study may be 
performed within the framework of the study if deemed necessary for accurate 
interpretation of the data or should such assay(s) become available at GSK. These assays 
may not be represented in the objectives/endpoints of the study protocol.
Sera will be archived at GSK laboratory or its designated lab for future research on 
immunogenicity of the Shigella vaccine. Study-related future research may include 
additional evaluation of immunogenicity on S. sonnei (i.e., IgM, sIgA against the OAg or 
IgG against other antigens of S. sonnei, sIgA from stimulated lymphocytes supernatant, 
FACS/CyTOF Phenotyping (Cytokine stimulation). Non-study related future research 
may include serology on other Shigella serotypes and other bacteria causing infectious 
diseases in developing countries (e.g., Salmonella typhi, Salmonella paratyphi, non-
typhoidal Salmonella, meningitis) to inform development of other vaccines relevant to 
the populations in developing countries.
The GSK Biologicals’ clinical laboratories have established a Quality System supported 
by procedures. The activities of GSK Biologicals’ clinical laboratories are audited 
regularly for quality assessment by an internal (sponsor-dependent) but laboratory-
independent Quality Department.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
76
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
77
6.7.4.
Biological samples evaluation
6.7.4.1.
Immunological read-outs
Table 11
Immunological read-outs
Sampling timepoint
Sub-cohort name
No. 
subjects
Component
Components 
priority rank
Type of contact 
and timepoint
Sampling 
timepoint
Screening Visit
Screening
All screened 
subjects
NA
Anti HIV*
1
HBsAg*
1
Anti HCV*
1
Serum anti-S. sonnei LPS IgG*
1
HLA-B27
1
Visit 1 (Day1)
Pre-Vacc
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
Serum anti-S. sonnei
bactericidal antibodies
2
Serum for Fc Glycosylation
3
α4β7 plasmablast
2
Transcriptomics
2
All subjects enrolled
72
sIgA in stool
NA
Visit 2 (Day 8)
Post Vacc 1
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
sIgA in stool
NA
α4β7 plasmablast
2
Transcriptomics
2
Visit 3 (Day 29)
Post Vacc 1
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
Serum anti-S. sonnei
bactericidal antibodies
2
Visit 4 (36)
Post Vacc 2
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
α4β7 plasmablast
2
Transcriptomics
2
sIgA in stool
NA
Visit 5 (Day 57)
Pre-challenge All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
Serum anti-S. sonnei
bactericidal antibodies
2
Serum for Fc Glycosylation
3
Inpatient Stay 
(Day 64)
Inpatient Stay
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
1
sIgA in stool
NA
α4β7 plasmablast
2
Transcriptomics
2
Visit 6 (Day 85)
Post-
challenge
All subjects enrolled
72
Serum anti-S. sonnei LPS IgG
NA
Note: Anti-S. sonnei LPS IgG will be determined by local Screening-ELISA at screening and by GVGH ELISA for the 
rest of the timepoints.
*This testing is performed at screening and the results might potentially impact the subject medical care.
Vacc: Vaccination, Fc: Fragment crystallisable, LPS: Lipopolysaccharide, IgG: Immunoglobulin G, α4β7: Gut-homing 
integrin, sIgA: Secretory specific Immunoglobulin A, IgG: Immunoglobulin G, HIV: Human Immunodeficiency Virus; 
HBsAg: Hepatitis B surface Antigen; HCV: Hepatitis C Virus, NA: Not Applicable
In case of insufficient blood sample volume to perform assays, the samples will be 
analyzed according to priority ranking provided in Table 11.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
77
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
78
6.7.4.2.
Hematology/blood chemistry
Table 12
Hematology/Blood Chemistry read-outs
Blood sampling timepoint
No. 
subjects
Component
*Type of contact and timepoint
Sampling timepoint
Screening
Pre-Vacc 1
NA
Hematology
Chemistry
Visit 2 (Day 8)
Post-Vacc 1
72
Hematology
Visit 3 (Day 29)
Pre-Vacc 2
72
Hematology
Visit 4 (Day 36)
Post-Vacc 2
72
Hematology
Visit 5 (Day 57)
Pre-challenge
72
Hematology
Visit 8 (Day 237)
Post-challenge
72
Hematology
*Hematology is repeated at 7 and 28 days after each vaccination and repeated weekly until resolution if neutropenia
occurs.
Vacc: Vaccination, NA: Not applicable
6.7.5.
Immunological correlates of protection
No generally accepted immunological correlate of protection has been demonstrated so 
far for Shigellosis and consequently for the candidate vaccine. However, in GVGH Phase 
I clinical protocols a high seroresponse was defined as a post-vaccination level of 
121 serum IgG EU/mL against the S. sonnei OAg containing LPS used as coating 
antigen in GVGH ELISA. This concentration corresponds to a titer of 1:800 in the 
ELISA method published by Cohen [Cohen, 1989] and is the median antibody 
concentration of a set of 87 Israeli convalescent subjects previously exposed to S. sonnei. 
The value of 121 EU/mL in the GVGH ELISA (anti-S. sonnei LPS IgG-ELISA) has been 
determined by calibration against the Cohen ELISA (i.e., the GVGH standard serum was 
tested in Cohen’s lab using the Cohen’s methodology) [Gerke, 2015].
The availability of this threshold has allowed GVGH to correlate the immunogenicity 
data induced by 1790GAHB vaccine with antibody levels after natural exposure in 
humans, which are associated with clinical protection from subsequent infections with the 
same Shigella serotype [Cohen, 1991; Ferreccio, 1991]. To confirm the proof of concept 
outcome of GVGH Phase I studies (post-immunization median antibody titer in vaccinees 
121 EU/mL), as part of the objectives of this study, any potential correlation between 
antibody response (ELISA and SBA) after vaccination and likelihood of infection will be 
evaluated. Additionally, potential correlation between antibody response by ELISA and 
serum bactericidal activity will be explored. Further correlation can be established post-
challenge.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
78
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
79
7.
STUDY VACCINE/PRODUCTS AND ADMINISTRATION
7.1.
Description of study vaccine/placebo and challenge agent
The 1790GAHB candidate vaccine has been developed by GVGH, property of GSK 
Biologicals.
The S. sonnei 53G challenge strain was developed by Walter Reed Army Institute of 
Research (WRAIR), Silver Spring, Maryland, USA.
The Quality Control Standards and Requirements for the candidate vaccine/placebo and 
challenge agent are described in separate Quality Assurance documents (e.g., release 
certificate/certificate of compliance) and required approvals will be obtained before use.
The vaccine/placebo and challenge agent are labelled and packed according to applicable 
regulatory requirements.
Table 13
Study vaccine/placebo and challenge agent
Treatment 
name*
Vaccine/
placebo 
and 
challenge 
agent name
Formulation
Presentation
Volume to be 
administered
Numbe
r of 
doses
S. sonnei*
Shigella 
sonnei 
1790GAHB
200 g 1790-GMMA 
protein adsorbed to 
0.7 mg aluminum3+/mL
White opalescent sterile 
suspension for injection
0.5 mL after 1:4 
dilution with 
GVGH Placebo
2
Placebo*
GAHB-
Placebo
Aluminum hydroxide 
(wet gel suspension 
Alhydrogel 2.0%) 0.7 
mg aluminum3+/mL of 
constituted vaccine
White opalescent sterile 
suspension for injection
0.5 mL
2
S. sonnei 
53G 
challenge 
strain**
S. sonnei 
53G
Challenge
S. sonnei strain 53G
1 mL of the inoculum 
(CFU TBD) will be 
added to 30 mL of 
sterile normal saline 
0.9% for administration
1500 CFU
1
*The supply is managed by GVGH with the support of a local Contract Manufacturing Organization.
**S. sonnei 53G strain will be used for the challenge.
7.2.
Storage and handling of study vaccine/placebo and 
challenge agent
The study vaccine/placebo and challenge agent must be stored at the respective label 
storage temperature conditions in a safe and locked place. Access to the storage space 
should be limited to authorized study personnel. The storage conditions will be assessed 
during pre-study activities under the responsibility of the sponsor study contact. The 
storage temperature should be continuously monitored with calibrated (if not validated) 
temperature monitoring device(s) and recorded. Refer to the Module on Clinical Trial 
Supplies in the SPM for more details on storage of the study vaccine/placebo and 
challenge agent.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
79
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
80
Temperature excursions must be reported in degree Celsius.
Any temperature excursion outside the range of +2 to +8C (for +2 to +8°C label storage 
condition) impacting 1790GAHB vaccine and placebo or -80°C 10°C for the challenge 
agent must be reported to GSK using the appropriate temperature excursion form. The 
impacted IMPs must not be used and must be stored in quarantine at label temperature 
conditions until usage approval has been obtained from the sponsor.
Refer to the Module on Clinical Trial Supplies in the SPM for details and instructions on 
the temperature excursion reporting and usage decision process, packaging and 
accountability of the study vaccine/placebo and challenge agent.
7.3.
Dosage and administration of study vaccine/placebo and 
challenge agent
7.3.1.
Vaccine/placebo preparation
Bedside mixing and vaccine/placebo administration at the study site will be performed 
according to the Sponsor instructions by trained site staff. The site staff responsible for 
these activities will be personnel who are qualified according to applicable laws and 
regulations and will not be involved in the clinical assessment of the subjects. The 
Sponsor, or its authorized delegate, will provide specific procedures and training for these 
activities.
7.3.2.
Preparation of challenge agent
Preparation and administration of the challenge agent at the study site will be performed 
according to study site instructions by trained site staff. The site staff responsible for 
these activities will be personnel who are qualified according to applicable laws and 
regulations. S. sonnei 53G is classified as a BSL-2 category organism. Personnel will take 
appropriate precautions for working with BSL-2 organisms and wear proper protective 
equipment such as lab coats, gloves and, if necessary, masks to shield themselves and 
others from spills and inadvertent mishaps. Spills will be treated according to Standard 
Operating Procedure (SOP). All unused reconstituted inoculum and materials containing 
the bacteria will be disposed of properly in biohazard bags. All exposed materials and all 
disposable materials will be discarded in the biohazard waste for pick up and 
decontamination as per CCHMC policy. At the study site specific procedures are 
available and site staff will be appropriately trained.
7.3.3.
Vaccine/placebo dosage and administration
The investigator or designee will be responsible for the oversight of the administration of 
vaccine/placebo to subjects enrolled in the study according to the procedures stipulated in 
this study protocol. All vaccines/placebos will be administered only by personnel who are 
qualified to perform that function under applicable local laws and regulations for the 
specific study site.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
80
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
81
7.3.4.
Challenge agent dosage and administration
The investigator or designee will be responsible for the oversight of the administration of 
the challenge agent to subjects enrolled in the study according to the procedures 
stipulated at the study site. The challenge agent will be administered only by personnel 
who are qualified to perform that function under applicable local laws and regulations for 
the specific study site.
Table 14
Dosage and administration
Type of contact 
and timepoint
Study 
group
Treatment name
Volume to be 
administered
Route1
Site
Location Directionality2
Laterality3
Visit 1 (Day 1)
S. sonnei
GVGH 1790GAHB 
S. sonnei vaccine
(1:4 diluted)
0.5 mL
IM
Deltoid
Upper
Non-
dominant
Placebo
GAHB-Placebo
0.5 mL
IM
Deltoid
Upper
Non-
dominant
Visit 3 (Day 29)
S. sonnei
GVGH 1790GAHB 
S. sonnei vaccine
(1:4 diluted)
0.5 mL
IM
Deltoid
Upper
Non-
dominant
Placebo
GAHB-Placebo
0.5 mL
IM
Deltoid
Upper
Non-
dominant
Visit 5 (Day 57)
S. sonnei
S. sonnei 53G
1500 CFU 
O
NA
NA
NA
Placebo
S. sonnei 53G
1500 CFU 
O
NA
NA
NA
1IM: intramuscular / O: oral
2Directionality is a qualifier for further detailing the location of the vaccine/placebo administration
3The non-dominant arm is the preferred arm of injection. In case it is not possible to administer the vaccine/placebo in 
the non-dominant arm, an injection in the dominant arm may be performed.
Precautions to be observed in administering study vaccine/placebo or challenge 
agent:
Prior to administration of the vaccine/placebo or challenge agent, subjects must be 
determined to be eligible and it must be clinically appropriate in the judgment of the 
investigator to vaccinate/challenge. Eligibility for vaccination/challenge is determined by 
evaluating the entry criteria outlined in protocol Sections 5.2, 5.3, 6.6.11 and 6.6.12.
Study vaccine/placebo or challenge agent should not be administered to individuals with 
known hypersensitivity to any component of the vaccine/placebo or challenge agent. 
Standard immunization practices are to be observed and care should be taken to 
administer the vaccine/placebo intramuscularly. Before administering vaccine/placebo, 
the vaccination site is to be disinfected with a skin disinfectant (e.g., 70% alcohol). Allow 
the skin to dry. DO NOT inject intravascularly.
As with all injectable vaccines/products, trained medical personnel and appropriate 
medical treatment should be readily available in case of anaphylactic reactions following 
vaccine/placebo administration. For example, epinephrine 1:1000, diphenhydramine, 
and/or other medications for treating anaphylaxis should be available.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
81
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
82
7.4.
Replacement of unusable vaccine/placebo doses and 
challenge agent
In addition to the vaccine/placebo doses provided for the planned number of subjects
(including over-randomization when applicable), at least 5% additional vaccine/placebo
doses will be supplied to replace those that are unusable. For the challenge agent, at least 
one back-up vial will be required.
The investigator will use SBIR to obtain the replacement vial number. The replacement 
numbers will be allocated by dose. The system will ensure, in a blinded manner that the 
replacement vial matches the formulation the subject was assigned to by randomization.
7.5.
Contraindications to subsequent vaccination or challenge
Eligibility to administration of a second dose of the vaccine and challenge agent should 
be reconfirmed. The following events constitute absolute contraindications to further 
administration of 1790GAHB vaccine or the placebo and the challenge agent. If any of 
these events occur during the study, the subject must not receive additional doses of 
vaccine/placebo and challenge agent but may continue other study procedures at the 
discretion of the investigator (see Section 9.5).

Anaphylaxis following the administration of vaccine/placebo.

Pregnancy (see Section 9.2.1).

Hepatomegaly, right upper quadrant abdominal pain or tenderness.

Any confirmed or suspected immunosuppressive or immunodeficient condition, 
including, HIV infection.

Any condition that in the judgment of the investigator would make intramuscular 
injection unsafe.
The following events constitute contraindications to administration of 1790GAHB 
vaccine or the challenge agent at that point in time; if any of these events occur at the 
time scheduled for vaccination, the subject may be vaccinated at a later date, within the 
time window specified in the protocol (see Section 6.5), or the subject may be withdrawn 
at the discretion of the investigator (see Section 9.5):

Neutropenia below 1800 cell/µL (LLN) based on most recent available laboratory 
results. Subjects with previous neutropenia or unresolved neutropenia may be re-
evaluated prior to vaccination or prior to challenge at the discretion of the 
investigator.

Acute disease and/or fever at the time of vaccination.

Fever is defined as temperature 38.0°C / 100.4°F. The preferred location for 
measuring temperature in this study will be the oral cavity.

Subjects with a minor illness (such as mild diarrhea, mild upper respiratory 
infection) without fever can be administered vaccine/placebo and challenge 
agent.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
82
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
83
7.6.
Concomitant medications/products and concomitant 
vaccinations
At each study visit/contact, the investigator or delegate should question the subject about 
any medications/products taken and vaccinations received by the subject.
7.6.1.
Recording of concomitant medications/products and 
concomitant vaccinations
The following concomitant medication(s)/product(s)/vaccine(s) must be recorded in the 
eCRF:

All concomitant medications/products, except vitamins and dietary supplements, 
administered during the period starting at vaccination day to 28 days following each 
dose of study vaccine/placebo (1 day to 28 days after each vaccination) and 
administration of challenge agent.

Relevant medications/products like vaccines, immunoglobulin, blood products, 
immunosuppressors, immunomodulators administered during the period starting 
from the administration of the first dose of the study vaccine/placebo and ending 28 
days after challenge.

Any concomitant vaccination administered in the period starting 28 days before the 
first dose of study vaccine/placebo and ending at 28 days after challenge with the 
exception of seasonal Flu vaccination.

Prophylactic medication (i.e. medication administered in the absence of ANY 
symptom and in anticipation of a reaction to the vaccination).
E.g., an anti-pyretic is considered to be prophylactic when it is given in the absence 
of fever and any other symptom, to prevent fever from occurring (fever is defined as 
temperature 38.0°C/100.4°F). The preferred location for measuring temperature in 
this study will be the oral cavity.

Any concomitant medications/products/vaccines relevant to a SAE to be reported as 
per-protocol or administered during the study period for the treatment of a SAE. In 
addition, concomitant medications relevant to SAEs need to be recorded on the 
expedited Adverse Event report.
7.6.2.
Concomitant medications/products/vaccines that may lead to the 
elimination of a subject from per-protocol analyses
The use of the following concomitant medications/products/vaccines will not require 
withdrawal of the subject from the study but may determine a subject’s evaluability in the 
per-protocol analysis. See Section 11.5 for analyses sets to be analyzed.

Any investigational or non-registered product (drug or vaccine) other than the study 
vaccine/products used during the study period.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
83
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
84

Immunosuppressants or other immune-modifying drugs administered chronically 
(i.e. more than 14 days in total) during the study period. For corticosteroids, this will 
mean prednisone 20 mg/day or equivalent. Inhaled, except for doses >800 g/day, 
and topical steroids are allowed.

Long-acting immune-modifying drugs administered at any time during the study 
period (e.g. infliximab).

A vaccine not foreseen by the study protocol administered during the period starting 
from the first dose and ending at the blood sample at Visit 8 or 28 days after the last 
dose of vaccine/placebo administration, with the exception of emergency mass 
vaccination and influenza vaccination.
In case an emergency mass vaccination for an unforeseen public health threat (e.g.: a 
pandemic) is organized by the public health authorities, outside the routine 
immunization program, the time period described above can be reduced if necessary 
for that vaccine provided it is licensed and used according to its Summary of Product 
Characteristics or Prescribing Information and according to the local governmental 
recommendations and provided a written approval of the Sponsor is obtained.

Immunoglobulins and/or any blood products administered during the study period.

Drug and/or alcohol abuse during the study period.
7.7.
Intercurrent medical conditions that may lead to elimination 
of a subject from per-protocol analyses
At each study visit subsequent to the first vaccination visit, it must be verified if the 
subject has experienced or is experiencing any intercurrent medical condition. If it is the 
case, the condition(s) must be recorded in the eCRF.
Subjects may be eliminated from the per-protocol cohort for immunogenicity if, during 
the study:

They incur a condition that has the capability of altering their immune response (i.e.,
varicella) or are confirmed to have an alteration of their initial immune status.

They have serious chronic or progressive disease according to judgment of the 
investigator (e.g., neoplasm, insulin dependent diabetes, cardiac, renal or hepatic 
disease).

They have any malignancy or lymphoproliferative disorder. 

They have any confirmed or suspected immunosuppressive or immunodeficient 
condition, based on physical examination.
8.
HEALTH ECONOMICS
Not applicable.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
84
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
85
9.
SAFETY
The investigator or site staff is/are responsible for the detection, documentation and 
reporting of events meeting the criteria and definition of an adverse event (AE) or serious 
adverse event (SAE) as provided in this protocol.
Each subject will be instructed to contact the investigator immediately should they/the 
subject manifest any signs or symptoms they perceive as serious.
9.1.
Safety definitions
9.1.1.
Definition of an adverse event
An AE is any untoward medical occurrence in a clinical investigation subject, temporally 
associated with the use of a medicinal product, whether or not considered related to the 
medicinal product.
An AE can therefore be any unfavorable and unintended sign (including an abnormal 
laboratory finding), symptom, or disease (new or exacerbated) temporally associated with 
the use of a medicinal product. For marketed medicinal products, this also includes 
failure to produce expected benefits (i.e., lack of efficacy), abuse or misuse.
Examples of an AE include:

Exacerbation of a chronic or intermittent pre-existing condition including either an 
increase in frequency and/or intensity of the condition.

New conditions detected or diagnosed after study vaccine/placebo administration 
even though they may have been present prior to the start of the study.

Signs, symptoms, or the clinical sequelae of a suspected interaction.

Signs, symptoms, or the clinical sequelae of a suspected overdose of either study
vaccine/placebo or a concurrent medication (overdose per se should not be reported 
as an AE/SAE).

Signs, symptoms temporally associated with study vaccine/placebo.

Pre- or post-treatment events that occur as a result of protocol-mandated procedures 
(i.e. invasive procedures, modification of subject’s previous therapeutic regimen).
AEs to be recorded as endpoints (solicited AEs) are described in Section 9.1.3. All other 
AEs will be recorded as UNSOLICITED AEs.
Examples of an AE DO NOT include:

Medical or surgical procedures (e.g., endoscopy, appendectomy); the condition that 
leads to the procedure is an AE/SAE.

Situations where an untoward medical occurrence did not occur (e.g., social and/or 
convenience admission to a hospital, admission for routine examination).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
85
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
86

Anticipated day-to-day fluctuations of pre-existing disease(s) or condition(s) present 
or detected at the start of the study that do not worsen. 

Pre-existing conditions or signs and/or symptoms present in a subject prior to the 
first study vaccination. These events will be recorded in the medical history section 
of the eCRF.
9.1.2.
Definition of a serious adverse event 
A SAE is any untoward medical occurrence that:
a.
Results in death,
b.
Is life-threatening,
Note: The term ‘life-threatening’ in the definition of ‘serious’ refers to an event in 
which the subject was at risk of death at the time of the event. It does not refer to an 
event, which hypothetically might have caused death, had it been more severe.
c.
Requires hospitalization or prolongation of existing hospitalization,
Note: In general, hospitalization signifies that the subject has been admitted at the 
hospital or emergency ward for observation and/or treatment that would not have 
been appropriate in the physician’s office or in an outpatient setting. Complications 
that occur during hospitalization are also considered AEs. If a complication prolongs 
hospitalization or fulfils any other serious criteria, the event will also be considered 
serious. When in doubt as to whether ‘hospitalization’ occurred or was necessary, the 
AE should be considered serious.
Hospitalization for elective treatment of a pre-existing condition (known or 
diagnosed prior to informed consent signature) that did not worsen from baseline is 
NOT considered an AE.
d.
Results in disability/incapacity, OR
Note: The term disability means a substantial disruption of a person’s ability to 
conduct normal life functions. This definition is not intended to include experiences 
of relatively minor medical significance such as uncomplicated headache, nausea, 
vomiting, diarrhea, influenza like illness, and accidental trauma (e.g., sprained ankle) 
which may interfere or prevent everyday life functions but do not constitute a 
substantial disruption.
e.
Is a congenital anomaly/birth defect in the offspring of a study subject.
Medical or scientific judgment should be exercised in deciding whether reporting is 
appropriate in other situations, such as important medical events that may not be 
immediately life-threatening or result in death or hospitalization but may jeopardize the 
subject or may require medical or surgical intervention to prevent one of the other 
outcomes listed in the above definition. These should also be considered serious. 
Examples of such events are invasive or malignant cancers, intensive treatment in an 
emergency room or at home for allergic bronchospasm, blood dyscrasias or convulsions 
that do not result in hospitalization.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
86
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
87
9.1.3.
Solicited adverse events
The term “reactogenicity” refers to solicited signs and symptoms (“solicited AEs”) 
occurring in the hours and days following a vaccination, to be collected by the subjects
for 7 consecutive days, using a predefined Subject Diary.
The study staff must review the data entered into the Subject Diary as described in 
Section 12.2.
Note: Any solicited AE that meets any of the following criteria must be entered into 
subjects’ source document (see Section 12.2) and also as an AE on the Adverse Event 
CRF:

Solicited local or systemic AE that continues beyond day 7 after vaccination.

Solicited local or systemic AE that leads to a visit to a healthcare provider (medically 
attended AE, see Section 9.3.3.4).

Solicited local or systemic AE leading to the subject withdrawing from the study or 
the subject being withdrawn from the study by the investigator (AE leading to 
withdrawal).

Solicited local or systemic AE that otherwise meets the definition of a SAE (see 
Section 9.1.2).
Solicited AEs after vaccination are included in the Subject Diary. Each AE is to be 
assessed using the scoring system reported in Section 9.3.3.2.1.
9.1.3.1.
Solicited local Adverse events
The following local (injection site) AEs will be solicited:
Table 15
Solicited local adverse events
Both study arms
Pain at injection site
Erythema at injection site
Induration at injection site
9.1.3.2.
Solicited systemic Adverse events
The following systemic AEs will be solicited:
Table 16
Solicited systemic adverse events
Both study arms
Arthralgia
Chills
Fatigue
Malaise
Myalgia
Fever
Headache
Note: Subjects will be instructed to measure and record oral body temperature in the evening 6 hours after vaccination 
and daily during the following 6 days. Subjects will be instructed to record the highest temperature in the diary card.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
87
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
88
9.1.3.3.
Solicited events after challenge phase
During the challenge phase after the subjects have received the challenge agent, events 
associated with the administration of the challenge agent will be collected and recorded 
by the investigator in the CRF. These events include diarrhea, abdominal pain, abdominal 
cramps, gas, anorexia, nausea, headache, myalgia, malaise, arthralgia, fever, and 
vomiting beginning the day of administration of study challenge agent until 7 days after 
challenge (i.e., Day 64). Any unresolved events will be followed to resolution or 
stabilization. Oral rehydration will be initiated and recorded for subjects with a Grade 2 
or higher AE of diarrhea, vomiting, dysentery or dehydration. The hydration of subjects 
developing diarrhea will be maintained with oral electrolyte solutions by offering at least 
1.5 mL for each gram of diarrheal stool lost, as tolerated. Subjects who develop vomiting 
will be offered at least 1.0 mL for each gram of emesis lost, as tolerated. Subjects will be 
evaluated by a physician who will consider intravenous hydration for subjects who:

Cannot tolerate oral fluids,

Experience fluids loss that exceeds their ability to drink replacement fluids,

Have > 1000 mL deficit in intake in a 24 hour period,

Experience weight loss of more than 5%,

Have urine specific gravity > 1.030 for 12 hours,

Have syncope or near-syncope,

Grade 3 tachycardia, or

Grade 3 hypotension.
If the subject is unable to tolerate fluids by mouth and intravenous fluids are deemed 
necessary by the assessing physician, a 0.9% sterile saline solution 1-liter bolus will be 
administered intravenously. This bolus will be repeated as needed to resolve Grade 2 and 
above symptoms at the discretion of assessing physician. Fluid maintenance will be 
continued using 0.45% NaCl, 5% dextrose, and 20 mEq KCL per liter at a rate of 
100 mL/hour until subject is able to resume oral rehydration. If the subject develops 
grade 4 hypotension despite the aggressive fluid management, the subject will be
transferred from the inpatient unit to a hospital setting.
9.1.4.
Unsolicited Adverse Events
An unsolicited AE is an AE that was not solicited using a Subject Diary and that was 
spontaneously communicated by a subject who has signed the informed consent or a 
solicited local or systemic AE that continues beyond the solicited period at day 7 after 
vaccination.
Potential unsolicited AEs may be medically attended (defined as symptoms or illnesses 
requiring hospitalization, or emergency room visit, or visit to/by a health care provider), 
or were of concern to the subjects. In case of such events, subjects will be instructed to 
contact the site as soon as possible to report the event(s). The detailed information about 
the reported unsolicited AEs will be collected by the qualified site personnel during the 
interview and will be documented in the subject’s records.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
88
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
89
Unsolicited AEs that are not medically attended nor perceived as a concern by subjects
will be collected during interview with the subjects and by review of available medical 
records at the next visit.
Unsolicited AEs will be collected until 28 days after each vaccination and until 28 days 
after challenge.
9.1.5.
Clinical laboratory parameters and other abnormal assessments 
qualifying as adverse events or serious adverse events
In absence of diagnosis, abnormal laboratory findings (e.g., clinical chemistry, 
hematology, urinalysis) or other abnormal assessments that are judged by the investigator 
to be clinically significant will be recorded as AE or SAE if they meet the definition of an 
AE or SAE (refer to Sections 9.1.1 and 9.1.2). Clinically significant abnormal laboratory 
findings or other abnormal assessments that are present at baseline and significantly 
worsen following the start of the study will also be reported as AEs or SAEs.
The investigator will exercise his or her medical and scientific judgment in deciding 
whether an abnormal laboratory finding or other abnormal assessment is clinically 
significant. Clinically significant modifications in hematology will be assessed by 
medical judgment based on interpretation of deviations from institution’s normal values 
and recommendations from CBER FDA GUIDANCE FOR INDUSTRY: Toxicity 
Grading Scale for Healthy Adults and Adolescent Volunteers Enrolled in Preventive 
Vaccine Clinical Trials and predefined list of sign and symptoms related to neutropenia.
9.1.6.
Adverse events of special interest
Adverse events of special interest (AESIs) are predefined (serious or non-serious) AEs of 
scientific and medical concern specific to the product or program, for which ongoing 
monitoring and rapid communication by the investigator to the sponsor can be 
appropriate, because such an event might warrant further investigation in order to 
characterize and understand it.
During the two Phase I studies with the study vaccine, no SAE were reported. Two 
subjects of African descent experienced a transient and clinically asymptomatic Grade 3 
neutropenia (the two episodes were graded as SAEs) that was finally classified as 
“benign ethnic neutropenia”. In addition to these two Grade 3 cases (one in each study), a 
total of 6 cases of transient and clinically asymptomatic Grade 2 neutropenia (one case in 
H03_01TP and 5 cases in H03_02TP) has been reported. GVGH has defined neutropenia 
as AESI. In the phase 2 study in endemic population, there have been 10 cases of 
neutropenia from 6 subjects of which one was severe, three moderate and 6 mild. All of 
these events were clinically asymptomatic.
During the course of this study, symptomatic neutropenia will be considered as AESIs.
Table 17
List of potential AESI to be followed during the study
Blood disorders
Symptomatic neutropenia (all Grades)
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
89
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
90
Neutropenia is defined as a decrease of neutrophil count asymptomatically or 
symptomatically. This is completely diagnosed by laboratory testing for complete blood 
count. However, only symptomatic neutropenia cases will be considered as AESI and 
reported as such.
The following grading will be used to classify neutropenia:

Grade 1: 1800 -1500 cells/µL.

Grade 2: 1499-1000 cells/µL.

Grade 3: 999-500 cells/µL.

Grade 4: < 500 cells/µL.
In performing their assessment of symptomatic neutropenia cases, investigators are 
strongly advised to use the table below.
Table 18
Evaluation of symptomatic neutropenia
Common presenting symptoms of neutropenia
Physical findings on examination of a patient with 
neutropenia
Low-grade fever
Fever
Sore mouth
Stomatitis
Odynophagia
Periodontal infection
Gingival pain and swelling
Cervical lymphadenopathy
Skin abscesses
Skin infection: The skin examination focuses on rashes, 
ulcers, or abscesses
Recurrent sinusitis and otitis
Splenomegaly
Symptoms of pneumonia (e.g., cough, dyspnea)
Associated petechial bleeding
Perirectal pain and irritation
Perirectal infection
Neutropenic sepsis
Other according to Investigator’s opinion
Neutropenic infection
Neutropenic colitis
Other according to Investigator’s opinion
In order to facilitate the documentation of AESI in the eCRF, a list of MedDRA preferred 
terms (PTs) and PT codes corresponding to the above diagnoses will be available to 
investigators at study start.
When there is enough evidence to make any of the above diagnoses, the AE must be 
reported as AESI. Symptoms, signs or conditions which might (or might not) represent 
the above diagnoses, should be recorded and reported as AEs but not as AESI until the 
final or definitive diagnosis has been determined, and alternative diagnoses have been 
eliminated or shown to be less likely.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
90
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
91
9.2.
Events or outcomes not qualifying as adverse events or 
serious adverse events
9.2.1.
Pregnancy
Female subjects who become pregnant before the 2nd vaccination and before the 
challenge must not receive additional doses of study vaccine/placebo, nor the challenge 
agent, but may continue other study procedures at the discretion of the investigator.
While pregnancy itself is not considered an AE or SAE, any adverse pregnancy outcome 
or complication or elective termination of a pregnancy for medical reasons will be 
recorded and reported as an AE or a SAE.
Note: The pregnancy itself should always be recorded on an electronic pregnancy report.
The following should always be considered as SAE and will be reported as described in 
Sections 9.4.1 and 9.4.3:

Spontaneous pregnancy loss, including:

Spontaneous abortion, (spontaneous pregnancy loss before/at 22 weeks of 
gestation)

Ectopic and molar pregnancy

Stillbirth (intrauterine death of fetus after 22 weeks of gestation).
Note: the 22 weeks cut-off in gestational age is based on WHO-ICD 10 noted in the 
EMA Guideline on pregnancy exposure [EMA, 2006]. It is recognized that national 
regulations might be different.

Any early neonatal death (i.e. death of a live born infant occurring within the first 7 
days of life). 

Any congenital anomaly or birth defect (as per [CDC MACDP] guidelines) 
identified in the offspring of a study subject (either during pregnancy, at birth or 
later) regardless of whether the fetus is delivered dead or alive. This includes 
anomalies identified by prenatal ultrasound, amniocentesis or examination of the 
products of conception after elective or spontaneous abortion.
Furthermore, any SAE occurring as a result of a post-study pregnancy AND considered 
by the investigator to be reasonably related to the study vaccine/placebo or challenge 
agent will be reported to GSK Biologicals as described in Section 9.4.3. While the 
investigator is not obligated to actively seek this information from former study 
participants, he/she may learn of a pregnancy through spontaneous reporting.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
91
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
92
9.3.
Detecting and recording adverse events, serious adverse 
events and pregnancies
9.3.1.
Time period for detecting and recording adverse events, serious 
adverse events and pregnancies
All AEs starting within 28 days following administration of each dose of study 
vaccine/placebo (day of vaccine/placebo administration to 28 days after administration)
and challenge agent administration must be recorded into the appropriate section of the 
eCRF, irrespective of intensity or whether or not they are considered vaccination-related.
The time period for collecting and recording SAEs will begin at the first receipt of study 
vaccine/placebo and will end at the conclusion of the study for each subject. See Section 
9.4 for instructions on reporting of SAEs.
In addition to the above-mentioned reporting requirements and in order to fulfil 
international reporting obligations, SAEs that are related to study participation (i.e. 
protocol-mandated procedures, invasive tests, a change from existing therapy) or are 
related to a concurrent GSK medication/vaccine will be collected and recorded from the 
time the subject consents to participate in the study until she/he is discharged from the 
study.
The time period for collecting and recording pregnancies will begin at the first receipt of 
study vaccine/placebo and will end at the conclusion of the study. See Section 9.4 for 
instructions on reporting of pregnancies.
The time period for collecting and recording of AESIs will begin at the first receipt of 
study vaccine/placebo and will end at the conclusion of the study. See Section 9.4 for 
instructions on reporting of AESIs.
An overview of the protocol-required reporting periods for AEs, SAEs, and pregnancies 
is given in Table 19.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
92
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
93
Table 19
Reporting periods for collecting safety information
Timepoints
Scr
D1
D8
D29
D36
D57
D57-D64
D85
D237 (M8)
Solicited local and systemic AEs
Unsolicited AEs
AEs/SAEs leading to withdrawal from the 
study
AESI
SAEs
Pregnancies
SAEs related to study participation or 
concurrent GSK medication/vaccine
Scr: Screening
D: Day
M: Month
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
93
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
94
9.3.2.
Post-study adverse events and serious adverse events
A post-study AE/SAE is defined as any event that occurs outside of the AE/SAE 
reporting period defined in Table 19. Investigators are not obligated to actively seek AEs 
or SAEs in former study participants. However, if the investigator learns of any SAE at 
any time after a subject has been discharged from the study, and he/she considers the 
event reasonably related to the study vaccine/placebo or challenge agent, the investigator 
will promptly notify the Study Contact for Reporting SAEs.
9.3.3.
Evaluation of adverse events and serious adverse events
9.3.3.1.
Active questioning to detect adverse events and serious adverse 
events
As a consistent method of collecting AEs, the subject should be asked a non-leading 
question such as:
‘Have you felt different in any way since receiving the vaccine/placebo or since the 
previous visit?’
When an AE/SAE occurs, it is the responsibility of the investigator to review all 
documentation (e.g. hospital progress notes, laboratory and diagnostics reports) relative 
to the event. The investigator will then record all relevant information regarding an 
AE/SAE in the eCRF. The investigator is not allowed to send photocopies of the 
subject’s medical records to GSK Biologicals instead of appropriately completing the
eCRF. However, there may be instances when copies of medical records for certain cases 
are requested by GSK Biologicals. In this instance, all subject identifiers will be blinded 
on the copies of the medical records prior to submission to GSK Biologicals.
The investigator will attempt to establish a diagnosis pertaining to the event based on 
signs, symptoms, and/or other clinical information. In such cases, the diagnosis should be 
documented as the AE/SAE and not the individual signs/symptoms.
9.3.3.2.
Assessment of adverse events
9.3.3.2.1.
Assessment of intensity
The intensity of the following solicited AEs will be assessed as described:
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
94
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
95
Table 20
Intensity scales for solicited symptoms
Adverse Event
Intensity 
grade
Parameter
After vaccine/placebo administration
Pain at injection site
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Erythema at injection site
Record greatest surface diameter in mm
Induration at injection site
Record greatest surface diameter in mm
Fever#*
Record temperature in °C/°F
Headache#
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Fatigue#
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Arthralgia#
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Malaise#
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Myalgia#
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Chills
0
Absent 
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
After challenge agent administration
Nausea
0
Absent 
1
Mild or transient; maintains reasonable intake
2
Moderate discomfort; intake decreased significantly; some activity limited
3
No significant intake and requires medical intervention
4
Hospitalization required
Abdominal cramping
0
Absent 
1
No interference with daily activities
2
Some interference with daily activities not requiring medical intervention
3
Prevents daily activities and requires medical intervention
4
ER visit or hospitalization
Abdominal pain
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Gas
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
95
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
96
Adverse Event
Intensity 
grade
Parameter
Anorexia
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Vomiting
0
Absent 
1
One episode within a 24-hour period Vomiting
2
2 episodes within a 24-hour period
3
>2 episodes within a 24-hour period and requires medical intervention
4
ER visit or hospitalization for hypotensive shock
Diarrhea**
0
Absent 
1
2-3 Grade 3-5 stools (loose or watery) or <400 g/Grade 3-5 (loose or watery) 
stools per 24 hours
2
4-5 Grade 3-5 stools (loose or watery) or 400-800 g/ (loose or watery) Grade 3-5 
stools per 24 hours
3
6 or more Grade 3-5 stools (loose or watery) or >800 g/Grade 3-5 (loose or 
watery) stools per 24 hours or requires medical intervention
4
10 loose stools (Grade 3 to 5) or 1000 grams of Grade 3 to 5 stools within 
24 hours
#Same grading is used for events present both post-vaccination and post-challenge.
*Fever is defined as temperature 38.0°C / 100.4°F. The preferred location for measuring temperature in this study 
will be the oral cavity.
**The end of a diarrheal episode occurs when a volunteer does not pass any Grade 3-5 stool within 24 hours.
ER: emergency room.
The maximum intensity of local injection-site erythema/induration/fever will be scored at 
GSK Biologicals as follows:
Erythema/Induration
0:
< 25 mm
1:
25 - 50 mm
2:
> 50 - 100 mm
3:
> 100 mm
Fever
Grade 0
Absent
Grade 1
Mild
Grade 2
Moderate
Grade 3
Severe
37.9°C
38.0°C – 38.9°C
39.0°C – 39.9°C
40.0°C
The investigator will assess the maximum intensity that occurred over the duration of the 
event for all unsolicited AEs (including SAEs) recorded during the study. The assessment 
will be based on the investigator’s clinical judgment.
Every effort should be made by the investigator to evaluate safety information reported 
by a subject for an underlying diagnosis and to capture this diagnosis as the event in the 
AE page. In other words, the practice of reporting only symptoms (e.g., “cough” or “ear 
pain”) are better reported according to the underlying cause (e.g., “asthma exacerbation” 
or “otitis media”).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
96
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
97
The severity of events reported on the Adverse Events eCRF will be determined by the 
investigator as:
Mild:
Transient with no limitation in normal daily activity
Moderate:
Some limitation in normal daily activity
Severe:
Unable to perform normal daily activity
9.3.3.2.2.
Assessment of causality
Alternative plausible causes, such as natural history of the underlying diseases, 
concomitant therapy, other risk factors, and the temporal relationship of the event to the 
study vaccine/placebo or challenge agent will be considered and investigated. The 
investigator will also consult the IB to determine his/her assessment.
There may be situations when a SAE has occurred, and the investigator has minimal 
information to include in the initial report to GSK Biologicals. However, it is very 
important that the investigator always makes an assessment of causality for every event 
prior to submission of the Expedited Adverse Events Report to GSK Biologicals. The 
investigator may change his/her opinion of causality in light of follow-up information and 
update the SAE information accordingly. The causality assessment is one of the criteria 
used when determining regulatory reporting requirements.
All solicited reactions will be considered causally related to vaccination or challenge. 
Causality of all other AEs should be assessed by the investigator using the following 
question:
Is there a reasonable possibility that the AE may have been caused by the study
vaccine/placebo or challenge agent?
YES:
There is a reasonable possibility that the study vaccine/placebo or challenge 
agent contributed to the AE. 
NO:
There is no reasonable possibility that the AE is causally related to the 
administration of the study vaccine/placebo or challenge agent. There are 
other, more likely causes and administration of the study vaccine/placebo or 
challenge agent is not suspected to have contributed to the AE.
If an event meets the criteria to be determined as ‘serious’ (see Section 9.1.2), additional 
examinations/tests will be performed by the investigator in order to determine ALL 
possible contributing factors for each SAE.
Possible contributing factors include:

Medical history.

Other medication.

Protocol-required procedure.

Other procedure not required by the protocol.

Lack of efficacy of the vaccine, if applicable.

Erroneous administration.

Other cause (specify).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
97
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
98
9.3.3.3.
Assessment of outcomes
The investigator will assess the outcome of all unsolicited AEs (including SAEs) 
recorded during the study as:

Recovered/resolved.

Recovering/resolving.

Not recovered/not resolved.

Recovered with sequelae/resolved with sequelae.

Fatal (SAEs only).
9.3.3.4.
Medically attended visits
For each solicited and unsolicited symptom the subject experiences, the subject will be 
asked if he/she received medical attention defined as hospitalization, or an otherwise 
unscheduled visit to or from medical personnel for any reason, including emergency 
room visits. This information will be recorded in the eCRF.
9.4.
Reporting of serious adverse events, pregnancies, and 
other events
9.4.1.
Prompt reporting of serious adverse events, pregnancies, and 
other events to GSK Biologicals
SAEs that occur in the time period defined in Section 9.3 will be reported promptly to 
GSK within the timeframes described in Table 21, once the investigator determines that 
the event meets the protocol definition of a SAE. Time of onset of SAE will allow 
distinguishing whether the SAE happened before or after challenge including any 
possible exacerbation of events following challenge.
Pregnancies that occur in the time period defined in Section 9.3 will be reported promptly 
to GSK within the timeframes described in Table 21, once the investigator becomes 
aware of the pregnancy. 
AESIs that occur in the time period defined in Section 9.3 will be reported promptly to 
GSK within the timeframes described in Table 21, once the investigator determines that 
the event meets the protocol definition of an AESI.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
98
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
99
Table 21
Timeframes for submitting serious adverse event, pregnancy and 
other events reports to GSK Biologicals
Type of Event
Initial Reports
Follow-up of Relevant Information on a 
Previous Report
Timeframe
Documents
Timeframe
Documents
SAEs
24 hours* ‡
electronic Expedited 
Adverse Events Report
24 hours*
electronic Expedited Adverse 
Events Report
Pregnancies
2 weeks*
electronic pregnancy report
2 weeks*
electronic pregnancy report
AESIs
24 hours** ‡
electronic Expedited 
Adverse Events Report
24 hours*
electronic Expedited Adverse 
Events Report
*Timeframe allowed after receipt or awareness of the information.
**Timeframe allowed once the investigator determines that the event meets the protocol definition of a AESI.
‡ The investigator will be required to confirm review of the SAE/AESI causality by ticking the ‘reviewed’ box in the 
electronic Expedited Adverse Events Report within 72 hours of submission of the SAE/AESI.
9.4.2.
Contact information for reporting serious adverse events,
pregnancies and AESIs
Study Contact for Reporting SAEs, AESIs and pregnancies 
Refer to the local study contact information document.
Back-up Study Contact for Reporting SAEs, AESIs and pregnancies 
24/24 hour and 7/7 day availability:
GSK Biologicals Clinical Safety & Pharmacovigilance
US sites only:
Email address: 
Fax: 
9.4.3.
Completion and transmission of SAE reports to GSK Biologicals
Once an investigator becomes aware that a SAE has occurred in a study subject, the 
investigator (or designate) must complete the information in the electronic Expedited 
Adverse Events Report WITHIN 24 HOURS. The report will always be completed as 
thoroughly as possible with all available details of the event. Even if the investigator does 
not have all information regarding a SAE, the report should still be completed within 
24 hours. Once additional relevant information is received, the report should be updated 
WITHIN 24 HOURS.
The investigator will always provide an assessment of causality at the time of the initial 
report. The investigator will be required to confirm the review of the SAE causality by 
ticking the ‘reviewed’ box in the electronic Expedited Adverse Events Report within 
72 hours of submission of the SAE.
9.4.3.1.
Back-up system in case the electronic reporting system does not work
If the electronic reporting system does not work, the investigator (or designate) must 
complete, then date and sign a paper Expedited Adverse Events Report and fax it to the 

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
99
23-JUL-2019
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
100
Study Contact for Reporting SAEs (refer to the Sponsor Information) or to GSK 
Biologicals Clinical Safety and Pharmacovigilance department within 24 hours.
This back-up system should only be used if the electronic reporting system is not working 
and NOT if the system is slow. As soon as the electronic reporting system is working 
again, the investigator (or designate) must complete the electronic Expedited Adverse 
Events Report within 24 hours. The final valid information for regulatory reporting will 
be the information reported through the electronic SAE reporting system.
9.4.4.
Completion and transmission of pregnancy reports to GSK 
Biologicals
Once the investigator becomes aware that a subject is pregnant, the investigator (or 
designate) must complete the required information onto the electronic pregnancy report 
WITHIN 2 WEEKS.
Note: Conventionally, the estimated gestational age (EGA) of a pregnancy is dated from 
the first day of the last menstrual period (LMP) of the cycle in which a woman conceives. 
If the LMP is uncertain or unknown, dating of EGA and the estimated date of delivery 
(EDD) should be estimated by ultrasound examination and recorded in the pregnancy 
report.
9.4.5.
Reporting of AESIs to GSK Biologicals
Once an AESI is diagnosed (serious or non-serious) in a study subject, the investigator 
(or designate) must complete the information in the electronic Expedited Adverse Events 
Report WITHIN 24 HOURS after he/she becomes aware of the diagnosis. The report 
allows to specify that the event is an AESI and whether it is serious or non-serious. The 
report will always be completed as thoroughly as possible with all available details of the 
event. Even if the investigator does not have all information regarding an AESI, the 
report should still be completed within 24 hours. Once additional relevant information is 
received, the report should be updated WITHIN 24 HOURS.
The investigator will always provide an assessment of causality at the time of the initial 
report. The investigator will be required to confirm the review of the AESI causality by 
ticking the ‘reviewed’ box in the electronic Expedited Adverse Events Report within 
72 hours of submission of the AESI.
Refer to Section 9.4.3.1 for back-up system in case the electronic reporting system does 
not work.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
100
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
101
9.4.6.
Updating of SAE, pregnancy, and AESI information after removal 
of write access to the subject’s eCRF
When additional SAE, pregnancy, or AESI information is received after removal of the 
write access to the subject’s eCRF, new or updated information should be recorded on the 
appropriate paper report, with all changes signed and dated by the investigator. The 
updated report should be faxed to the Study Contact for Reporting SAEs (refer to the 
Sponsor Information) or to GSK Biologicals Clinical Safety and Pharmacovigilance 
department within the designated reporting time frames specified in Table 21.
9.4.7.
Regulatory reporting requirements for serious adverse events
The investigator will promptly report all SAEs to GSK in accordance with the procedures 
detailed in Section 9.4.1. GSK Biologicals has a legal responsibility to promptly notify, 
as appropriate, both the local regulatory authority and other regulatory agencies about the 
safety of a product under clinical investigation. Prompt notification of SAEs by the 
investigator to the Study Contact for Reporting SAEs is essential so that legal obligations 
and ethical responsibilities towards the safety of other subjects are met.
Investigator safety reports are prepared according to the current GSK policy and are 
forwarded to investigators as necessary. An investigator safety report is prepared for a 
SAE(s) that is both attributable to the study vaccine/placebo or challenge agent and 
unexpected. The purpose of the report is to fulfil specific regulatory and GCP 
requirements, regarding the product under investigation.
9.5.
Follow-up of adverse events, serious adverse events, and 
pregnancies
9.5.1.
Follow-up of adverse events and serious adverse events
9.5.1.1.
Follow-up during the study
After the initial AE/SAE report, the investigator is required to proactively follow each 
subject and provide additional relevant information on the subject’s condition to GSK 
Biologicals (within 24 hours for SAEs; refer to Table 21).
All SAEs and AESIs (serious or non-serious) documented at a previous visit/contact and 
designated as not recovered/not resolved or recovering/resolving will be reviewed at 
subsequent visits/contacts until the last visit of the subject.
All AEs documented at a previous visit/contact and designated as not recovered/not 
resolved or recovering/resolving will be reviewed at subsequent visits/contacts until 30 
days after the last vaccination.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
101
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
102
9.5.1.2.
Follow-up after the subject is discharged from the study
The investigator will follow subjects:

With SAEs, AESIs (serious or non-serious), or subjects withdrawn from the study as 
a result of an AE, until the event has resolved, subsided, stabilized, disappeared, or 
until the event is otherwise explained, or the subject is lost to follow-up.

With other non-serious neutropenia cases, until the event is otherwise explained or 
they are lost to follow-up.
If the investigator receives additional relevant information on a previously reported SAE, 
he/she will provide this information to GSK Biologicals using a paper/electronic 
Expedited Adverse Events Report and/or pregnancy report as applicable.
GSK Biologicals may request that the investigator performs or arranges the conduct of 
additional clinical examinations/tests and/or evaluations to elucidate as fully as possible 
the nature and/or causality of the AE or SAE. The investigator is obliged to assist. If a 
subject dies during participation in the study or during a recognized follow-up period, 
GSK Biologicals will be provided with any available post-mortem findings, including 
histopathology.
9.5.2.
Follow-up of pregnancies
Pregnant subjects will be followed to determine the outcome of the pregnancy. At the end 
of the pregnancy, whether full-term or premature, information on the status of the mother 
and child will be forwarded to GSK Biologicals using the electronic pregnancy report and 
the Expedited Adverse Events Report if applicable. Generally, the follow-up period 
doesn’t need to be longer than six to eight weeks after the estimated date of delivery.
Regardless of the reporting period for SAEs for this study, if the pregnancy outcome is a 
SAE, it should always be reported as SAE.
9.6.
Treatment of adverse events
Treatment of any AE is at the sole discretion of the investigator and according to current 
good medical practice. Any medication administered for the treatment of a SAE/AESIs 
should be recorded in Expedited Adverse Event Report of the subject’s eCRF (refer to 
Section 7.6).
9.7.
Unblinding
GSK Biologicals’ policy (which incorporates ICH E2A guidance, EU Clinical Trial 
Directive and US Federal Regulations) is to unblind the report of any SAE which is 
unexpected and attributable/suspected to be attributable to the study vaccine/placebo or 
challenge agent, prior to regulatory reporting. The GSK Biologicals’ Central Safety 
Physician is responsible for unblinding the treatment assignment in accordance with the 
specified timeframes for expedited reporting of SAEs (refer to Section 9.4.1).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
102
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
103
9.8.
Emergency unblinding
Unblinding of a subject’s individual treatment code should occur only in the case of a 
medical emergency, or in the event of a serious medical condition, when knowledge of 
the treatment is essential for the clinical management or welfare of the subject, as judged 
by the investigator.
The emergency unblinding process consists of an automated system SBIR that allows the 
investigator to have unrestricted, immediate and direct access to the subject’s individual 
study treatment.
The investigator has the option of contacting a GSK Biologicals’ On-call Central Safety 
Physician (or Backup) if he/she needs medical advice or needs the support of GSK to 
perform the unblinding (i.e. he/she cannot access the automated Internet-based system).
Any emergency unblinding must be fully documented by using the Emergency 
Unblinding Documentation Form, which must be appropriately completed by the 
investigator and sent within 24 hours to GSK Biologicals.
GSK Biologicals’ Contact information for Emergency Unblinding
24/24 hour and 7/7 day availability
GSK Biologicals’ Central Safety Physician:
For US/Canada only:
 (GSK Biologicals Central Safety Physician on-call)
GSK Biologicals’ Central Safety Physician Back-up:
US/Canada only:
Emergency Unblinding Documentation Form transmission:
US/Canada only:
Fax: 
9.9.
Subject card
Study subjects must be provided with the address and telephone number of the main 
contact for information about the clinical study.
The investigator (or designate) must therefore provide a “subject card” to each subject. In 
an emergency situation this card serves to inform the responsible attending physician that 
the subject is in a clinical study and that relevant information may be obtained by 
contacting the investigator.
Subjects must be instructed to keep subject cards in their possession at all times during 
the study duration.

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
103
23-JUL-2019
PPD
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
104
9.10.
Holding rule and safety monitoring
9.10.1.
Holding rule
The following holding rule has been defined for the study:

At least one subject developing a Grade 3 symptomatic neutropenia considered 
possibly, probably or definitely related to vaccination.
The Investigator must notify GVGH/GSK immediately if the holding rule is met and 
should halt any further vaccination until further notice. Vaccination can only be resumed 
after formal review of unblinded data by the IDMC and formal greenlight to proceed with 
further vaccination (please refer to the IDMC charter).
9.10.2.
Safety monitoring
The SRT will monitor the safety of subjects throughout the study. The SRT will review 
blinded data, assess safety signals and make recommendations to the IDMC and to the 
Sponsor concerning continuation, termination, or other modifications of the study based 
on the observed adverse effects.
An IDMC will be established by GSK Biologicals for the purpose of monitoring the 
study and to provide independent, non-binding advice on safety and ethics. The IDMC 
will provide recommendations about stopping, holding, continuing or modifying the trial.
The frequency of IDMC sessions and other operational details are described in the IDMC 
charter. In case of a serious safety issue during the study, GSK Biologicals will inform 
the IDMC as well as fulfil its regulatory obligation expeditiously.
10.
SUBJECT COMPLETION AND WITHDRAWAL
10.1.
Subject completion
A subject who returns for the concluding visit foreseen in the protocol is considered to 
have completed the study.
10.2.
Subject withdrawal
Withdrawals will not be replaced.
10.2.1.
Subject withdrawal from the study
From an analysis perspective, a ‘withdrawal’ from the study refers to any subject who did 
not come back for the concluding visit foreseen in the protocol.
All data collected until the date of withdrawal/last contact of the subject will be used for 
the analysis.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
104
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
105
A subject is considered a ‘withdrawal’ from the study when no study procedure has 
occurred, no follow-up has been performed and no further information has been collected 
for this subject from the date of withdrawal/last contact.
Investigators will make an attempt to contact those subjects who do not return for
scheduled visits or follow-up.
Information relative to the withdrawal will be documented in the eCRF. The investigator 
will document whether the decision to withdraw a subject from the study was made by 
the subject himself/herself, or by the investigator, as well as which of the following 
possible reasons was responsible for withdrawal:

Serious adverse event.

Unsolicited non-serious adverse event.

Solicited adverse event.

Protocol violation (specify).

Consent withdrawal, not due to an adverse event*.

Moved from the study area.

Lost to follow-up.

Other (specify).
*In case a subject is withdrawn from the study because he/she has withdrawn consent, the 
investigator will document the reason for withdrawal of consent, if specified by the 
subject, in the eCRF.
Subjects who are withdrawn from the study because of SAEs/AEs must be clearly 
distinguished from subjects who are withdrawn for other reasons. Investigators will 
follow subjects who are withdrawn from the study as result of a SAE/AE until resolution 
of the event (see Section 9.5.1.2).
10.2.2.
Subject withdrawal from study vaccine/placebo or challenge 
agent
A ‘withdrawal’ from the study vaccine/placebo or challenge agent refers to any subject 
who does not receive the complete treatment, i.e. when no further planned dose or 
challenge is administered from the date of withdrawal. A subject withdrawn from the 
study vaccine/placebo or challenge agent may not necessarily be withdrawn from the 
study as further study procedures or follow-up may be performed (safety or 
immunogenicity) if planned in the study protocol.
Information relative to premature discontinuation of the study vaccine/placebo or 
challenge agent will be documented on the Vaccine Administration page/screen of the 
eCRF. The investigator will document whether the decision to discontinue further 
vaccination/challenge administration was made by the subject himself/herself, or by the 
investigator, as well as which of the following possible reasons was responsible for 
withdrawal:
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
105
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
106

Serious adverse event.

Unsolicited non-serious adverse event.

Solicited adverse event.

Not willing to be vaccinated or to receive the challenge agent.

Other (specify).
11.
STATISTICAL METHODS
11.1.
Primary endpoint
Efficacy
VE will be evaluated with:

Rate of shigellosis (fulfilling the protocol primary case definition) occurring within a 
period starting with the challenge visit and lasting up to the end of the inpatient stay, 
in all subjects.
11.2.
Secondary endpoints
Efficacy
VE, in subjects receiving the 1790GAHB vaccine vs. placebo, will be also measured
during inpatient stay (Day 57 to Day 64) against:

Rate of shigellosis as defined by the CHIM working group case definition for 
shigellosis occurring within a period starting with challenge visit and lasting until the 
end of the inpatient stay, in all subjects. (Amended: 23 July 2019)

Rate of shigellosis, as defined by: severe diarrhea OR moderate diarrhea with fever 
or with one or more moderate constitutional/enteric symptom OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 reportable 
constitutional/enteric symptom]].

Rate of more severe shigellosis as defined by: severe or moderate diarrhea with fever 
or with one or more severe constitutional/enteric symptom OR dysentery [[≥2 loose 
stools with gross blood (hemoccult positive) in 24 hours] AND [oral temperature 
≥38.0oC OR ≥1 severe constitutional/enteric symptom]]. (Amended: 23 July 2019)

Shedding of S. sonnei strain 53G.
Shedding of S. sonnei strain 53G is defined as positivity of at least one stool sample 
either by culture or qPCR or both.

Severe diarrhea.

More severe diarrhea.

Dysentery.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
106
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
107

Weight of all grade 3-5 stools.

Total number of all grade 3-5 stools.

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR dysentery 
OR presence of oral temperature 38.5°C OR presence of one or more severe 
intestinal symptoms (abdominal pain, cramping, nausea, vomiting, gas, anorexia).

Disease not fulfilling the protocol primary case definition for shigellosis associated 
or not with mild to moderate symptoms including: passing loose stool (not meeting 
the protocol definition of moderate or severe diarrhea), abdominal pain, abdominal 
cramps, gas, anorexia, nausea, headache, myalgia, malaise, arthralgia, fever,
vomiting and IV fluid administration.

Time to onset of shigellosis after challenge, according to the protocol primary case 
definition.
Safety
Solicited adverse events

Occurrence of each solicited local and systemic adverse event within 7 days after 
each vaccination.
Unsolicited adverse events

Occurrence of unsolicited AEs within 28 days after vaccination and after challenge, 
according to Medical Dictionary for Regulatory Activities (MedDRA) classification.
Serious adverse events

Occurrence of all SAEs and related SAEs from Day 1 to study end.
Adverse events of special interest

Occurrence of AESI (i.e., symptomatic neutropenia) from Day 1 to study end.
Laboratory parameters

Out of laboratory reference range and/or clinically significant value (according to 
local ranges) for hematology at 7 days after first and second vaccination and at last 
study visit (Visit 8).
Immunogenicity
The measures of immunogenicity, against the LPS of S. sonnei, will include:

IgG geometric mean concentrations (GMCs) pre-vaccination (Day 1), 7 and 28 days 
after first and second vaccination by antibody concentration at baseline (i.e., above 
vs. below the assay detection limit), as determined by anti-S. sonnei LPS IgG 
ELISA.

IgG GMC pre-challenge (Day 57), 7 and 28 days after challenge (Day 64 and Day 
85) as determined by anti-S. sonnei LPS IgG ELISA.

Number and percentage of subjects achieving a post vaccination anti- S. Sonnei LPS 
concentration ≥ 121 EU/ml at 28 days after first and second vaccination.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
107
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
108

Number and percentage of seroresponders* for anti-S. sonnei LPS at 28 days after 
first and second vaccination.
*Seroresponse is aimed to define a significant increase in anti S. sonnei LPS IgG 
concentration in post-vaccination samples and relies on the definition already used in 
a previous phase II study in Kenyan population. For the purpose of this study 
seroresponse is defined as:

If the baseline value is greater than 50 EU/mL then an increase of at least 50% 
in the post-vaccination sample as compared to baseline.

If the baseline value is less or equal to 50 EU/mL then an increase of at least 
25 EU/mL in the post-vaccination sample as compared to baseline.
Note: Threshold values/increases given in the definition of seroresponse might be 
subject to change during the course of the study (e.g., in case of 
optimization/qualification/validation of the anti S. sonnei LPS IgG ELISA).
11.3.
Tertiary endpoints

Specific anti-S. sonnei LPS sIgA antibody concentration in stool samples at Day 1, 7
days after first and second vaccination and 7 days after challenge (Day 64).

Frequency of S. sonnei LPS specific IgG α4β7+/- antibody secreting cells per 10^6 
PBMC plasmablast at Day 1 and 7 days after first and second vaccination and 7 days 
after challenge (Day 8, Day 36 and Day 64). (Amended: 23 July 2019)

Glycosylation profiles of IgG antibodies at Day 1 and 28 days after second 
vaccination (Visit 5; Day 57).

Number and percentage of subjects that show correlation between serum anti-S. 
sonnei LPS IgG concentration, SBA titer, shigellosis, shedding, MSD, dysentery and
mild diarrhea after challenge.

Concentration of stool markers of intestinal inflammation (e.g. calprotectin and 
myeloperoxidase) before oral challenge with S. sonnei, 53G at Visit 5 (Day 57) and 
daily during the post-challenge inpatient stay (Day 57 to Day 64).

The number of differential expressed genes 7 days after first and second vaccination 
and 7 days after challenge by comparing the relative abundance of mRNA sequences 
compared to Day 1 (pre-vaccination baseline).

Diversity and frequency of microbiome components (taxa and/or genes according to 
technology) at Day 1 prior to vaccination and 28 days after second vaccination (Visit 
5; Day 57).
Exploratory analysis for hypotheses generation will include the evaluation of the 
association of the microbiome components with efficacy and immunogenicity 
described above.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
108
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
109
11.4.
Determination of sample size
Primary objective - Efficacy
In comparing the protective efficacy of 1790GAHB vaccine against the placebo group the 
following assumptions will be made:
Assuming a true VE of 70%, a total number of 21 confirmed cases will be needed to 
demonstrate that the LL of the two-sided 90% CI for the VE is above 0% with 80% 
power (by Pass 2013, One Proportion Power Analysis, one-sided test, one-sided alpha =
5%).
Based on the results obtained by the Cincinnati Children’s Hospital Medical Center, 
where the challenge model was developed, in subjects receiving a challenge with 1500 
CFU of S. sonnei 53G, the attack rate for the primary case definition of this study is 58%.
Thus considering an AR of 58% in the placebo group and a percentage of non-evaluable 
subjects of 22%, approximately 72 subjects (36 per group) will be recruited to reach these 
21 cases.
The assumption on the value of true VE is based on the percentage of subjects with 
seroresponse observed in previous studies where the 1.5/25 µg OAg/protein dose of 
1790GAHB vaccine was evaluated. In the phase I study in Europe, the observed 
percentage of subjects with seroresponse was 63% and 88% after 1st and 2nd vaccination 
respectively. In the Phase IIa study, conducted in endemic region, the observed 
percentage of subjects with seroresponse was 68% and 90% after 1st and 2nd vaccination,
respectively.
11.5.
Analysis sets
11.5.1.
All Enrolled Set
All screened subjects who provide informed consent, and provide demographic and/or 
baseline screening assessments, regardless of the subject’s randomization and treatment 
status in the study and received a Subject ID.
11.5.2.
All Exposed Set
All subjects in the enrolled set who receive a study vaccination.
11.5.3.
Safety set
11.5.3.1.
Solicited Safety Set (solicited local and systemic adverse events and 
other solicited adverse events)
All subjects in the Exposed Set with any solicited AE data and/or indicators of solicited 
AEs.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
109
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
110
11.5.3.2.
Unsolicited Safety Set (unsolicited adverse events)
All subjects in the Exposed Set with unsolicited AE data.
11.5.3.3.
Overall safety set
All subjects who are in the Solicited Safety Set and/or Unsolicited Safety Set.
Subjects will be analyzed as “treated” (i.e., according to the vaccine* a subject received, 
rather than the vaccine* to which the subject may have been randomized).
*Vaccine refers to study vaccine or placebo.
11.5.4.
Full analysis set (FAS) efficacy/Immunogenicity set
11.5.4.1.
Full analysis set efficacy 
All subjects in the All Enrolled Set who are randomized, receive a study vaccination and 
provide efficacy data.
11.5.4.2.
Full analysis set Immunogenicity
All subjects in the All Enrolled Set who are randomized, receive at least one study 
vaccination and provide immunogenicity data at the relevant timepoints.
In case of vaccination error, subjects in the FAS sets will be analyzed “as randomized” 
(i.e., according to the vaccine* a subject was designated to receive, which may be 
different from the vaccine* the subject actually received).
*Vaccine refers to study vaccine or placebo.
11.5.5.
Per-protocol (PP) set for efficacy/Immunogenicity set
All subjects in the FAS Efficacy / Immunogenicity who:

Correctly receive the vaccine* (i.e., receive the vaccine* to which the subjects is 
randomized and at the scheduled timepoints).
*Vaccine refers to study vaccine or placebo.

Have no protocol deviations leading to exclusion as defined prior to unblinding / 
analysis.

Are not excluded due to other reasons defined prior to unblinding or analysis.
PPS are subsets of FAS and should be always defined even if the objectives do not 
require it.
Examples for subjects excluded due to other reasons than protocol deviations are:

Subjects who withdrew informed consent.
The primary analysis will be based on the PP cohort for efficacy and immunogenicity. 
However efficacy and immunogenicity analyses will be performed on both FAS and PP 
sets.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
110
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
111
11.5.6.
Other analysis sets
There are no additional analysis sets for analysis in this study.
All subjects who are screened, i.e., consented but not yet randomized/enrolled.
11.5.7.
Sub-groups
The analysis for the primary efficacy endpoint will be repeated for the two subgroups of 
subjects who were responders or non-responders at the immunogenicity assessment of the 
pre-challenge visit.
11.6.
Derived and transformed data

Screening (anti S. sonnei LPS IgG Screening-ELISA)

The cut-off value for the anti S. sonnei LPS IgG Screening-ELISA is defined by 
the laboratory.

A seronegative subject is a subject whose titer is below the cut-off value.

A seropositive subject is a subject whose titer is greater than or equal to the cut-
off value.

Immunogenicity (anti S. sonnei LPS IgG-ELISA):

The cut-off value for the anti S. sonnei LPS IgG-ELISA is defined by the 
laboratory.
Seroresponse is aimed to define a significant increase in anti S. sonnei LPS IgG 
concentration in post-vaccination samples and relies on the definition already used in 
a previous phase II study in Kenyan population. For the purpose of this study 
seroresponse is defined as:

If the baseline value is greater than 50 EU/mL then an increase of at least 50% 
in the post-vaccination sample as compared to baseline.

If the baseline value is less or equal to 50 EU/mL then an increase of at least 
25 EU/mL in the post-vaccination sample as compared to baseline.
Note: Threshold values/increases given in the definition of seroresponse might be 
subject to change during the course of the study (e.g., in case of 
optimization/qualification/validation of the anti S. sonnei LPS IgG ELISA).

The GMC calculations are performed by taking the anti-log of the mean of the 
log concentration transformations. Values to be used for the antibody 
concentrations below the assay cut-off will be described in the Statistical 
Analysis Plan (SAP).

Handling of missing data: for a given subject and a given immunogenicity 
measurement, missing or non-evaluable measurements will not be replaced.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
111
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
112

Reactogenicity and safety:

Handling of missing data: subjects who missed reporting symptoms 
(solicited/unsolicited or concomitant medications) will be treated as subjects 
without symptoms (solicited/unsolicited or concomitant medications, 
respectively). In case of significant non-compliance of study procedures for 
reporting symptoms, the analysis plan will be reassessed to ensure more accurate 
reporting of study data by further analysis.

For the analysis of solicited symptom, missing or non-evaluable measurements 
will not be replaced. Therefore, the analysis of the solicited symptoms based on 
the All Enrolled Set will include only subjects/doses with documented safety 
data (i.e., symptom screen completed).
11.7.
Analysis of demographics
Descriptive statistics (mean, standard deviation, median, minimum and maximum) for 
age, height and weight at enrolment will be calculated overall and by vaccine/placebo 
group.
Distributions of subjects by gender and geographic ancestry will be summarized.
11.8.
Analysis of efficacy
VE will be evaluated at the end of study period. VE will be estimated as 1-RR where RR 
is the risk ratio (proportion of subjects reporting the disease in the vaccinated group over 
the proportion in the placebo group) together with 90% CIs.
11.9.
Analysis of immunogenicity
Analysis of binary variables:
The number and percentages of subjects will be summarized. Two-sided 95% CIs for the 
percentages will be computed.
Antibody titers/concentration below the limit of detection in the respective assay will be 
set to half the limit for the purposes of analysis. Missing values of immunogenicity will 
be excluded from analyses (i.e. complete-case analysis) since they are considered missing 
completely at random, i.e. not informative and with no impact on inferences.
Analysis of continuous variables:
The antibody concentrations/titers will be logarithmically transformed (base10) (to fulfil 
the normal distribution assumption). GMCs will be calculated, with their associated two-
sided 95% CIs, by exponentiating the corresponding log-transformed means and their 
95% CI.
Additionally, within-subject geometric mean ratios (GMRs) will be computed for 
geometric mean titers/GMCs at each time point after vaccination versus baseline (Day 1). 
The GMRs and 95% CIs will be constructed by exponentiating the mean within-subject 
differences in log-transformed titers and the corresponding 95% CIs.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
112
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
113
11.10.
Analysis of safety
The primary analysis will be performed on the All Exposed Set.
Analysis of solicited local and systemic adverse events and other reactions:
Solicited AEs will be summarized according to defined severity grading scales.
Frequencies and percentages of subjects experiencing each AE will be presented for each 
symptom severity. Summary tables showing the occurrence of any local or systemic AE 
overall and at each timepoint will also be presented.
Post-vaccination/challenge solicited AE reported from Day 1 to 7 days post-
vaccination/challenge will be summarized by maximal severity and by vaccine/placebo
group. The severity of solicited local AE will be summarized according to categories 
based on linear measurement.
Injection-site pain and systemic reactions occurring up to 7 days after each vaccination 
will be summarized according to “mild”, “moderate” or “severe”.
Each solicited local and systemic AE will also be further summarized as “none” versus 
“any”.
Analysis of unsolicited AEs:
All the AEs occurring during the study, judged either as probably related, possibly 
related, or not related to vaccination/challenge by the investigator, will be recorded.
The original verbatim terms used by investigators to identify AEs in the eCRFs will be 
mapped to preferred terms using the MedDRA dictionary. The AEs will then be grouped 
by MedDRA preferred terms into frequency tables according to system organ class. All 
reported AEs, as well as AEs judged by the investigator as at least possibly related to 
study vaccine/placebo or challenge agent, will be summarized according to system organ 
class and preferred term within system organ class. These summaries will be presented by 
vaccination group. When an AE occurs more than once for a subject, the maximal 
severity and strongest relationship to the vaccine/placebo group will be counted.
Separate summaries will be produced for the following categories:

SAEs.

AEs that are possibly or probably related to vaccine/placebo or challenge agent.

AEs leading to withdrawal from the study.
Data listings of all AEs will be provided by subject. In addition, AEs in the categories 
above will be provided as listed data.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
113
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
114
11.11.
Interpretation of analyses
Except for analyses on objectives with a predefined success criterion and an appropriate 
type I error control (see Section 2), comparative analyses will be descriptive with the aim 
to characterize the difference in reactogenicity and immunogenicity efficacy between 
groups. These descriptive analyses should not be interpreted.
11.12.
Conduct of analyses
Any deviation(s) or change(s) from the original statistical plan outlined in this protocol 
will be described and justified in the final study report.
11.12.1.
Sequence of analyses
The total of 72 subjects will be divided in 4 cohorts of 18 subjects each (for bed 
availability at the study site). The vaccination and challenge will be done per cohort.
However, if for any reason, a cohort does not reach the planned 18 subjects, additional 
subjects can be added in the next cohorts. The maximum number of subjects must not be 
more than 20 (maximum number of beds in the clinic) in each cohort.
The following 2 interim analyses are planned:
1.
After completion of the Visit 5 (Day 64): post-challenge efficacy data of all 
subjects (all 4 cohorts) 
2.
After Visit 6 (Day 85): secondary immunogenicity data and tertiary SBA 
immunogenicity data of all subjects (all 4 cohorts).
(Amended: 23 July 2019)
All analyses will be conducted before unblinding on clean and final data. (Amended: 23 
July 2019)
An integrated Clinical Study Report containing all data will be written after the End of 
Study and made available to the investigators. (Amended: 23 July 2019)
If the data for tertiary endpoints become available at a later stage, (an) additional 
analysis/analyses will be performed. These data will be documented in annex(es) to the 
study report and will be made available to the investigators at that time.
11.12.2.
Statistical considerations for interim analyses
No statistical adjustment will be made for the interim analyses, which are intended to 
provide final outputs related to the different endpoints and timepoints in a phased 
manner.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
114
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
115
12.
ADMINISTRATIVE MATTERS
To comply with ICH GCP administrative obligations relating to data collection, 
monitoring, archiving data, audits, confidentiality, public disclosure requirements and 
publications must be fulfilled.
12.1.
Electronic case report form instructions
A validated GSK defined electronic data collection tool will be used as the method for 
data collection.
In all cases, subject initials will not be collected nor transmitted to GSK. Subject data 
necessary for analysis and reporting will be entered/transmitted into a validated database 
or data system. Clinical data management will be performed in accordance with 
applicable GSK standards and data cleaning procedures.
While completed eCRFs are reviewed by a GSK Biologicals’ Site Monitor at the study 
site, omissions or inconsistencies detected by subsequent eCRF review may necessitate 
clarification or correction by the investigator or appropriately qualified designee. In all 
cases, the investigator remains accountable for the study data. 
The investigator will be provided with an electronic format in read only mode of the final 
version of the data generated at the investigational site once the database is archived and 
the study report is complete and approved by all parties.
12.2.
Subject Diary
Paper Diaries (pDiaries), hereafter referred to as Subject Diaries will be the only source 
document allowed for solicited local and systemic adverse events (including body 
temperature measurements), starting after the initial 30 minute post-vaccination period at 
the clinic. The following additional rules apply to documentation of safety information 
collected in the Subject Diary.
The Investigator or delegated staff should monitor the Subject’s Diary status throughout 
the study for compliance and any solicited local and systemic adverse events that were of 
concern to the subject.

No corrections or additions to the information recorded by the subject within the 
Subject Diary will be allowed after it is delivered to the site.

Any blank or illegible fields on the Subject Diary must be described as missing in the 
eCRF.
The following additional rules apply to documentation of Subject Diary information 
collected in the eCRFs:

The site must enter all readable entries in the Subject Diary into the eCRF, including 
those values that may be biologically implausible (e.g. body temperature: 400°C).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
115
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
116

Any illegible or implausible data should be reviewed with the Subject. If an 
underlying solicited or unsolicited AE is described on review with the subject, this 
should be described in the source document and reported as an unsolicited AE in the 
Adverse Event eCRF (e.g., if the subject above confirms body temperature of 40°C 
on the day in which body temperature: 400°C was written into his/her Subject Diary, 
this fever of 40°C should be recorded in the Adverse Event eCRF).

Any newly described safety information (including a solicited AE) must not be 
written into the Subject Diary and must be described in the study file as a verbally 
reported AE. Any AE reported in this fashion must be described as an unsolicited AE 
and therefore entered on the Adverse Event eCRF.
12.3.
Study monitoring by GSK biologicals
GSK will monitor the study to verify that, among other items, the:

Data are authentic, accurate, and complete.

Safety and rights of subjects are being protected.

Study is conducted in accordance with the currently approved protocol, any other 
study agreements, GCP and all applicable regulatory requirements.
The investigator and the head of the medical institution (where applicable) agrees to 
allow the monitor direct access to all relevant documents.
The investigator must ensure provision of reasonable time, space and qualified personnel 
for monitoring visits.
Direct access to all study-site related and source data is mandatory for the purpose of 
monitoring review. The monitor will perform an eCRF review and a Source Document 
Verification (SDV). By SDV we understand verifying eCRF entries by comparing them 
with the source data that will be made available by the investigator for this purpose.
The Source Documentation Agreement Form describes the source data for the different 
data in the eCRF. This document should be completed and signed by the site monitor and 
investigator and should be filed in the investigator’s study file. Any data item for which 
the eCRF will serve as the source must be identified, agreed and documented in the 
source documentation agreement form. 
Upon completion or premature discontinuation of the study, the monitor will conduct site 
closure activities with the investigator or site staff, as appropriate, in accordance with 
applicable regulations, GCP, and GSK procedures.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
116
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
117
12.4.
Record retention
Following closure of the study, the investigator must maintain all site study records 
(except for those required by local regulations to be maintained elsewhere) in a safe and 
secure location. The records must be easily accessible, when needed (e.g. audit or 
inspection), and must be available for review in conjunction with assessment of the 
facility, supporting systems, and staff. Where permitted by applicable laws/regulations or 
institutional policy, some or all of these records can be maintained in a validated format 
other than hard copy (e.g. microfiche, scanned, electronic); however, caution needs to be 
exercised before such action is taken. The investigator must ensure that all reproductions 
are legible and are a true and accurate copy of the original and meet accessibility and 
retrieval standards, including re-generating a hard copy, if required. Furthermore, the 
investigator must ensure that an acceptable back-up of the reproductions exists and that 
there is an acceptable quality control procedure in place for making these reproductions.
GSK will inform the investigator/institution of the time period for retaining these records 
to comply with all applicable regulatory requirements. The minimum retention time will 
meet the strictest standard applicable to a particular site, as dictated by ICH GCP, any 
institutional requirements, applicable laws or regulations, or GSK standards/procedures, 
otherwise, the minimum retention period will default to 25 years after completion of the 
study report.
The investigator/institution must notify GSK of any changes in the archival 
arrangements, including, but not limited to archival at an off-site facility, transfer of 
ownership of the records in the event the investigator leaves the site. 
12.5.
Quality assurance
To ensure compliance with GCP and all applicable regulatory requirements, GSK may 
conduct a quality assurance audit. Regulatory agencies may also conduct a regulatory 
inspection of this study. Such audits/inspections can occur at any time during or after 
completion of the study. If an audit or inspection occurs, the investigator and institution 
agree to allow the auditor/inspector direct access to all relevant documents and to allocate 
his/her time and the time of his/her staff to the auditor/inspector to discuss findings and 
any relevant issues.
12.6.
Posting of information on publicly available clinical trial 
registers and publication policy
GSK assures that the key design elements of this protocol will be posted on the GSK 
website and in publicly accessible database(s) such as clinicaltrials.gov, in compliance 
with the current regulations.
GSK also assures that results of this study will be posted on the GSK website and in 
publicly accessible regulatory registry(ies) within the required timeframe, in compliance 
with the current regulations. The minimal requirement is to have primary endpoint 
summary results disclosed at latest 12 months post PCD and to have secondary endpoint 
disclosed at latest 12 months after the Last Subject Last Visit as described in the protocol.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
117
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
118
GSK also aims to publish the results of these studies in searchable, peer reviewed 
scientific literature and follows the guidance from the International Committee of 
Medical Journal Editors.
12.7.
Provision of study results to investigators
Where required by applicable regulatory requirements, an investigator signatory will be 
identified for the approval of the study report. The investigator will be provided 
reasonable access to statistical tables, figures, and relevant reports and will have the 
opportunity to review the complete study results at a GSK site or other mutually-
agreeable location.
GSK Biologicals will also provide the investigator with the full summary of the study 
results. The investigator is encouraged to share the summary results with the study 
subjects, as appropriate.
12.8.
Data sharing
Under the framework of the SHARE initiative, results of GSK studies may be combined 
with non- GSK studies, to investigate further about the study product(s) and other 
product(s), and /or the disease/condition under investigation and related diseases and 
conditions.
12.9.
Pharmacogenomics
As part of the sequencing for the microbiome, human genome will be sequenced as 
bypass product but the intent is not to analyze the data which will be stored securely.
Analyses of the transcriptomics signals evaluating the number of differential expressed 
genes by comparing the relative abundance of mRNA sequences are also considered a 
pharmacogenomics experiment.
By United States federal regulation, annual reports must include relevant 
pharmacogenomics results experiment. Refer to the US Guidance for industry 
“Pharmacogenomic data submissions” for more information on the process and format 
for submission of such data.
13.
COUNTRY SPECIFIC REQUIREMENTS
Not applicable.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
118
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
119
14.
REFERENCES
Bodhidatta L, Pitisuttithum P, Chamnanchanant S, Chang K, Islam D, Bussaratid V, 
Venkatesan M, Hale T. Establishment of a S. sonnei human challenge model in Thailand. 
Vaccine. 2012 Nov; 30 (49): 7040-5.
Centers for Disease Control and Prevention Metropolitan Atlanta Congenital Defects 
Program (CDC MACDP) guidelines. Birth defects and genetic diseases branch 6-digit 
code for reportable congenital anomalies; 
http://www.cdc.gov/ncbddd/birthdefects/documents/MACDPcode0807.pdf
Cohen D, Block C, Green MS, Lowell G, Ofek I. Immunoglobulin M, A, and G antibody 
response to lipopolysaccharide O antigen in symptomatic and asymptomatic Shigella 
infections. J Clin Microbiol. 1989 Jan; 27 (1): 162–167.
Cohen D, Green M, Block C, Slepon R, Ambar R, Wasserman SS, Levine MM. 
Reduction of transmission of shigellosis by control of houseflies (Musca domestica). 
Lancet. 1991 Apr 27; 337 (8748): 993-7.
EMA Guideline on the exposure to medicinal products during pregnancy: need for post-
authorization data (Doc. Ref. EMEA/CHMP/313666/2005) ‘adopted at Community level 
in May 2006);
http://www.ema.europa.eu/docs/en_GB/document_library/Regulatory_and_procedural_g
uideline/2009/11/WC500011303.pdf
Ferreccio C, Prado V, Ojeda A, Cayyazo M, Abrego P, Guers L, Levine MM. 
Epidemiologic patterns of acute diarrhea and endemic Shigella infections in children in a 
poor periurban setting in Santiago, Chile. Am J Epidemiol. 1991 Sep 15; 134 (6): 614-27.
GBD 2015 Mortality and Causes of Death Collaborators. Global, regional, and national 
life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 
1980–2015: a systematic analysis for the Global Burden of Disease Study 20. Lancet. 
2016; 388: 1459-544
Gerke C, Colucci AM, Giannelli C, Sanzone S, Vitali CG, Sollai L, Rossi O, Martin LB, 
Auerbach J, Di Cioccio V, Saul A. Production of a Shigella sonnei Vaccine Based on 
Generalized Modules for Membrane Antigens (GMMA), 1790GAHB. PLoS One. 2015; 
10 (8): e0134478.
Pitisuttithum P, Islam D, Chamnanchanunt S, Ruamsap N, Khantapura P, Kaewkungwal 
J, Kittitrakul C, Luvira V, Dhitavat J, Venkatesan MM, Mason CJ, Bodhidatta L. Clinical 
trial of an oral live Shigella sonnei vaccine candidate, WRSS1, in Thai adults. Clin 
Vaccine Immunol. 2016; 23: 564-575.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
119
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
120
Appendix A
LABORATORY ASSAYS
Hematology, Virology, Blood chemistry, HLA-B27, anti S. sonnei LPS IgG-Screening, 
urinalysis:
Hematology, Virology, Blood chemistry, HLA-B27, urinalysis and anti S. sonnei LPS 
IgG Screening-ELISA will be done at the local site according to the methods available 
there. The anti S. Sonnei LPS IgG Screening-ELISA will be done locally for the anti-S. 
sonnei LPS IgG antibody determination at screening.
HEMATOLOGY
White Blood Cells (WBC)
Red Blood Cells (RBC)
Hemoglobin
Hematocrit
Platelets
Eosinophils
Basophils
Neutrophils
Monocytes
Lymphocytes
CLINICAL CHEMISTRY
Total bilirubin
Aspartic Aminotransferase (ASAT/GOT)
Alanine Aminotransferase (ALAT/GPT)
γ-Glutamyl Transferase (γ-GT)
Lactic Dehydrogenase (LDH)
Alkaline Phosphatase (AP)
Total Proteins
Glucose (random glucose)
Blood Urea Nitrogen (BUN)
Creatinine
Sodium
Potassium
Prothrombin time (only at screening)
SEROLOGY for VIROLOGY
HBsAg
HCV antibodies
HIV antibodies
PREGNANCY TEST
Human chorionic gonadotropin (hCG) in urine
HLA-B27
HLA-B27
URINE DIPSTICK
Glucose
Proteins
pH
Ketones
Nitrites
Blood
URINALYSIS: Microscopic test on urine
(performed if urine dipstick shows deviations from normal values)
Leucocytes (WBC)
Erythrocytes (RBC)
Epithelial Cells
Casts
Bacteria
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
120
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
121
Anti S. sonnei LPS antibody determination from serum:
Anti-S. sonnei LPS IgG antibodies in serum (for all timepoints except screening) will be 
measured by ELISA in the GVGH-Laboratories (Siena, Italy). The ELISA is performed 
using S. sonnei LPS as coating antigen. A standard curve is run in duplicate on each 
plate. Results are expressed in ELISA units (EU) /mL of serum. 1 unit equals the 
reciprocal of the dilution to give an OD of 1.
Serum Bactericidal Activity in serum:
Serum bactericidal activity against S. sonnei will be measured by serum bactericidal 
assay. This assay is currently in development in a GVGH laboratory. 
S. sonnei determination from stool:

Culture: The presence of S. sonnei in stool samples will be assessed using a 
qualitative procedure and following the SOPs of the local or designated laboratory 
for culture, isolation and identification of S. sonnei from stool specimens.

qPCR: S. sonnei qPCR determination will be done following the SOPs of the local or 
designated laboratory for identification of S. sonnei by a qPCR from stool 
specimens.

S. sonnei sIgA and total sIgA determination from stool: S. Sonnei ELISA will be 
performed following the SOPs of the local or designated laboratory for ELISA assay 
from stool specimens. The S. sonnei sIgA result will be normalized to the total sIgA.
Stool inflammatory markers assay
Inflammatory markers including calprotectin and myeloperoxidase levels in stools 
(ng/mL) will be measured using commercially available (Epitope Diagnostics, Inc.) 
quantitative ELISA kits according to the manufacturer’s instructions.
α4β7 plasmablast ELISA (Amended: 23 July 2019)
Anti-S. sonnei LPS-specific IgG titers will be determined in plasmablasts, in both α4β7
positive and α4β7negative populations. The titers provided will be measured by ELISA 
assay in the culture supernatant of 5x10^6 cells, by using an in-house method 
developed in WRAIR. (Amended: 23 July 2019)
Transcriptomics
The transcriptomics signals analysis will be performed evaluating the number of 
differential expressed genes by comparing the relative abundance of mRNA sequences.
Gut Microbiome profile:
Gut microbiome analysis in stool using 16s ribosomal DNA amplicon sequencing and/or 
shotgun whole genome sequencing (refer to Section 6.7.3).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
121
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
122
Glycosylation profiles of IgG antibodies:
The activity of IgG antibody is mediated through two functional domains, the Fab and the 
Fc. The Fc domain mediates effector functions though specific interactions with FcγRs 
expressed on the surface of leukocytes, and activation of diverse immunomodulatory 
pathways impacting both innate and adaptive immunity [1]. The mechanisms of Fc 
domain diversification that determine Fc-FcγR interaction include IgG subclass and Fc-
associated glycan structure [2]. Distinct profiles are enriched following vaccination or 
during inflammatory diseases or infection. Vaccination with 1790GAHB is hypothesized 
to enrich certain IgG subclasses and Fc glycan structures and specific profiles of elicited 
IgG will contribute to clinical protection observed in controlled human infection models.
References for Appendix A:
1.
Bournazos S and Ravetch JV. Fcγ receptor pathways during active and passive 
immunization. Immunol Rev. 2015; 268:88-103.
2.
Pincetic A et al. Type I and type II Fc receptors regulate innate and adaptive 
immunity. Nat Immunol. 2014; 15:707-716.
Appendix B
CLINICAL LABORATORIES
Table 22
GSK Biologicals’ laboratories
Laboratory
Address
GSK Biological’s Clinical Laboratory Sciences, 
Rixensart 
Biospecimen Reception - B7/44
Rue de l'Institut, 89 - B-1330 Rixensart – Belgium
GVGH Laboratory
Via Fiorentina 1
53100 Siena
Italy
Table 23
Outsourced laboratories
Laboratory
Address
Cincinnati Children's Hospital Medical Center
Core Laboratories
3333 Burnet Avenue, 
Building B, MLC 1010
Cincinnati, Ohio 45229-3039, USA
Cincinnati Children's Hospital Medical Center
Clinical site Laboratories
619 Oak street, Room 2803
Cincinnati, Ohio, 45206, USA
Rockefeller University
1230 York Avenue
New York, NY 10065, USA
WRAIR
503 Robert Grant Avenue
Silver Spring, MD 20910
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
122
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
123
Appendix C
AMENDMENTS AND ADMINISTRATIVE 
CHANGES TO THE PROTOCOL
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 1
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 1
Amendment date:
08 February 2018
Coordinating author:
(XPE Pharma for GSK Biologicals)
Rationale/background for changes:
!
To increase the yield of the peripheral blood mononuclear cell (PBMC) analysis, 
volume of the blood collected for PBMC analysis has been changed from 40 mL 
to 50 mL.
!
To make the definition of the primary objective more conclusive, the wording of 
the primary objective definition has been updated.
!
The case definition of shigellosis has been also reworded to make it complete and 
more conclusive.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
Section 2.1
Primary objective (+ in synopsis)
!
To demonstrate the efficacy of two vaccinations with 25 μg of 1790GAHB vaccine 
in healthy adults compared to placebo in preventing (reduction of shigellosis, 
fulfilling according to the protocol primary case definition, i.e. moderate or severe 
diarrhea, OR oral temperature of ∀38°C after challenge with S. sonnei strain 53G).
Section 2.2
Secondary objective (+ in synopsis)
Efficacy
!
To determine the efficacy of the 1790GAHB vaccine compared to placebo against:
#
[…]
#
Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR 
dysentery AND OR presence of fever ∀38°C OR presence of one or more 
severe intestinal symptoms (abdominal pain, cramping, tenesmus, nausea, 
vomiting …).

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
123
23-JUL-2019
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
124
Section 3
Study design overview (+ in synopsis)

Sampling schedule:

[…]

40 50 mL of peripheral venous blood for α4β7 plasmablast flow-cytometry and 
RNA extraction from PBMCs for gene expression profiling: Visit 1, Visit 2, 
Visit 4 and 7 days after Visit 5 (Day 64).
Section 3.2
Challenge phase
Four weeks after completion of the two-dose vaccination schedule (approximately 28 
days after Visit 4 3) subjects will be admitted the day before the challenge date […]
Section 4
Case definitions (+ in synopsis)
Shigellosis
For the challenge phase of the study, the protocol primary case definition for shigellosis 
is:

Moderate or severe diarrhea OR fever (oral temperature 38°C).
Section 5.6
Outline of study procedures
Table 4
List of study procedures
Blood sampling for PBMC isolation (α4β7 plasmablasts response and transcriptomics) (~40 50 mL)
Section 6.6.10.1
Blood sampling for safety or immune response assessments

An overall volume of 360 400 mL will be collected per subject during the entire 
study period (8 months).
Section 6.7.2 Biological samples
Table 6
Biological samples
Sample type (analysis) (All subjects)
Quantity
Unit
Timepoint
Blood (PBMC for α4β7 plasmablasts response and transcriptomics)
~ 40 50
mL
scheduled
[…]
**Includes anti S. sonnei LPS IgG-ELISA (Clinical Laboratory Sciences)
Section 6.7.3 Laboratory assays
Table 10
Hematology, Serum Chemistry, Virology, HLA-B27 test, Urine and 
Stool tests
System
Component
Method
Laboratory
EDTA Blood
HLA-B27
Flow Cytometry PCR
Study site
[…], PCR: Polymerase Chain Reaction
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
124
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
125
Section 6.7.4.1
Immunological read-outs
Table 11
Immunological read-outs
Note: Anti-S. sonnei LPS IgG will be determined by local Screening-ELISA at screening and by Clinical Laboratory 
Sciences GVGH ELISA for the rest of the timepoints.
Section 11.2
Secondary endpoints (+ in synopsis)
Efficacy
VE, in subjects receiving the 1790GAHB vaccine vs. placebo, will be also measured 
against:

[…]

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR dysentery 
AND OR presence of fever 38°C OR presence of one or more severe intestinal 
symptoms (abdominal pain, cramping, tenesmus, nausea, vomiting …).
Section 12.9
Pharmacogenomics
As part of the sequencing for the microbiome, human genome will be sequence
sequenced as bypass product but the intent is not to analyze the data which will be store 
securely.
Analyses of the transcriptomics signals evaluating the number of differential expressed 
genes by comparing the relative abundance of mRNA sequences are also considered a 
pharmacogenomics experiment.
Appendix A
Laboratory assays
Anti S. sonnei LPS antibody determination from serum:
Anti-S. sonnei LPS IgG antibodies in serum (for all timepoints except screening) will be 
measured by ELISA in the Clinical Laboratory Sciences laboratories of GSK Biologicals
GVGH-Laboratories, Siena. The ELISA is performed using S. sonnei LPS […]
Appendix B
Clinical laboratories
Table 22
GSK Biologicals’ laboratories
Laboratory
Address
GSK Vaccines GmbH
Clinical Laboratory Sciences, Marburg, Germany
Emil-von-Behring-Str. 76
35041 Marburg
Germany
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
125
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
126
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 2
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 2
Amendment date:
22 June 2018
Coordinating author:
Rationale/background for changes:
!
To address FDA comment that the case definition as stated in Protocol 
Amendment 1 did not appear to be sufficiently specific for shigellosis versus 
other causes of fever: therefore shedding has been added to address the deficiency 
in the primary case definition.
!
The definition of fever in the previous case definition (Temperature ≥38°C) has 
been changed to (Temperature ≥38.5°C) to be in line with the definition of fever 
used for the challenge model set up at Cincinnati.
!
To address FDA comment on performing screening safety laboratories but not 
proposing eligibility criteria based on them.
!
To address the FDA request to provide a sample size calculation based on human 
challenge data relevant to the primary endpoint case definition in this study.
!
To incorporate FDA recommendation on definition of holding rule for the study.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
Section 2.1
Primary objective (+ in synopsis)
!
To demonstrate the efficacy of two vaccinations with 25 μg of 1790GAHB vaccine 
in healthy adults compared to placebo (Reduction of shigellosis according to the 
protocol primary case definition, i.e. Shedding of S. sonnei 53G accompanied by 
moderate or severe diarrhea, OR shedding with an oral temperature of ∀38.5°C
after challenge with S. sonnei strain 53G).
Section 2.2
Secondary objective (+ in synopsis)
Efficacy
!
To determine the efficacy of the 1790GAHB vaccine compared to placebo against:
#
[…]

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
126
23-JUL-2019
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
127

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR 
dysentery OR presence of fever 38.5°C OR presence of one or more severe 
intestinal symptoms (abdominal pain, cramping, tenesmus, nausea, vomiting 
…).
Section 4
Case definitions (+ in synopsis)
Shigellosis
For the challenge phase of the study, the protocol primary case definition for shigellosis 
is:

Shedding of S. sonnei 53G accompanied by mModerate or severe diarrhea OR 
shedding with fever (an oral temperature of 38.5°C).
Section 5.3
Exclusion criteria
Subjects with a baseline neutrophil count below 1800 cells/µL LLN OR with clinically 
significant abnormalities in other laboratory values (CBC, CMP, UA ), according to 
local reference ranges and investigator judgment)
Section 9.10.1 Holding rule
The following holding rule has been defined for the study: at least one subject developing 
a ≥Grade 3 symptomatic neutropenia considered possibly, probably or definitely related 
within 7 days after to vaccination
Section 11.2
Secondary endpoints
Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR dysentery OR 
presence of fever ≥38.5°C OR presence of one or more severe intestinal symptoms 
(abdominal pain, cramping, tenesmus, nausea, vomiting …).
Section 11.4 Determination of sample size
Based on the results obtained by the Cincinnati Children’s Hospital Medical Center, 
where the challenge model was developed, in subjects receiving a challenge with 1500 
CFU of S. sonnei 53G, the attack rate for the primary case definition of this study is 
58%. Thus considering an AR of 6058% in the placebo group and a percentage of non-
evaluable subjects of 22%, approximately 72 subjects (36 per group) will be recruited to 
reach these 21 cases.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
127
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
128
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 3
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 3
Amendment date:
07 September 2018
Coordinating author:
Rationale/background for changes:
!
To address a comment made by the FDA asking if listings of unblinded unsolicited 
adverse events after challenge are made available to the IDMC.
!
To add a secondary objective for evaluating efficacy of the vaccine also against a 
consensus definition of shigellosis by the Controlled Human Infection Model 
(CHIM) expert working group that was convened by the Gates Foundation, the 
funder of the study, on 06 February 2018.
!
To clarify that regarding weight and number of stools, the interest is in total 
number and weight of all grade 3-5 stools, and not only in grade 3-5 stools 
concurring in diarrhea episodes.
!
To further harmonize the protocol with the challenge model established at the 
Cincinnati Children’s Hospital Medical Center with previous GVGH studies in 
terms of grading of events and immunological parameters evaluated, and with 
GSK standards.
!
To introduce a mitigation strategy in case the site is not able to include the 
required number of subjects in a given cohort.
!
To add a tertiary objective to evaluate inflammatory response in stools as 
discussed with the funder of the study and other partners.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
Cover Page:
Investigational New Drug
IND18163
(IND) number
Contributing authors
, 
, GVGH 
Serology Representatives (Scientific Technical Leaders)

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
128
23-JUL-2019
PPD
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
129
List of Abbreviations
CHIM:
ICH:
Controlled Human Infection Model
International Council for Harmonisation Conference on 
Harmonization
Section 1.3.1
Risk Assessment
The most common symptoms that happen after taking Bactrim TMP-SMX are nausea, 
vomiting, loss of appetite, skin rash and itching.
Section 1.3.3
Overall Benefit: Risk Conclusion
However the S. sonnei 53G challenge strain used in the challenge phase is known to be 
susceptible to multiple antimicrobial agents including TMP-SMX and quinolones which 
will be used in this study and will be given to all challenged subjects at Day 5 of the 
challenge phase (4th day after administration of the challenge agent) 5 days after 
administration of the challenge agent (day 62) or earlier if medically needed.
Section 2.2
Secondary objectives (+ in synopsis)
Efficacy

To determine the efficacy of the 1790GAHB vaccine compared to placebo against:

Shigellosis as defined by the CHIM expert working group on case definition.*

[…]

Weight of all grade 3-5 diarrhea episodes stools.

Total number of all grade 3-5 diarrhea episodes stools.

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR 
dysentery OR presence of oral temperature fever ≥ 38.5°C OR presence of one 
or more severe intestinal symptoms (abdominal pain, cramping, tenesmus,
nausea, vomiting…, gas, and anorexia).

[…]

Time to onset of shigellosis after challenge, according to the primary case 
definition.
*According to the working group, the participant must fulfil any one of the three 
following possible endpoints to qualify as having reached the CHIM case definition for
this objective:
1.
Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose 
stools in 24 hours] 
2.
Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours] 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
129
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
130
3.
Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature 38.0oC OR 1 moderate constitutional/enteric 
symptom OR 2 episodes of vomiting in 24 hours].
Safety

To assess the safety and reactogenicity of the 1790GAHB vaccine in terms of 
solicited symptomsadverse events, unsolicited symptomsadverse events, serious 
adverse events (SAEs), adverse events of special interest (AESI) and laboratory 
parameters.

To assess safety after challenge in terms of SAEs, unsolicited adverse events, AESI, 
and laboratory parameters.
Immunogenicity

To evaluate the IgG ELISA immunogenicity profile of the 1790GAHB vaccine at 7 
days and 28 days after the first and second vaccination (IgG ELISA coated with 
OAg containing LPS).

[…]

To assess anti- S.sonnei LPS concentration ≥ 121 EU/ml at 28 days after first and 
second vaccination.
Section 2.3
Tertiary objectives (+ in synopsis)

[…]

Evaluate inflammatory response from stools collected before challenge at Visit 5 
(Day 57) and daily, post challenge, during inpatient stay (Day 57 to Day 64)

[…]
Section 3
Study Design Overview
The total of 72 subjects will be divided in 4 cohorts of 18 subjects each (for logistical 
reasons due to bed capacity at the study site). The vaccination and challenge will be done 
in overlapping cohorts and randomization will ensure there is the same number of 
vaccinees and controls in each cohort. However, if for any reason, a cohort does not 
reach the planned 18 subjects, additional subjects can be added in the next cohorts. 
The maximum number of subjects must not be more than 20 (maximum number of 
beds in the clinic) in each cohort.
Section 3.2
Challenge Phase

Sampling schedule:

[…]

Stool sample for inflammatory response before challenge at Visit 5 (Day 57) 
and daily, post challenge, during inpatient stay (Day 57 to Day 64)

[…]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
130
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
131

Safety monitoring:

[…]
The safety review team (SRT) will monitor the safety of subjects throughout the study. 
The SRT will review blinded data, assess safety signals and make recommendations to 
the IDMC and Sponsor concerning continuation, termination, or other modifications of 
the study based on the observed adverse effects.
Section 4.1
Diarrhea (+ in synopsis)
For the purpose of this study, diarrhea is defined as:

[…]

Severe diarrhea: 6 or more loose or watery (Grade 3 to 5) stools or > 800 grams of 
Grades 3 to 5 stools within 24 hours or required medical intervention. In case of 
severe diarrhea, medical intervention is defined as intravenous (IV) fluids 
administration or anticipation of antibiotic treatment before the 5th day after 
challenge.

More severe diarrhea: 10 loose 10 or more loose or watery (Grade 3 to 5) stools or 
1000 grams of Grade 3 to 5 stools within 24 hours or required medical 
intervention. In case of more severe diarrhea, medical intervention is defined as 
ER visit or hospitalization for hypotensive shock.
Section 4.3
Shigellosis (+ in synopsis)
For the primary and secondary objectives in the challenge phase of the study, the 
protocol primary case definition for shigellosis is:

Shedding of S. sonnei 53G accompanied by moderate or severe diarrhea OR 
shedding with an oral temperature of 38.5°C).
For the secondary objectives in the challenge phase of the study, the CHIM working 
group case definition will require the participant to fulfil any one of the three following 
possible endpoints: 
1.
Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose 
stools in 24 hours] 
2.
Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours]  
3.
Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature 38.0oC0 °C OR 1 moderate constitutional/enteric 
symptom OR 2 episodes of vomiting in 24 hours].
Section 5.1
Number of subjects/center
Enrolment will take place in 4 overlapping cohorts of 18 subjects each to accommodate 
for the availability of beds required for the challenge phase of the study at the clinical 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
131
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
132
site (see also Section 11.12.1). However, if for any reason, a cohort does not reach the
planned 18 subjects, additional subjects can be added in the next cohorts. The 
maximum number of subjects must not be more than 20 (maximum number of beds in 
the clinic) in each cohort. The vaccination and challenge will be done per cohort.
Section 6.2.2.2.1
Study group and treatment allocation
Subjects will be enrolled in 4 overlapping cohorts of 18 subjects each, for logistical 
reasons at the clinical site, therefore a 1:1 ratio should be maintained at the cohort level.
However, if for any reason, a cohort does not reach the planned 18 subjects, additional 
subjects can be added in the next cohorts. The maximum number of subjects must not 
be more than 20 (maximum number of beds in the clinic) in each cohort. 
Table 4
List of Study Procedures
Record any concomitant medications/vaccinations
●Visit 8
Stool sample for inflammatory response 
● Visit 5, ● Inpatient Stay 
Recording of solicited adverse events within 7 days post-vaccination
Recording of non-serious unsolicited adverse events within 28 days post-vaccination
Recording of solicited adverse events within 7 days post-challenge
●Inpatient Stay
Recording of unsolicited adverse events within 28 days post-challenge
●Inpatient Stay  ●Visit 6
Recording of AESI, SAEs and pregnancies ●Phone call (Day 3 and Day 7) ●Phone call (Day 31 and 
Day 35) 
Recording of SAEs related to study participation, 
●Phone call (Day 3 and 
or to a concurrent GSK medication/vaccine
Day 7) ●Phone call (Day
                                                                                                                                 31 and Day 35) 
7Before vaccination/challenge (Day 1/Day 57 sample can be collected by the subject at most a week before and stored 
as described in the Investigator Manual and SPM.
Table 5
Intervals between study visits
Interval
Optimal length of interval
Allowed interval
Visit 5 Visit 7
56 days
5649 days - 7063 days
Visit 5 Visit 8
180 days
180166 days - 194 days
Section 6.6.8
Assess pre-vaccination body temperature
The oral body temperature of each subject needs to be measured prior to any study 
vaccine/placebo or challenge agent administration. If the subject has fever (fever is 
defined as temperature 38.0°C/100.4°F regardless the location of measurement) on the 
day of vaccination, the visit will be rescheduled within the allowed interval (see Table 5).
Section 6.6.10.3
Stool sampling
Aliquots of stool will be collected for fecal sIgA, inflammatory response, culture and 
qPCR, at each predefined timepoint (see Table 4). If, during the inpatient stay, no stools 
are passed on a given day, up to two rectal swabs can be collected for culture and qPCR
(see also Section 3.2). The aliquots for fecal sIgA and inflammatory markers should be 
frozen at -80°C as soon as possible at the clinical site.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
132
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
133
Section 6.6.12
Challenge administration and inpatient stay
Refer to Section 3.2 and SPM for more details related to challenge administration and the 
preparation and administration of the challenge agent and the collection of samples 
during the inpatient stay.
Section 6.6.14.1
Subject Diary
Subject Diary training should be directed at the individual(s) who will perform the 
measurements of adverse events and who will enter the information into the Subject 
Diary. This individual may not be the subject, but if a person other than the subject enters 
information into the Subject Diary, this person’s identity must be documented in the
Subject Diary Subject’s source records. Any individual that makes entries into the 
Subject Diary must receive training on completion of the Subject Diary at the time of the 
visit when Subject Diary is dispensed. This training must be documented in the subject’s 
source record.
Section 6.7
Biological sample handling and analysis
Please refer to the SPM and Investigator Manual for details on biospecimen 
management (handling, storage and shipment).
Table 6
Biological samples
Stool*** (sIgA, microbiome, inflammatory markers, weight, 
consistency and blood assessment, culture and qPCR)
scheduled
Table 10   
Hematology, Serum Chemistry, Virology, HLA-B27 test, Urine and 
Stool tests
Stool 
Inflammatory markers
ELISA 
WRAIR or GVGH 
designated lab
ELISA: Enzyme-Linked Immunosorbent Assay, WRAIR: Walter Reed Army Institute of Research (US)
Section 6.7.3
Laboratory assays

[…]
Fecal markers of intestinal inflammation will be measured as a sensitive predictor for 
inflammatory activities in the gastrointestinal tract. This analysis will assess if 
concentrations of inflammatory markers such as calprotectin and myeloperoxidase will 
increase after oral challenge with S. sonnei 53G and will additionally investigate if the 
S. sonnei 1790GAHB vaccine can reduce or abrogate the inflammatory response in the 
intestine after oral challenge.
Table 12
Hematology/Blood Chemistry read-outs
Visit 8 (Day 240 237) 
Post-challenge
72
Hematology
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
133
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
134
Section 7.6.1 Recording of concomitant medications/products and concomitant 
vaccinations

Prophylactic medication (i.e. medication administered in the absence of ANY 
symptom and in anticipation of a reaction to the vaccination).
E.g., an anti-pyretic is considered to be prophylactic when it is given in the absence of 
fever and any other symptom, to prevent fever from occurring (fever is defined as 
temperature 38.0°C/100.4°F regardless the location of measurement). The preferred 
location for measuring temperature in this study will be the oral cavity.
Section 9.1.3
Solicited adverse events
The following solicited AEsSolicited AEs after vaccination are included in the Subject 
Diary. Each AE is to be assessed using the scoring system reported in parentheses 
belowSection 9.3.3.2.1.
Section 9.1.3.3
Solicited events after challenge phase
The hydration of subjects developing diarrhea will be maintained with oral electrolyte 
solutions (i.e., Pedialyte, Gatorade)by offering at least 1.5 mL for each gram of diarrheal 
stool lost, as tolerated.
Section 9.1.4
Unsolicited adverse events
Unsolicited AEs will be collected until 28 days after each vaccination and until 28 
days after challenge.
Table 19
Reporting periods for collecting safety information
Timepoints
Scr
D1
D8
D29
D36
D57
D57-
D64
D85
D237
(M8)
Solicited local and systemic 
AEs
Unsolicited AEs
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
134
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
135
Table 20
Intensity scales for solicited symptoms
Pain at injection site
0
NoneAbsent
1
Mild: Any pain neither interfering with nor preventing normal every day activities.
Easily tolerated.
2
Moderate: Painful when limb is moved and interferes with every day activities
Interferes with normal activity
3
Severe: Significant pain at rest. Prevents normal every day activities.Prevents 
normal activity.
Headache#
0
NormalAbsent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
Fatigue#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
Arthralgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
Malaise#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
Myalgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
Chills
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That Prevents normal activity
After challenge agent administration
Nausea
0
NormalAbsent
1
Mild or transient; maintains reasonable intake
2
Moderate discomfort; intake decreased significantly; some activity limited
3
No significant intake and requires medical intervention
4
Hospitalization required
Abdominal cramping
0
NormalAbsent
1
No interference with daily activities
2
Some interference with daily activities not requiring medical intervention
3
Prevents daily activities and requires medical intervention
4
ER visit or hospitalization
Abdominal pain
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Gas
0
NormalAbsent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Anorexia
0
NormalAbsent
1
Easily tolerated
2
Interferes with normal activity
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
135
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
136
3
Prevents normal activity
Vomiting
0
NormalAbsent
1
One episode within a 24-hour period Vomiting
2
2 episodes within a 24-hour period
3
>2 episodes within a 24-hour period and requires medical intervention
4
ER visit or hospitalization for hypotensive shock
Diarrhea**
0
NormalAbsent
1
2-3 Grade 3-5 stools (loose or watery) or <400 g/Grade 3-5 (loose or watery) 
stools per 24 hours
2
4-5 Grade 3-5 stools (loose or watery) or 400-800 g/ (loose or watery) Grade 3-5 
stools per 24 hours
3
6 or more Grade 3-5 stools (loose or watery) or >800 g/Grade 3-5 (loose or 
watery) stools per 24 hours and or requires medical intervention
4
10 loose stools (Grade 3 to 5) or 1000 grams of Grade 3 to 5 stools within 
24 hours or ER visit or hospitalization for hypotensive shock
Section 9.3.3.2.1
Assessment of intensity
Erythema/Induration
0:
20 < 25 mm 
1:
> 20 25 - 50 mm 
2:
> 50 - 100 mm
3:
> 100 mm
Section 9.10.2
Safety monitoring
The SRT will monitor the safety of subjects throughout the study. The SRT will review 
blinded data, assess safety signals and make recommendations to the IDMC and to the 
Sponsor concerning continuation, termination, or other modifications of the study based 
on the observed adverse effects.
Section 11.1 
Primary endpoint (plus Synopsis)

Rate of shigellosis (fulfilling the protocol primary case definition) occurring within a 
period starting with the challenge visit and lasting up to the end of the inpatient stay, 
in all subjects.
Section 11.2 
Secondary endpoints (plus Synopsis)
VE, in subjects receiving the 1790GAHB vaccine vs. placebo, will be also measured
during inpatient stay (Day 57 to Day 64) against:

Rate of shigellosis (fulfilling the CHIM working group case definition for 
shigellosis) occurring within a period starting with challenge visit and lasting until 
the end of the inpatient stay, in all subjects. 

[…]

Weight of all grade 3-5 diarrhea episodesstools.

Total number of all grade 3-5 diarrhea episodesstools.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
136
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
137

Confirmed S. sonnei 53G shedding AND moderate or severe diarrhea OR dysentery 
OR presence of oral temperature fever 38.5°C OR presence of one or more severe 
intestinal symptoms (abdominal pain, cramping, tenesmus, nausea, vomiting, …gas, 
anorexia). 

Disease not fulfilling the protocol primary case definition for shigellosis associated 
or not with mild to moderate symptoms including: passing loose stool (not meeting 
the protocol definition of moderate or severe diarrhea), abdominal pain, abdominal 
cramps, gas, anorexia, nausea, headache, myalgia, malaise, arthralgia, fever, 
vomiting and IV fluid administration.

Time to onset of shigellosis after challenge, according to the protocol primary case
definition. 
Safety
Solicited adverse events

Occurrence of each solicited local and systemic adverse event within 7 days after 
each vaccination.
Unsolicited adverse events

Occurrence of unsolicited AEs within 28 days after any vaccination and after 
challenge, according to Medical Dictionary for Regulatory Activities (MedDRA) 
classification. 

[…]
Immunogenicity
The measures of immunogenicity, against the LPS of S. sonnei, will include:

IgG geometric mean concentrations (GMCs) pre-vaccination (Day 1), 7 and 28 days
after first and 28 days after second vaccination by antibody concentration at baseline 
(i.e., above vs. below the assay detection limit), as determined by anti-S. sonnei LPS 
IgG ELISA.

[…]

Number and percentage of subjects achieving a post vaccination anti- S. Sonnei 
LPS concentration ≥ 121 EU/ml at 28 days after first and second vaccination. 

Number and percentage of seroresponders* for anti-S. sonnei LPS at 28 days after 
first and second vaccination. 
*Seroresponse is aimed to define a significant increase in anti S. sonnei LPS IgG 
concentration in post-vaccination samples and relies on the definition already used in a 
previous phase II study in Kenyan population. […]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
137
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
138
Section 11.3 
Tertiary endpoints (plus Synopsis)

[…]

Glycosylation profiles of IgG antibodies at Day 1 and 28 days after second 
vaccination (Visit 5; Day 57).

[…]

Concentration of stool markers of intestinal inflammation (e.g. calprotectin and 
myeloperoxidase) before oral challenge with S. sonnei, 53G at Visit 5 (Day 57) and 
daily during the post-challenge inpatient stay (Day 57 to Day 64)

[…]

Diversity and frequency of microbiome components (taxa and/or genes according to 
technology) at Day 1 prior to vaccination and 28 days after second vaccination (Visit 
5; Day 57).
Section 11.5.7
Sub-groups
There are no intended sub-groups for analysis in this study.The analysis for the primary 
efficacy endpoint will be repeated for the two subgroups of subjects who were 
responders or non-responders at the immunogenicity assessment of the pre-challenge 
visit. 
Section 11.12.1
Sequence of analyses
The total of 72 subjects will be divided in 4 cohorts of 18 subjects each (for bed 
availability at the study site). The vaccination and challenge will be done per cohort.
However, if for any reason, a cohort does not reach the planned 18 subjects, additional 
subjects can be added in the next cohorts. The maximum number of subjects must not 
be more than 20 (maximum number of beds in the clinic) in each cohort. 
One interim analysis is intended and will include post-challenge efficacy data of all 
subjects (all 4 cohorts) and immunogenicity data up to 28 days after second vaccination 
for the first 3 vaccinated cohorts. Further serological results will follow after the 
conclusion of the study..
Appendix A
Laboratory Assays
[…]
Stool inflammatory markers assay
Inflammatory markers including calprotectin and myeloperoxidase levels in stools 
(ng/mL) will be measured using commercially available (Epitope Diagnostics, Inc.) 
quantitative ELISA kits according to the manufacturer’s instructions. 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
138
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
139
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 4
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 4
Amendment date:
19 February 2019
Coordinating author:
(XPE Pharma for GSK Biologicals)
Rationale/background for changes:
!
Subjects of African descent are known to have a lower Absolute Neutrophil Count 
(ANC) than subjects of European descent. African Americans represent about 75% 
of all included subjects in the study so far, which is more than was initially 
anticipated. Furthermore, all cases of neutropenia recorded so far in the study 
occurred in African-American subjects. The threshold and grading scale, 
appropriate for this population, in line with the recommended criteria of the 
Division of AIDS (DAIDS), have been added to the protocol. This change will 
provide a more appropriate definition of neutropenia for African-American 
subjects as a basis to decide on eligibility for participation in the study and for 
vaccination and administration of the challenge agent, and will mitigate the risk 
that African-American subjects are excluded from the study due to episodes of 
neutropenia that are not clinically relevant.
!
The current definition of “more severe diarrhea” was inconsistent with the 
definition of “Shigellosis”. A change has been introduced to the definition of 
“more severe diarrhea” for a clear classification of cases.
!
Minor editorial mistakes are corrected.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
Contributing Authors
!
, Safety Scientist, Safety Evaluation and Risk Management team
List of Abbreviations
DAIDS:
Division of Acquired Immunodeficiency Syndrome

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
139
23-JUL-2019
PPD
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
140
Section 1.3.1 Risk Assessment
Important 
Potential/Identified Risk
Data/Rationale for Risk
Mitigation Strategy
Investigational vaccine: 1790GAHB vaccine
Symptomatic Neutropenia
Eight cases of Grade 2 or Grade 3 
neutropenia were reported from 
Phase 1 clinical trials 
(asymptomatic).
All cases occurred in the first 20 days 
after administration of first vaccine 
dose, and reversed after 
discontinuation.
Literature review of reports of 
neutropenia in association with 
vaccination indicates factors noted to 
be associated with neutropenia 
(including ethnicity, and low baseline 
counts) with the majority of cases 
detected within 2 weeks of the 
vaccination. None of the reported 
cases was clinically symptomatic.
Five cases of asymptomatic 
neutropenia (Grade 1 and 2) have 
been reported at Day 7 after receipt 
of the first dose in 5 subjects.
One of the 5 subjects had an 
additional Grade1 neutropenia 
episode at Day 28, and another one 
had two additional episodes, one of 
which was Grade 3 (940 cells/mL) at 
7 days after the second dose and the 
second was Grade 2 (1,410 cells/mL) 
at 28 days after second vaccination. 
All cases were resolved before last 
study visit.
Exclusion criteria for this clinical 
studiesstudy include:

Subjects with a low baseline 
neutrophil (below 1800 cells/µl 
LLN 1000 cells/µL for African-
American subjects or other 
subjects of African descent 
and 1800 cells/µL for subjects 
of other ethnicity). As guidance,
the WHO criteria should be 
followed Division of Acquired 
Immunodeficiency Syndrome 
(DAIDS) criteria [DAIDS, 2017] 
should be followed for African-
American subjects or other 
subjects of African descent, 
whereas WHO criteria should 
be followed for all other 
subjects.

Previous history of Benign Ethnic 
Neutropenia, or drug related 
Neutropenia.

Concomitant treatment with 
neutropenic agents.
Monitoring for this clinical study to include:

Baseline neutrophil counts.

Full blood counts with differential 
measured at 7 days post each 
scheduled vaccination.

Assessment of clinical impact of 
neutropenia.
Subjects will be closely monitored during 
the entire study and have hematology 
repeated every 7 days when neutropenia is 
identified until resolution. If a case of 
neutropenia does not resolve based on 
most recent available laboratory results,
before the second vaccination, or 
challenge agent administration, the 
subject will not be re-vaccinated or 
administered the challenge agent.
Section 4.1 (+Synopsis)
Diarrhea
For the purpose of this study, diarrhea is defined as:

[…]

More severe diarrhea: 10 or more loose or watery (Grade 3 to 5) stools or 1000 
grams of Grade 3 to 5 stools within 24 hours or required medical intervention. In 
case of more severe diarrhea, medical intervention is defined as ER visit or 
hospitalization for hypotensive shock.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
140
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
141
Section 5.3
Exclusion criteria

[…]

Subjects with a baseline neutrophil below 1800 1000 cells/L LLN for African-
American subjects or other subjects of African descent, and 1800 cells/L for 
subjects of other ethnicity OR with clinically significant abnormalities in other 
laboratory values (CBC, CMP, UA), according to local reference ranges and 
investigator judgment).
Section 7.5
Contraindications to subsequent vaccination or challenge

[…]

Neutropenia below 1800 cells/L LLN.

[…]
The following events constitutes contraindications to administration of 1790GAHB 
vaccine or the challenge agent at that point in time; if this any of these events occurs at 
the time scheduled for vaccination, the subject may be vaccinated at a later date, within 
the time window specified in the protocol (see Section 6.5), or the subject may be 
withdrawn at the discretion of the investigator (see Section 9.5):

Neutropenia (for threshold values refer to Section 9.1.6) based on most recent 
available laboratory results. Subjects with previous neutropenia or unresolved 
neutropenia may be re-evaluated prior to vaccination or prior to challenge at the 
discretion of the investigator.

[…]
Section 9.1.6 Adverse events of special interest

[…]
Neutropenia is defined as a decrease of neutrophil count asymptomatically or 
symptomatically. Available local laboratory ranges will be used to define neutropenia. 
This is completely diagnosed by laboratory testing for complete blood count. However,
only symptomatic neutropenia cases will be considered as AESI and reported as such.
The following grading will be used to classify neutropenia in African-American subjects 
or other subjects of African descent:

Grade 1: 1000-800 cells/µL.

Grade 2: 799-600 cells/µL.

Grade 3: 599-400 cells/µL.

Grade 4: < 400 cells/µL.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
141
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
142
The following grading will be used to classify neutropenia for subjects of other 
ethnicity:

Grade 1: 1800-1500 cells/µL.

Grade 2: 1499-1000 cells/µL.

Grade 3: 999-500 cells/µL.

Grade 4: < 500 cells/µL.
Section 9.3.3.2.1, Table 20
Intensity scales for solicited symptoms
Diarrhea**
0
Absent 
1
2-3 Grade 3-5 stools (loose or watery) or <400 g/Grade 3-5 (loose or watery) 
stools per 24 hours
2
4-5 Grade 3-5 stools (loose or watery) or 400-800 g/ (loose or watery) Grade 3-5 
stools per 24 hours
3
6 or more Grade 3-5 stools (loose or watery) or >800 g/Grade 3-5 (loose or 
watery) stools per 24 hours or requires medical intervention
4
10 loose stools (Grade 3 to 5) or 1000 grams of Grade 3 to 5 stools within 24 
hours or ER visit or hospitalization for hypotensive shock
References
U.S. Department of Health and Human Services, National Institutes of Health, 
National Institute of Allergy and Infectious Diseases, Division of AIDS. Division of 
AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events, 
Corrected Version 2.1. (July 2017). 
https://rsc.niaid.nih.gov/sites/default/files/daidsgradingcorrectedv21.pdf
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
142
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
143
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 5
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 5
Amendment date:
15 April 2019
Coordinating author:
(XPE Pharma for GSK 
Biologicals)
Rationale/background for changes:
!
To meet a FDA request for removing the DAIDS thresholds and criteria specific 
for African-American subjects that had been added in Amendment 4.
!
To add secondary endpoints and case definitions for shigellosis that would 
facilitate comparison of results with other CHIM studies.
!
To specify that stool samples will be analyzed for both S. sonnei secretory IgA 
(sIgA) and total sIgA (S. sonnei sIgA to be normalized for total sIgA). 
!
Minor editorial mistakes are corrected.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
List of Abbreviations
DAIDS:
Division of Acquired Immunodeficiency Syndrome
Section 1.3.1. Risk Assessment (in the column “Mitigation Strategy)
Exclusion criteria for this clinical study include:
!
Subjects with a low baseline neutrophil count below 10001800 cells/μL (LLN) for 
African-American subjects or other subjects of African descent and 1800 cells/μL 
for subjects of other ethnicity). As guidance, the Division of Acquired 
Immunodeficiency Syndrome (DAIDS) criteria [DAIDS, 2017] should be followed 
for African-American subjects or other subjects of African descent, whereas WHO 
criteria should be followed for all other subjects.
Section 2.2 Secondary objectives (+ in synopsis) 
!
To determine the efficacy of the 1790GAHB vaccine compared to placebo against:
#
Shigellosis as defined by the CHIM expert working group on case definition.* 

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
143
23-JUL-2019
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
144

Shigellosis, as defined by: severe diarrhea OR moderate diarrhea with fever or 
with one or more moderate constitutional/enteric symptoms OR dysentery [[ 
≥2 loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 
reportable constitutional/enteric symptom]].

More severe shigellosis, as defined by: severe or moderate diarrhea with fever 
or with one or more severe constitutional/enteric symptoms OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 severe 
constitutional/enteric symptom]].

Shedding of S. sonnei strain 53G.

[…]
Section 2.3 Tertiary objective (+ in synopsis)
The following tertiary objectives which are part of the study exploratory objectives may 
be evaluated in addition to the primary and secondary objectives and will complement 
assessment of the vaccine immunogenicity profile:

Evaluate S. sonnei specific secretory immunoglobulin A (sIgA) in stool at Day 1 
and 7 days after first and second vaccination and 7 days after challenge (Day 64).

[…]
Section 3
Study design overview (+ in synopsis)

Sampling schedule:

[…]

Stool sample: for microbiome testing at Visit 1 and Visit 5, for S. sonnei 
specific sIgA at Visit 1, Visit 2, Visit 4 and 7 days after challenge (Day 64) and 
stool analysis, culture and qPCR daily during inpatient stay (from Visit 5 to 7 
days after challenge [Day 57 to Day 64] or prolonged until 2 consecutive 
negative stool samples if subject still shedding).
Section 4.2 Dystentery (+ in synopsis)
For the purpose of this study, dysentery is defined as:

A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours and 
presence of constitutional/enteric symptoms (e.g., fever, vomiting, chills, fatigue…, 
refer to Table 23).
Section 4.3 Shigellosis (+ in synopsis)
For the primary and secondary objectives in the challenge phase of the study, the protocol 
primary case definition for shigellosis is:

Shedding of S. sonnei 53G accompanied by moderate or severe diarrhea OR 
shedding with an oral temperature of 38.5°C).
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
144
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
145
For the secondary objectives in the challenge phase of the study, 2 definitions of 
shigellosis are used:
1.
CHIM working group case definition for shigellosis as defined by any one of the 
three following possible endpoints:

Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose 
stools in 24 hours]

Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours]  

Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [oral temperature 38.0°C OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours].
2.
Shigellosis as defined by any one of the three following possible endpoints:

Severe diarrhea defined as [≥6 loose stools in 24 hours OR ˃800 grams loose 
stools in 24 hours]

Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams 
loose stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 moderate 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [≥1 reportable constitutional/enteric symptom].
For the secondary objectives in the challenge phase of the study, more severe 
shigellosis is defined by any one of the two following possible endpoints:

Moderate OR severe diarrhea [≥4 loose stools in 24 hours OR ≥400 grams 
loose stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 severe 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [≥1 severe constitutional/enteric symptom].
the CHIM working group case definition will require the participant to fulfil any one of 
the three following possible endpoints: 
Severe diarrhea defined as [6 loose stools in 24 hours] OR [˃800 grams loose stools in 
24 hours] 
Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams loose 
stools in 24 hours] AND [oral temperature 38.0oC OR 1 moderate 
constitutional/enteric symptom OR 2 episodes of vomiting in 24 hours] 
Dysentery defined as [2 loose stools with gross blood (hemoccult positive) in 24 hours] 
AND [oral temperature 38.0oC0 °C OR 1 moderate constitutional/enteric symptom OR 
2 episodes of vomiting in 24 hours]. 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
145
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
146
Section 5.3 Exclusion criteria

[…]

Subjects with a baseline neutrophil count below 1000 cells/L for African-American 
subjects or other subjects of African descent, and 1800 cells/L (LLN) for subjects 
of other ethnicity OR with clinically significant abnormalities in other laboratory 
values (CBC, CMP, UA), according to local reference ranges and investigator 
judgment).

[…]
Section 6.7.3, Table 7  Immunity (Antibody determination)
System
Component
Method
Kit/
Manufacturer
Unit2
Cut-off2
Laboratory3
Serum
(screening)
Anti-S. sonnei
LPS IgG
ELISA1
WRAIR
Endpoint 
titer
plate 
dependent
CCHMC
Serum
(except 
screening)
Anti-S. sonnei
LPS IgG
ELISA
In-house
EU/mL
plate 
dependent
GVGH4 or GVGH 
designated lab
Serum
Bactericidal 
antibodies
SBA
In-house
Dilution 
Factor 
(titer)
NA
GVGH4 or GVGH 
designated lab
Stool
Anti-S. sonnei
LPS sIgA
ELISA
WRAIR
Titer
EU/mL
10 0.200 
OD
CCHMC or 
GVGH 
designated lab
Stool
Anti-total sIgA
ELISA
WRAIR
mg/mL
0.001
CCHMC
1 Local Screening-ELISA will be used for this testing.
2Assay cut-off and unit might be subject to change during the course of the study (e.g. in case of requalification, 
revalidation or standardization). In this case, this will be documented in the clinical report.
3Refer to Appendix B for the laboratory addresses.
4 GVGH laboratory refers to the GVGH-laboratories in Siena, Italy.
ELISA: enzyme-linked immunosorbent assay, NA: not applicable, EU: ELISA unit, LPS: lipopolysaccharide, IgA/G: 
immunoglobulin A/G, SBA: serum bactericidal Assay, WRAIR: Walter Reed Army Institute of Research (US), GVGH: 
GSK Vaccines Institute for Global Health, CCHMC: Cincinnati Children’s Hospital Medical Center; sIgA: secretory 
Immunnoglobulin A
Section 7.5 Contraindications to subsequent vaccination or challenge
[…]
The following events constitute contraindications to administration of 1790GAHB 
vaccine or the challenge agent at that point in time; if any of these events occur at the 
time scheduled for vaccination, the subject may be vaccinated at a later date, within the 
time window specified in the protocol (see Section 6.5), or the subject may be withdrawn 
at the discretion of the investigator (see Section 9.5):

Neutropenia (for threshold values refer to Section 9.1.6)below 1800 cell/µL based on 
most recent available laboratory results. Subjects with previous neutropenia or 
unresolved neutropenia may be re-evaluated prior to vaccination or prior to challenge 
at the discretion of the investigator.

[…]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
146
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
147
Section 9.1.6 Adverse events of special interest
[…]
The following grading will be used to classify neutropenia: in African-American subjects 
or other subjects of African descent:
Grade 1: 1000-800 cells/µL. 
Grade 2: 799-600 cells/µL.
Grade 3: 599-400 cells/µL.
Grade 4: < 400 cells/µL. 
The following grading will be used to classify neutropenia for subjects of other ethnicity:

Grade 1: 1800 -1500 cells/µL.

Grade 2: 1499-1000 cells/µL. 

Grade 3: 999-500 cells/µL.

Grade 4: < 500 cells/µL.
[…]
Section 11.2 Secondary endpoints (+ in Synopsis)
VE, in subjects receiving the 1790GAHB vaccine vs. placebo, will be also measured
during inpatient stay (Day 57 to Day 64) against:

Rate of shigellosis (fulfilling the CHIM working group case definition for 
shigellosis) occurring within a period starting with challenge visit and lasting until 
the end of the inpatient stay, in all subjects.

Rate of shigellosis, as defined by severe diarrhea OR moderate diarrhea with fever 
or with one or more moderate constitutional/enteric symptom OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 reportable 
constitutional/enteric symptom]].

Rate of more severe shigellosis as defined by: severe or moderate diarrhea with 
fever or with one or more severe constitutional/enteric symptom OR dysentery [[≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 severe 
constitutional/enteric symptom]].

[…]
Section 11.3
Tertiary endpoints (+ in Synopsis)

Specific anti-S. sonnei LPS sIgA antibody concentration in stool samples at Day 1, 7 
days after first and second vaccination and 7 days after challenge (Day 64).

[…]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
147
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
148
Section 14 References
U.S. Department of Health and Human Services, National Institutes of Health, National 
Institute of Allergy and Infectious Diseases, Division of AIDS. Division of AIDS 
(DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events, 
Corrected Version 2.1. (July 2017). 
https://rsc.niaid.nih.gov/sites/default/files/daidsgradingcorrectedv21.pdf
Appendix A
LABORATORY ASSAYS
[…]
S. sonnei determination from stool:

Culture: The presence of S. sonnei in stool samples will be assessed using a 
qualitative procedure and following the SOPs of the local or designated laboratory 
for culture, isolation and identification of S. sonnei from stool specimens.

qPCR: S. sonnei qPCR determination will be done following the SOPs of the local or 
designated laboratory for identification of S. sonnei by a qPCR from stool 
specimens.

S. sonnei sIgA and total sIgA determination from stool: S. Sonnei ELISA will be 
performed following the SOPs of the local or designated laboratory for ELISA assay 
from stool specimens. The S. sonnei sIgA result will be normalized to the total 
sIgA.
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
148
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
149
GlaxoSmithKline Biologicals SA
Vaccines R&D
Protocol Amendment 6
eTrack study number 
and Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Amendment number:
Amendment 6
Amendment date:
23 July 2019
Coordinating author:
(Modis for GSK Biologicals)
Rationale/background for changes:
!
To add an additional interim analysis for immunogenicity data, which will allow a 
faster interpretation of study results and planning of subsequent follow-up studies.
!
To correct an error in the definitions of dysentery and more severe shigellosis, and 
align these definitions to other CHIM studies; oral temperature ≥ 38.0°C (fever) is 
added to the definitions.
!
To correct an error in the primary completion date of the study.
!
To clarify the different applicable case definitions of dysentery in the study.
!
To provide clarification in the study design by showing the inpatient stay in the 
study design figure as per the Schedule of Activities table.
!
To specify the allowed time interval window for the blood draw that occurs during 
the inpatient stay.
!
To specify the assay used for the α4β7 plasmablast analysis as measuring both 
positive and negative cells by ELISA, and not using flow cytometry.
!
To change the assay used for HLA-B27 testing from PCR to qualitative flow 
cytometry.
Amended text has been included in bold italics and deleted text in strikethrough in 
the following sections:
List of Abbreviations
ELISPOT:
Enzyme-linked immunospot assay
Section 2.2
Secondary objectives (+Synopsis)
!
To determine the efficacy of the 1790GAHB vaccine compared to placebo against:
#
[…]
#
More severe shigellosis, as defined by: severe or moderate diarrhea with fever or 
with one or more severe constitutional/enteric symptoms OR dysentery [[≥2 

CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
149
23-JUL-2019
PPD
_5HGDFWHG3URWRFRO$PHQGPHQW$SU_70)_


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
150
loose stools with gross blood (hemoccult positive) in 24 hours] AND [oral 
temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]].

[…]
Section 2.3
Tertiary objectives (+Synopsis)
The following tertiary objectives which are part of the study exploratory objectives may 
be evaluated in addition to the primary and secondary objectives and will complement 
assessment of the vaccine immunogenicity profile:

[…]

Evaluate S. Sonnei LPS IgG-specific presence and migration of α4β7+/- plasmablast 
response at Day 1 and 7 days after first and second vaccination and 7 days after 
challenge (Day 64).

[…]
Section 3.2, Figure 1 Study design
[…]
[…]
Inpatient stay*
Day 57 to Day 65
B & S
*Refer to Section 3.2 for details of procedures during the inpatient stay
Section 3.2 Challenge phase
[…]
Study Design

Primary completion date (PCD): Visit 8 End of inpatient stay (Visit 5, 6 months 
after challengeDay 64).
[…]

Sampling schedule:

[…]

50 mL of peripheral venous blood for α4β7+/- plasmablast flow-
cytometryanalysis by ELISA and RNA extraction from PBMCs for gene 
expression profiling: Visit 1, Visit 2, Visit 4 and 7 days after Visit 5 (Day 64).

[…]
Section 4.2
Dysentery (+Synopsis)
For the purpose of this study, dysentery is defined :
A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours and 
presence of constitutional/enteric symptoms (e.g., fever, vomiting, chills, fatigue…, refer 
to 23).For the purpose of the endpoint “Rate of shigellosis as defined by the CHIM 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
150
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
151
expert working group occurring within a period starting with challenge visit and 
lasting until the end of the inpatient stay, in all subjects”, dysentery is defined as 
follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [oral 
temperature ≥38.0oC OR ≥1 moderate constitutional/enteric symptom OR ≥2 
episodes of vomiting in 24 hours]. In this case constitutional/enteric symptom are 
the following: nausea, abdominal pain, abdominal cramping, myalgia, arthralgia, 
malaise.
For the purpose of the endpoint “Rate of shigellosis, as defined by: severe diarrhea OR 
moderate diarrhea with fever or with one or more moderate constitutional/enteric 
symptoms OR dysentery”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [≥1 
reportable constitutional/enteric symptom]. In this case constitutional/enteric 
symptom are the following: headache, fatigue, arthralgia, malaise, myalgia, chills, 
nausea, abdominal cramping, abdominal pain, gas, anorexia, vomiting.
For the purpose of the endpoint “Rate of more severe shigellosis as defined by: severe 
or moderate diarrhea with fever or with one or more severe constitutional/enteric 
symptom OR dysentery [[≥2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric 
symptom]].”, dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours] AND 
[oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]. In this 
case constitutional/enteric symptom are the following: headache, fatigue, 
arthralgia, malaise, myalgia, chills, nausea, abdominal cramping, abdominal pain, 
gas, anorexia, vomiting.
For the purpose of the endpoints “Dysentery” and “Confirmed S. sonnei 53G shedding 
AND moderate or severe diarrhea OR dysentery OR presence of oral temperature ≥ 
38.5°C OR presence of one or more severe intestinal symptoms (abdominal pain, 
cramping, nausea, vomiting, gas, and anorexia)”, dysentery is defined as follows:

A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours 
and presence of constitutional/enteric symptoms. In this case, 
constitutional/enteric symptoms consist of headache, fatigue, arthralgia, malaise, 
myalgia, chills, nausea, abdominal cramping, abdominal pain, gas, anorexia, 
vomiting, and fever.
Section 4.3
Shigellosis (+Synopsis)
For the secondary objectives in the challenge phase of the study, more severe shigellosis 
is defined by any one of the two following possible endpoints: 

[…]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
151
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
152

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 
24 hours] AND [oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric 
symptom].
Section 6.5, Table 4 List of study procedures
Blood sampling for PBMC isolation (α4β7+/- plasmablasts response and transcriptomics) (~50 mL) 
Section 6.5 Table 5
Intervals between study visits
Visit 5 Visit 5 post-challenge 
blood draw
7 days
7 days – 10 days
Section 6.7.2, Table 6
Biological samples
Blood (PBMC) for α4β7+/- plasmablasts response and 
transcriptomics)
~ 50
ml
scheduled
Section 6.7.3, Table 8
Cell-Mediated Immunity (CMI) using ELISPOT
System
Component
Method
Unit
Laboratory
PBMC
α4β7 positive 
plasmablast
ELISPOTELISA
Anti- S. sonnei 
LPS specific Titer/ 
5x10^6 cellsspot-
forming units
WRAIR or GVGH designated lab
PBMC
α4β7 negative 
plasmablast
ELISA
Anti- S. sonnei 
LPS specific Titer/ 
5x10^6 cells
WRAIR or GVGH designated lab
PBMC
Gene expression 
(transcriptomics) 
study
NextGen 
sequencing/ 
microarray
Sequencing or 
fluorescent intensity
GVGH* or GVGH designated lab
ELISA: Enzyme-Linked Imunosorbent Assay; PBMC: peripheral blood mononuclear cells, Elispot: enzyme-linked 
immunospot assay, WRAIR: Walter Reed Army Institute of Research (US), GVGH: GSK Vaccines Institute for Global 
Health.
*GVGH laboratory refers to the GVGH-laboratories in Siena, Italy.
Section 6.7.3, Table 10
Hematology, Serum Chemistry, HLA-B27 test, Urine 
and Stool tests
EDTA Blood
HLA-B27
PCRQualitative flow cytometry
Study site
PCR: Polymerase Chain Reaction,
Section 11.2
Secondary endpoints (+Synopsis)
Efficacy 
VE, in subjects receiving the 1790GAHB vaccine vs. placebo, will be also measured
during inpatient stay (Day 57 to Day 64) against:

Rate of shigellosis (fulfilling as defined by the CHIM working group case definition 
for shigellosis) occurring within a period starting with challenge visit and lasting 
until the end of the inpatient stay, in all subjects.

[…]
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
152
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
23-JUL-2019
153

Rate of more severe shigellosis as defined by: severe or moderate diarrhea with fever 
or with one or more severe constitutional/enteric symptom OR dysentery [[≥2 loose 
stools with gross blood (hemoccult positive) in 24 hours] AND [oral temperature 
≥38.0oC OR ≥1 severe constitutional/enteric symptom]].

[…]
Section 11.3
Tertiary endpoints (+Synopsis)

[…]

Frequency of S. sonnei LPS specific IgG α4β7+/- antibody secreting cells per 10^6 
PBMC plasmablast at Day 1 and 7 days after first and second vaccination and 7 days 
after challenge (Day 8, Day 36 and Day 64).

[…]
Section 11.12.1
Sequence of analyses
[…]
One interim analysis is intended and will include post-challenge efficacy data of all 
subjects (all 4 cohorts).
The following 2 interim analyses are planned:
1.
After completion of the Visit 5 (Day 64): post-challenge efficacy data of all 
subjects (all 4 cohorts) 
2.
After Visit 6 (Day 85): secondary immunogenicity data and tertiary SBA 
immunogenicity data of all subjects (all 4 cohorts).
All analyses will be conducted before unblinding on clean and final data as clean as 
possible.
An integrated Cclinical Sstudy Rreport containing all data will be written after the End 
of Study and made available to the investigators.
[…]
Appendix A
Laboratory Assays
α4β7 plasmablast ELISA
Anti-S. sonnei LPS-specific IgG titers will be determined in plasmablasts, in both α4β7
positive and α4β7 negative populations. The titers provided will be measured by ELISA 
assay in the culture supernatant of 5x10^6 cells, by using an in-house method 
developed in WRAIR. 
 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Protocol Amendment 6 Final
5889c076f178fb77b7f8644dc83edbbe4030715b
153
23-JUL-2019
205626 | Redacted Protocol Amendment 6 28 Apr 2020 | TMF-831981 | 1.0

SAP_001.pdf: 
CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 1 of 57
Statistical Analysis Plan
Detailed Title:
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population.
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Scope:
All primary and secondary objectives pertaining to the 
above study and a subset of the tertiary objectives. The 
Analysis Plan for remaining tertiary objectives will be 
part of a separate SAP.
Date of Statistical Analysis 
Plan
Amendment 1 Final: 03-Sep-2019
APP 9000058193 Statistical Analysis Plan Template ( Effective date: 14 April 2017)


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 2 of 57
TABLE OF CONTENTS
PAGE
LIST OF ABBREVIATIONS.............................................................................................7
1.
DOCUMENT HISTORY............................................................................................9
2.
STUDY DESIGN ......................................................................................................9
3.
OBJECTIVES.........................................................................................................16
3.1.
Primary objective ........................................................................................16
3.2.
Secondary objectives..................................................................................16
3.3.
Tertiary objectives.......................................................................................17
4.
ENDPOINTS ..........................................................................................................18
4.1.
Case Definitions..........................................................................................18
4.2.
Primary endpoint.........................................................................................20
4.3.
Secondary endpoints ..................................................................................20
4.4.
Tertiary endpoints.......................................................................................23
5.
ANALYSIS SETS ...................................................................................................23
5.1.
Definition.....................................................................................................23
5.1.1.
All Enrolled Set ............................................................................23
5.1.2.
All Exposed Set ...........................................................................24
5.1.3.
Safety Set....................................................................................24
5.1.3.1.
Solicited Safety Set (solicited local and 
systemic adverse events and other solicited 
adverse events)..........................................................24
5.1.3.2.
Unsolicited Safety Set (unsolicited adverse 
events) .......................................................................24
5.1.3.3.
Overall Safety Set ......................................................24
5.1.4.
Full Analysis Set (FAS) for Efficacy/Immunogenicity....................24
5.1.4.1.
Full Analysis Set for Efficacy ......................................24
5.1.4.2.
Full Analysis Set for Immunogenicity..........................24
5.1.5.
Per-Protocol Set (PPS) for Efficacy/Immunogenicity....................24
5.2.
Criteria for eliminating data from Analysis Sets...........................................25
5.2.1.
Elimination from Exposed Set (ES)..............................................25
5.2.2.
Safety Set....................................................................................25
5.2.3.
Elimination from Full Analysis Set (FAS) for Efficacy ...................26
5.2.3.1.
Excluded subjects ......................................................26
5.2.4.
Elimination from Per-protocol analysis Set (PPS) for 
Efficacy........................................................................................26
5.2.4.1.
Excluded subjects ......................................................26
5.2.5.
Elimination from Full Analysis Set (FAS) for 
Immunogenicity............................................................................28
5.2.5.1.
Excluded subjects ......................................................28
5.2.6.
Elimination from Per-protocol analysis Set (PPS) for 
Immunogenicity............................................................................29
5.2.6.1.
Excluded subjects ......................................................29
5.3.
Important protocol deviation not leading to elimination from per-
protocol analysis set ...................................................................................31


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 3 of 57
6.
STATISTICAL ANALYSES.....................................................................................31
6.1.
Demography...............................................................................................31
6.1.1.
Analysis of demographics/baseline characteristics planned 
in the protocol..............................................................................31
6.1.2.
Additional considerations.............................................................31
6.2.
Exposure ....................................................................................................31
6.2.1.
Analysis of exposure planned in the protocol...............................31
6.2.2.
Additional considerations.............................................................31
6.3.
Efficacy/Effectiveness.................................................................................32
6.3.1.
Analysis of efficacy planned in the protocol..................................32
6.3.2.
Additional considerations.............................................................32
6.3.3.
Definition of shigellosis according to CHIM Expert Working 
Group ..........................................................................................34
6.4.
Immunogenicity...........................................................................................34
6.4.1.
Analysis of immunogenicity planned in the protocol.....................34
6.4.2.
Additional considerations.............................................................35
6.5.
Analysis of safety........................................................................................37
6.5.1.
Analysis of safety planned in the protocol ....................................37
6.5.2.
Additional considerations.............................................................38
6.5.2.1.
Exclusion of implausible solicited Adverse 
Event..........................................................................38
6.5.2.2.
Solicited Adverse Events............................................38
6.5.2.3.
Unsolicited Adverse Events........................................43
6.5.2.4.
Combined Solicited and Unsolicited Adverse 
Events ........................................................................45
6.5.2.5.
Clinical Safety Laboratory Investigations ....................45
6.5.2.6.
Concomitant Medication .............................................46
7.
ANALYSIS INTERPRETATION..............................................................................48
8.
CONDUCT OF ANALYSES....................................................................................48
8.1.
Sequence of analyses.................................................................................48
8.2.
Statistical considerations for interim analyses.............................................49
9.
CHANGES FROM PLANNED ANALYSES.............................................................49
10. NON-STANDARD DATA DERIVATION RULES AND STATISTICAL 
METHODS .............................................................................................................49
10.1.
Data derivation ...........................................................................................49
10.2.
Statistical Method .......................................................................................49
11. LIST OF FINAL REPORT TABLES, LISTINGS AND FIGURES .............................50
12. ANNEX 1 STANDARD DATA DERIVATION RULE AND STATISTICAL 
METHODS .............................................................................................................50
12.1.
Statistical Method References ....................................................................50
12.2.
Standard data derivation.............................................................................50
12.2.1.
Date derivation ............................................................................50
12.2.2.
Dose number...............................................................................51
12.2.3.
Demography................................................................................51
12.2.4.
Immunogenicity............................................................................52
12.2.5.
Safety ..........................................................................................52


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 4 of 57
12.2.6.
Number of decimals displayed:....................................................53
12.2.7.
Efficacy........................................................................................53
13. ANNEX 2: SUMMARY ON ELIMINATION CODES ................................................56
14. ANNEX 3: STUDY SPECIFIC MOCK TFL..............................................................56
15. REFERENCES.......................................................................................................57


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 5 of 57
LIST OF TABLES
PAGE
Table 1
Study groups and epochs foreseen in the study.....................................10
Table 2
Study groups and treatment foreseen in the study .................................10
Table 3
Blinding of study epochs ........................................................................10
Table 4
List of study procedures .........................................................................13
Table 5
Intervals between study visits.................................................................15
Table 6
CHIM Expert Working Group Diarrhea and Dysentery definitions...........34
Table 7
Implausible Solicited Adverse Events.....................................................38
Table 8
List of Local and Systemic solicited adverse events...............................39
Table 9
Intensity grade for Erythema/Induration..................................................39
Table 10
Intensity grade for fever..........................................................................39
Table 11
Intensity scales for solicited symptoms...................................................40
Table 12
List of potential AESI to be followed during the study .............................44
Table 13
Evaluation of symptomatic neutropenia..................................................44
Table 14
Reporting periods for collecting safety information .................................47
Table 15
Derivation of efficacy endpoints..............................................................53


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 6 of 57
LIST OF FIGURES
PAGE
Figure 1
Study Design..........................................................................................12


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 7 of 57
LIST OF ABBREVIATIONS
AE
Adverse Event
AESI
Adverse Events of Special Interest
ATC
Anatomical Therapeutic Chemical (ATC) Classification System
BMGF
Bill and Melissa Gates Foundation
CBER
FDA Center for Biologics Evaluation and Research
CHIM
Controlled Human Infection Model
CI
Confidence Interval
CTRS
Clinical Trial Registry Summary
eCRF
electronic Case Report Form
ELISA
Enzyme-linked immunosorbent assay
EoS:
End of Study
ER
Emergency Room
ES
Exposed Set
EU/ml
ELISA unit per milliliter
FAS
Full Analysis Set
Fc
Fragment crystallisable
FDA
Food and Drug Administration, United States of America
GMC
Geometric mean antibody concentration
GSK
GlaxoSmithKline
GMMA
Generalized Modules for Membrane Antigens
GMR
Geometric Mean Ratio
GMT
geometric mean titers
GVGH
GSK Vaccines Institute for Global Health
HBV
Hepatitis B Virus
HCV
Hepatitis C Virus
HIV
Human Immunodeficiency Virus
HLA
Human Leukocyte Antigen
ICF
Informed Consent Form
IDAC
Independent Data Analysis Center
IDMC
Independent Data Monitoring Committee
IgG
Immunoglobulin G
IM
Intramuscular


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 8 of 57
LL
Lower Limit of the confidence interval
LLOQ
Lower Limit of Quantification
LPS
Lipopolysaccharide
LSAF
Life Science Analytics Framework
L-SBA
Luminescent Serum Bactericidal Assay
MedDRA
Medical Dictionary for Regulatory Activities
MSD
Moderate to Severe Diarrhea
OAg
O antigen
PBMC
Peripheral Blood Mononuclear Cells
PCD
Primary Completion Date
PD
Protocol Deviation
PPS
Per Protocol Set
qPCR
quantitative Polymerase Chain Reaction
RCDC
Reverse Cumulative Distribution Curve
RR
Risk Ratio
S. sonnei
Shigella sonnei
SAE
Serious adverse event
SAP
Statistical Analysis Plan
SBA
Serum Bactericidal Assay
SBIR
System Built for Internet Randomization
SD
Standard Deviation
sIgA
Secretory Immunoglobulin A
TFL
Tables Figures and Listings 
TOC
Table of Content
UL
Upper Limit of the confidence interval
Vacc
Vaccination
VE
Vaccine Efficacy


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 9 of 57
1.
DOCUMENT HISTORY
Date
Description
Protocol Version
09-AUG-2018
Final Version
22-JUN-2018
Amendment 2 Final
03-SEP-2019
Amendment 1
23-JUL-2019 
Amendment 6 Final
2.
STUDY DESIGN
This is a randomized, placebo-controlled, single center, observer-blind, phase 2b human 
challenge trial. The study includes a screening visit (performed between study Days -45 
to -1), 2 clinical visits with vaccination (performed at study Day 1 and Day 29), 2 clinical 
visits 7 days after each vaccination (performed at study Day 8 and Day 36), 1 clinical 
visit with S. sonnei 53G Challenge administration during an 8-day inpatient stay 28 days 
after second vaccination (performed at study Day 57), and 3 visits after challenge, 28 
days (study Day 85), 56 days (study Day 113) and 6 months (study Day 237) after 
challenge.
This study will evaluate the efficacy, safety and immunogenicity of the 1790GAHB 
vaccine administered via intramuscular (IM) route to adults (18-50 years of age at 
enrolment). The objectives will be assessed through the conduct of the study in two 
phases: a vaccination phase with 1790GAHB vaccine or placebo followed by a challenge 
phase with S. sonnei strain 53G.
A total of 72 subjects will be divided in 4 cohorts of 18 subjects each. The vaccination 
and challenge will be done in overlapping cohorts and randomization will ensure there is 
the same number of vaccinees and controls in each cohort. However, if for any reason, a 
cohort did not reach the planned 18 subjects, additional subjects can be added to the 
following cohorts. The maximum number of subjects must not be more than 20 
(maximum number of beds) in each cohort.

Experimental design: Phase IIB, observer-blind, randomized, placebo control, 
mono-centric study with two parallel groups (S. sonnei group and placebo group).

Duration of the study: Each subject will be followed up for approximately 6 months 
after challenge with the pathogenic S. sonnei strain 53G, with a total study duration 
of approximately 32 weeks (i.e., 8 months) for each study subject.

Epoch 001: Starting at Screening Visit (Day -45 to Day -1) and ending before 
Visit 1 (Day 1).

Epoch 002: Starting the day of randomization and first vaccination (Visit 1) and 
ending before the receipt of the challenge agent, 28 days after second vaccination 
(Visit 5).

Epoch 003: Starting with the receipt of the challenge agent at 28 days after 
second vaccination (Visit 5) and ending 6 months after challenge (Visit 8).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 10 of 57

Primary completion date (PCD): Visit 8 (6 months after challenge).
Refer to Glossary Section of the protocol for the definition of PCD.

End of Study (EoS): Last testing results released of samples collected for primary 
and secondary objectives at Visit 8.
Refer to Glossary Section of the protocol for the definition of EoS.

Study groups:
Table 1
Study groups and epochs foreseen in the study
Study 
groups
Number of 
subjects
Age (Min - Max)
Epochs
Epoch 001
Epoch 002
Epoch 003
Screening
1st and 2nd vaccination
Challenge
S. sonnei
36
18 years – 50 years
x
x
x
Placebo
36
18 years – 50 years
x
x
x
Table 2
Study groups and treatment foreseen in the study
Treatment name
Vaccine/ placebo/
challenge agent name
Study Groups
S. sonnei
Placebo
S. sonnei
1790GAHB
x
Placebo
GAHB-Placebo
x
Challenge
S. sonnei 53G strain
x
x

Control: Placebo control with GAHB-Placebo with the same composition as the 
vaccine except the active ingredient. GAHB-Placebo will also be used as diluent for 
bed-side mixing of the vaccine.

Vaccination schedule: Subjects will receive 2 doses of either the study vaccine or 
placebo 28 days apart. At 28 days after the second dose, all subjects will receive the 
challenge dose.

Treatment allocation: Following the screening period before the first vaccination 
(Day -45 to Day -1), subjects will be randomized in a 1:1 ratio to receive either the 
study vaccine or the placebo.

Blinding: The study will be observer-blind.
Table 3
Blinding of study epochs
Study Epochs
Blinding
Screening (Epoch 001)
N/A
1st and 2nd vaccination (Epoch 002)
observer-blind
Challenge (Epoch 003)
observer-blind


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 11 of 57
An overview of the study design is given in Figure 1 and a list of study procedures is 
reported in Table 4. For further details please refer to Section 3 of the protocol.
Randomization
After obtaining the signed and dated ICF from the subject and having checked the 
eligibility of the subject, the site staff in charge of the vaccine administration will access 
GSK Biological’s Internet Randomization System (SBIR). Upon providing the subject 
identification number, the randomization system will determine the study group and will 
provide the treatment number to be used for each dose.
The number of each administered treatment must be recorded in the eCRF (electronic 
Case Report Form) on the Vaccine Administration screen.
The target will be to enroll approximately 72 eligible subjects (36 per treatment group) 
who will be randomly assigned to two study groups in a (1: 1) ratio. The randomization 
algorithm will use a minimization procedure accounting for study. The block size used
for the material randomization list is 6.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 12 of 57
Figure 1
Study Design
*Refer to Section 3.2 from Protocol for details of procedures during the inpatient stay (Amended: 23 July 2019)
Scr: Screening
N: Number of subjects
B: Blood sampling
S: Stool sampling
U: Urine sampling


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 13 of 57
Table 4
List of study procedures 
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient stay Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to 
Day -1
Day 1
Day 3 and 
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to 
Day 65 8
Day 
85
Day 
113
Day 237
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9 Inpatient stay
Post-challenge
Informed consent
●
Check inclusion/exclusion criteria
●
●
●
Collect demographic data
●
Measure/record height and weight
●
Medical history
●
History directed physical examination
O
O
O
O
O
O
Physical examination
●
●
●
●
Urine pregnancy test 1
●
●
●
●
●
Check contraindications to vaccination
O
O
O
Pre-vaccination/placebo/challenge agent 
administration body temperature
●
●
●
Vaccine/placebo/challenge agent administration
Study group and treatment number 
allocation
●
Recording of administered treatment 
number
●
●
Vaccine/placebo administration
●
●
Challenge with S. sonnei 53G
●
Laboratory assays
Blood sampling for antibody response 
(~20 mL)
●2, 3
●
●2
●
●2, 3
●4
●
Blood sampling for PBMC isolation (α4β7 
plasmablasts response and 
transcriptomics) (~50 mL)
●
●
●
●4
Blood sampling for hematology (~5 mL) 5
●
●
●
●
●
●
Blood sampling for biochemical analysis 
(~5 mL)
●


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 14 of 57
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient stay Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to 
Day -1
Day 1
Day 3 and 
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to 
Day 65 8
Day 
85
Day 
113
Day 237
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9 Inpatient stay
Post-challenge
Serology for virology: HIV, HBV, HCV 
(~10 mL)
●
Blood test for HLA-B27 and local anti S. 
sonnei LPS IgG (Screening-ELISA) (~15 
mL)
●
Urine sampling for urinalysis 6
●
●
Stool sample for sIgA
●
●
●
●4
Stool sample for microbiome testing 7
●
●
Stool assessment: weight, consistency, 
blood and S. sonnei by culture and qPCR
●
Safety assessment
Record any concomitant 
medications/vaccinations
●
●
●
●
●
●
●
●
●
Distribution of diary cards
O
O
Return of diary cards
●
●
Diary card transcription by investigator
●
●
Recording of solicited adverse events (1–
7 days post-vaccination)
●
●
Recording of non-serious adverse events 
within 28 days post-vaccination
●
●
●
●
Recording of AESI, SAEs and 
pregnancies
●
●
●
●
●
●
●
●
●
●
Recording of SAEs related to study 
participation, or to a concurrent GSK 
medication/vaccine
●
●
●
●
●
●
●
●
●
●
Study Conclusion
●
V: Visit, D: Day, Vacc: Vaccination; HIV: Human Immunodeficiency Virus, HCV: Hepatitis C Virus, HBV: Hepatitis B Virus, ELISA: Enzyme-linked immunosorbent assay, AESI: 
Adverse Events of Specific Interest, SAEs: Serious Adverse Events.
● is used to indicate a study procedure that requires documentation in the individual eCRF.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 15 of 57
O is used to indicate a study procedure that does not require documentation in the individual eCRF.
1Female subjects will be randomized and study vaccine/placebo or challenge agent may only be administered if the pregnancy test is negative.
2Serum bactericidal assay will be performed at these visits in addition to the S. sonnei LPS IgG antibody response.
3Fc glycosylation test on leftover serum samples will be performed at these visits in addition to the S. sonnei LPS IgG antibody response and serum bactericidal assay.
4Sampling to be done 7 days after challenge agent administration (i.e., Day 64).
5Additionally, hematology is repeated weekly until resolution if neutropenia occurs. On the day of vaccination/challenge, sampling will be done before vaccination/challenge
6Urine dipstick to be done for all subjects and, in case of abnormal results, a urine culture is to be performed (urinalysis).
7Before vaccination/challenge (Day 1/Day 57 sample can be collected by the subject at most a week before and stored in a freezer).
8Sampling to be done daily during inpatient stay and if subject is still shedding 7 days post-challenge administration (Day 64). However, all subjects even if not shedding anymore will 
remain in the inpatient stay until 7 days post-challenge and will be discharged on Day 65.
9 Samples collection can be performed between Day 56 and Day 57.
Whenever possible, the investigator should arrange study visits within the interval described in Table 5.
Table 5
Intervals between study visits
Interval
Optimal length of interval
Allowed interval
Screening visit .Visit 1
-7 days
-45 days – -1 days
Visit 1Phone Call
3 days
2 days - 6 days
Visit 1 .Visit 2
7 days
7 days - 10 days
Visit 1 Visit 3
28 days
26 days - 33 days
Visit 3 Phone call
3 days
2 days - 6 days
Visit 3 Visit 4
7 days
7 days - 10 days
Visit 3 Visit 5
28 days
26 days - 33 days
Visit 5 Inpatient stay
9 days
9 days - as needed
Visit 5 Visit 5 post-challenge 
blood draw
7 days
7 days - 10 days
Visit 5 Visit 6
28 days
28 days - 35 days
Visit 5 Visit 7
56 days
49 days - 63 days
Visit 5 Visit 8
180 days
166 days - 194 days


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 16 of 57
3.
OBJECTIVES
3.1.
Primary objective
Efficacy

To demonstrate the efficacy of two vaccinations with 25 µg of 1790GAHB vaccine 
in healthy adults compared to placebo in reducing shigellosis, fulfilling the primary 
protocol case definition (reported in Section 4.1), after challenge with S. sonnei 
strain 53G.
Criterion:

Vaccine efficacy (VE) of 1790GAHB vaccine will be shown if the lower limit (LL) 
of the 90% confidence interval (CI) of VE will be above zero.
Refer to Section 4.1 below for the protocol case definition of shigellosis and to Section 
4.2 for the definition of the primary endpoint.
3.2.
Secondary objectives
Efficacy

To determine the efficacy of the 1790GAHB vaccine compared to placebo against:

Shigellosis, as per definition requested by the Controlled Human Infection Model
(CHIM) expert working group (see Section 6.3.3).

Shigellosis, as defined by: severe diarrhea OR moderate diarrhea with fever or 
with one or more moderate constitutional/enteric symptoms OR dysentery [[ ≥2 
loose stools with gross blood (hemoccult positive) in 24 hours] AND [≥1 at least 
mild constitutional/enteric symptom]].

More severe shigellosis, as defined by: severe or moderate diarrhea with fever or 
with one or more at least severe constitutional/enteric symptoms OR dysentery 
[[≥2 loose stools with gross blood (hemoccult positive) in 24 hours] AND fever 
OR ≥1 at least severe constitutional/enteric symptom]].

Shedding of S. sonnei strain 53G

Severe diarrhea.

More severe diarrhea.

Dysentery.

Weight of all grade 3-5 stools.

The total number of grade 3-5 stools.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 17 of 57

Confirmed S. sonnei 53G shedding AND [moderate or severe diarrhea OR 
dysentery OR presence of fever 38.5°C OR presence of one or more severe 
intestinal symptoms (abdominal pain, cramping, nausea, vomiting, gas, and 
anorexia)].

Disease not fulfilling the protocol primary case definition for shigellosis 
associated or not with mild to moderate symptoms including: passing loose stool 
(not meeting the protocol definition of moderate or severe diarrhea), abdominal 
pain, abdominal cramps, gas, anorexia, nausea, headache, myalgia, malaise, 
arthralgia, fever, vomiting and IV fluid administration.

Time to onset of shigellosis after challenge
Safety

To assess the safety and reactogenicity of the 1790GAHB vaccine in terms of 
solicited symptoms, unsolicited symptoms, serious adverse events (SAEs), adverse 
events of special interest (AESI) and laboratory parameters.

To assess safety after challenge in terms of SAEs, unsolicited symptoms, AESI and 
laboratory parameters.
Immunogenicity

To evaluate the IgG ELISA (Enzyme-linked immunosorbent assay) immunogenicity 
profile of the 1790GAHB vaccine at 7, and 28 days after the first and second 
vaccination (IgG ELISA coated with O antigen (OAg) containing 
Lipopolysaccharide (LPS)).

To evaluate the immunogenicity profile of the 1790GAHB vaccine at pre-challenge
and at 7 and 28 days after challenge (IgG ELISA coated with OAg containing LPS).

To assess seroresponse for anti-S. sonnei LPS at 7 and 28 days after first and second 
vaccination.

To assess post vaccination concentration ≥ 121 EU/ml for anti-LPS S. sonnei at 7 
and 28 days after first and second vaccination

To assess post challenge concentration ≥ 121 EU/ml for anti-LPS S. sonnei at 7 and 
28 days after challenge
Refer to Section 4.3 for the definition of the secondary endpoints.
3.3.
Tertiary objectives
The following tertiary objectives will be analyzed as part of this SAP:

Evaluate serum bactericidal activity against S. sonnei at Day 1 and 28 days after first 
and second vaccination.

Evaluate correlation between serum anti-S. sonnei LPS IgG level and serum 
bactericidal activity titer.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 18 of 57
The following and remaining tertiary objectives will complement assessment of the 
vaccine immunogenicity profile and will be part of a subsequent SAP:

Evaluate S. sonnei specific Secretory Immunoglobulin A (sIgA) in stool at Day 1 and 
7 days after first and second vaccination and 7 days after challenge (Day 64).

Evaluate S. Sonnei LPS IgG-specific α4β7+/- plasmablast at Day 1 and 7 days after 
first and second vaccination and 7 days after challenge (Day 64).

Evaluate correlation between serum anti-S. sonnei LPS IgG level, serum bactericidal 
activity titer, shigellosis, shedding, mild, moderate, severe or more severe diarrhea, 
and dysentery after challenge.

Evaluate glycosylation of fragment crystallisable (Fc) portion of IgG antibodies at 
Day 1 and 28 days after second vaccination and association with clinical protection 
and/or serological endpoints.

Evaluate gene expression signatures at Day 1 and 7 days after first and second 
vaccination and 7 days after challenge (Day 64).

Investigate gut microbiome at Day 1 and 28 days after second vaccination and its 
potential association with protection and immune response.
These last two tertiary objectives involve pharmacogenomics testing. Refer to the
Glossary of the protocol for the definition of Pharmacogenomics.
Refer to Section 4.4 for the definition of the tertiary endpoints.
4.
ENDPOINTS
4.1.
Case Definitions
Stools
Stools will be graded as follows:

Grade 1: firm formed;

Grade 2: soft formed;

Grade 3: viscous opaque liquid or semi-liquid which assumes the shape of the bowl;

Grade 4: watery opaque liquid;

Grade 5: clear watery or mucoid liquid.
Diarrhea
For the purpose of this study, diarrhea as used in the primary endpoint is defined as:

Moderate diarrhea: 4 to 5 loose or watery (Grade 3 to 5) stools or 400 to 800 grams 
of Grade 3 to 5 stools within 24 hours.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 19 of 57

Severe diarrhea: 6 or more loose or watery (Grade 3 to 5) stools or > 800 grams of 
Grades 3 to 5 stools within 24 hours or required medical intervention.

More severe diarrhea: 10 loose or watery (Grade 3 to 5) stools or 1000 grams of 
Grade 3 to 5 stools within 24 hours.

Note: Diarrhea severity classes are not mutually exclusive, as more severe diarrhea is 
a subset of severe diarrhea.

In case of severe diarrhea, medical intervention is defined as intravenous (IV) fluids 
administration or anticipation of antibiotic treatment before the 5th day after 
challenge.
Dysentery
For the purpose of the endpoint “Rate of shigellosis as defined by the CHIM expert 
working group occurring within a period starting with challenge visit and lasting until the 
end of the inpatient stay, in all subjects” (a), see Section 4.3), dysentery is defined as
follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [oral 
temperature ≥38.0oC OR ≥1 moderate constitutional/enteric symptom OR ≥2 
episodes of vomiting in 24 hours]. In this case constitutional/enteric symptom are the 
following: nausea, abdominal pain, abdominal cramping, myalgia, arthralgia, 
malaise.
For the purpose of the endpoint “Rate of shigellosis, as defined by: severe diarrhea OR 
moderate diarrhea with fever or with one or more moderate constitutional/enteric 
symptoms OR dysentery” (b), see Section 4.3), dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours AND [≥1 
reportable constitutional/enteric symptom]. In this case constitutional/enteric 
symptom are the following: headache, fatigue, arthralgia, malaise, myalgia, chills, 
nausea, abdominal cramping, abdominal pain, gas, anorexia, vomiting.
For the purpose of the endpoint “Rate of more severe shigellosis as defined by: severe or 
moderate diarrhea with fever or with one or more severe constitutional/enteric symptom 
OR dysentery [[≥2 loose stools with gross blood (hemoccult positive) in 24 hours] AND 
[oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]].” (c), see 
Section 4.3), dysentery is defined as follows:

At least 2 loose stools with gross blood (hemoccult positive) in 24 hours] AND [oral 
temperature ≥38.0oC OR ≥1 severe constitutional/enteric symptom]. In this case 
constitutional/enteric symptom are the following: headache, fatigue, arthralgia, 
malaise, myalgia, chills, nausea, abdominal cramping, abdominal pain, gas, anorexia, 
vomiting.
For the purpose of secondary efficacy objective g) and k) (see Section 4.3), dysentery is 
defined as:


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 20 of 57

A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours 
AND presence of constitutional/enteric symptoms (i.e. fever, headache, fatigue, 
arthralgia, malaise, myalgia, chills, nausea, abdominal cramping, abdominal pain, 
gas, anorexia, vomiting).
Shigellosis
For the challenge phase of the study, the protocol primary case definition for shigellosis 
is:

Shedding of S.sonnei 53G accompanied by moderate or severe diarrhea OR shedding 
with an oral temperature ≥ 38.5°C.
4.2.
Primary endpoint
Primary Efficacy endpoint
Vaccine efficacy (VE) will be evaluated in the 8-day post-challenge inpatient period after 
visit 5 (i.e. from challenge to discharge) by:

Attack Rate of shigellosis (fulfilling the protocol case definition) occurring within a 
period starting with the challenge visit and lasting up to the end of the inpatient stay, 
in all subjects. The attack rate of shigellosis is expressed as proportion of subjects 
per group with at least one episode of shigellosis after challenge.
4.3.
Secondary endpoints
Secondary Efficacy endpoints
All the secondary endpoints will be assessed in the 8-day post-challenge inpatient period
after visit 5 (i.e. from challenge to discharge).
All subjects receiving the 1790GAHB vaccine vs. placebo will be compared according to 
the following endpoints:
a)
Attack rate of shigellosis, as defined by CHIM expert working group (see Section 
6.3.3)
b)
Attack rate of shigellosis, as defined by any one of the three following possible 
endpoints:

Severe diarrhea defined as [≥6 loose stools in 24 hours OR ˃800 grams loose stools 
in 24 hours]

Moderate diarrhea defined as [4-5 loose stools in 24 hours OR 400-800 grams loose 
stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 at least moderate 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [≥1 at least mild constitutional/enteric symptom].


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 21 of 57
c)
Attack rate of More Severe Shigellosis, as defined by any one of the two following 
possible endpoints:

Moderate OR severe diarrhea [≥4 loose stools in 24 hours OR ≥400 grams loose 
stools in 24 hours] AND [oral temperature ≥38.0oC OR ≥1 at least severe 
constitutional/enteric symptom].

Dysentery defined as [≥2 loose stools with gross blood (hemoccult positive) in 24 
hours] AND [oral temperature ≥38.0oC OR ≥1 at least severe constitutional/enteric 
symptom].
d)
Proportion of subjects with shedding of S. sonnei strain 53G.
Shedding of S. sonnei strain 53G is defined as positivity of at least one stool sample 
either by culture or quantitative Polymerase Chain Reaction (qPCR).
e)
Proportion of subjects with at least one episode of severe diarrhea.
f)
Proportion of subjects with at least one episode of more severe diarrhea.
g)
Proportion of subjects with at least one episode of dysentery (as defined in Section 
4.1).
h)
Mean (arithmetic or geometric, according to distribution of the data) weight of grade 
3-5 stools per subject, for all subjects and for subjects with at least one grade 3-5 
stool (i.e. grade 3-5 stool).
i)
Mean weight per subject of all grade 3-5 stools accumulated from challenge to 
discharge
j)
Mean number of grade 3-5 stools per subject from challenge to discharge.
k)
Proportion of subjects with confirmed S. sonnei 53G shedding AND [moderate or 
severe diarrhea, OR dysentery (as defined in Section 4.1), OR presence of fever (oral 
temperature ≥ 38.5°C), OR presence of at least one intestinal symptom (abdominal 
pain, abdominal cramping, gas, nausea, vomiting, anorexia) graded as severe].
l)
Disease not fulfilling the protocol case definition for shigellosis associated or not 
with mild to moderate symptoms including: 
1.
Proportion of subjects with at least one stool (not meeting the protocol definition 
of moderate or severe or more severe diarrhea), 
2.
Proportion of subjects with at least one episode of abdominal pain, 
3.
Proportion of subjects with at least one episode of abdominal cramps, 
4.
Proportion of subjects with at least one episode of gas, 
5.
Proportion of subjects with at least one episode of anorexia, 
6.
Proportion of subjects with at least one episode of nausea, 
7.
Proportion of subjects with at least one episode of headache, 
8.
Proportion of subjects with at least one episode of myalgia, 
9.
Proportion of subjects with at least one episode of malaise, 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 22 of 57
10. Proportion of subjects with at least one episode of arthralgia, 
11. Proportion of subjects with at least one episode of fever (oral temperature ≥ 
38.5°C), 
12. Proportion of subjects with at least one episode of vomiting, and 
13. Proportion of subjects with at least one IV fluid administration.
m) Time to onset of Shigellosis during the post-challenge period
All endpoints are measured from challenge to discharge.
Note that in the primary and secondary efficacy endpoints #k and #l.11, fever is defined 
as oral temperature ≥ 38.5°C, in agreement with challenge model set up at Cincinnati. 
However, fever in other endpoints and as solicited event is defined as a body temperature 
of ≥38°C irrespective of route of measurement, in agreement with latest GSK standards 
and Brighton collaboration rules (see Section 6.5.2.2).
For derivation of the primary and secondary endpoints refer to Section 12.2.7.
Secondary Safety endpoints
The measures of safety will include:

Number of subjects with solicited local and systemic reactions during 7 days 
following each vaccination. Solicited local reactions include injection site erythema, 
injection site induration and injection site pain; solicited systemic reactions include 
headache, arthralgia, chills, fatigue, malaise, myalgia, and fever (as measured orally).

Number of subjects with reported unsolicited adverse events (of any nature and 
severity) during 28 days following vaccination and challenge, i.e. up to second 
vaccination visit (when evaluating after first vaccination) whichever comes first, and 
up to challenge visit (when evaluating after second vaccination) whichever comes
first, and up to 28th day after challenge.

Number of subjects with reported SAEs throughout the study duration.

Number of subjects with reported AESI (i.e., symptomatic neutropenia) throughout 
the study duration.

Number of subjects with deviations from normal values (i.e. reference range and/or 
clinically significant value, according to local ranges) of hematological tests at 7 
days after first and second vaccination (Visit 2 and Visit 4) and at last study visit 
(Visit 8).
Secondary Immunogenicity endpoints
The measures of immunogenicity, against the LPS of S. sonnei, will include:

IgG geometric mean concentrations (GMCs) pre-vaccination (Day 1), 7 days after 
first vaccination (Day 8), 28 days after first vaccination (Day 29), 7 days after 
second vaccination (Day 36), and 28 days after second vaccination (Day 57) overall 
and by antibody concentration at baseline (i.e., above vs. below ELISA Lower Limit 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 23 of 57
of Quantification, LLOQ, 22 EU/ml ), as determined by anti-S. sonnei LPS IgG 
ELISA and applicable within-subject geometric mean ratios (GMRs) between post 
vaccination and baseline samples (D8/D1, D29/D1, D36/D1 and D57/D1).

IgG GMC pre-challenge (Day 57), 7 and 28 days after challenge (Day 64 and Day 
85) as determined by anti-S. sonnei LPS IgG ELISA and applicable within-subject 
geometric mean ratios (GMRs) between post-challenge and pre-challenge samples 
(D64/D57, and D85/D57).

Number and percentage of seroresponders for anti-S. sonnei LPS at 7 and 28 days 
after first and second vaccination. Seroresponse is aimed to define a significant 
increase in anti S. sonnei LPS IgG concentration in post-vaccination samples and 
relies on the definition already used in a previous phase II study in Kenyan 
population. See Section 6.4.2 for definition of seroresponders.

Number and percentage of subjects with titers post vaccination concentration ≥ 121 
EU/ml for anti-LPS S. sonnei at 7 and 28 days after first and second vaccination 

Number and percentage of subjects with titers post challenge concentration ≥ 121 
EU/ml for anti-LPS S. sonnei at 7 and 28 days after challenge
4.4.
Tertiary endpoints
Below are reported the tertiary immunogenicity endpoints in scope of this SAP:

Luminescent Serum Bactericidal Assay (L-SBA) geometric mean titers (GMTs) pre-
vaccination (Day 1), 28 days after first vaccination (Day 29), and 28 days after 
second vaccination (Day 57) overall and by antibody concentration at baseline (i.e., 
above vs. below L-SBA LLOQ), as determined by L-SBA and applicable within-
subject geometric mean ratios (GMRs) between post vaccination and baseline 
samples (D29/D1 and D57/D1).

Correlation between bactericidal antibodies titers (as measured by L-SBA titres) and 
anti-LPS S. sonnei serum IgG antibody concentration (as measured by ELISA) will 
be assessed by Pearson correlation coefficient, calculated on the log10 transformed 
values for all the sample pooled together. Correlation will be also assessed by the 
treatment groups (shigella and placebo) and antibodies at baseline above and below 
LLOQ for L-SBA and ELISA. The correlation coefficients will be graphically 
supplemented by scatter plots
5.
ANALYSIS SETS
5.1.
Definition
5.1.1.
All Enrolled Set
All screened subjects who provide informed consent, and provide demographic and/or 
baseline screening assessments and received a Subject ID, regardless of the subject’s 
randomization and treatment status in the study.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 24 of 57
5.1.2.
All Exposed Set
All subjects in the enrolled set who receive a study vaccination. Please note that 
throughout Section 5, vaccine/study vaccination refer to study vaccine or placebo.
5.1.3.
Safety Set
5.1.3.1.
Solicited Safety Set (solicited local and systemic adverse events and 
other solicited adverse events)
All subjects in the All Exposed Set with any valid data on solicited AEs.
5.1.3.2.
Unsolicited Safety Set (unsolicited adverse events)
All subjects in the Exposed Set that do not withdraw early and are lost to follow-up on a 
vaccination visit.
5.1.3.3.
Overall Safety Set
All subjects who are in the Solicited Safety Set and/or Unsolicited Safety Set.
5.1.4.
Full Analysis Set (FAS) for Efficacy/Immunogenicity
5.1.4.1.
Full Analysis Set for Efficacy 
All subjects in the All Enrolled Set who are randomized, receive a study vaccination and 
provide efficacy data.
5.1.4.2.
Full Analysis Set for Immunogenicity
All subjects in the All Enrolled Set who are randomized, receive at least one study 
vaccination and provide post vaccination immunogenicity data at the relevant timepoints.
In case of vaccination error, subjects in the FAS sets will be analyzed “as randomized” 
(i.e. according to the vaccine a subject was designated to receive, which may be different 
from the vaccine the subject actually received).
5.1.5.
Per-Protocol Set (PPS) for Efficacy/Immunogenicity
All subjects in the FAS for Efficacy/Immunogenicity who:

Correctly receive the vaccines (i.e., receive the vaccine to which the subjects is 
randomized and at the scheduled timepoints).

Have no protocol deviations leading to exclusion as defined prior to unblinding / 
analysis.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 25 of 57

Are not excluded due to other reasons defined prior to unblinding or analysis.
PPS are subsets of FAS and should be always defined even if the objectives do not 
require it.
Examples for subjects excluded due to other reasons than protocol deviations are:

Subjects who withdrew informed consent.
The primary analysis will be based on the PPS for efficacy and immunogenicity. 
However, selected analyses will be performed on both FAS and PPS sets (more details in 
Section 6).
PPS for Immunogenicity will be furtherly categorized in PPS Post-Vaccination where 
Visit 1, 2, 3, 4, and 5 are analyzed, and in PPS Post-Challenge where Visit 5, Visit at the 
end of inpatient stay, and Visit 6 are analyzed.
5.2.
Criteria for eliminating data from Analysis Sets
Elimination codes are used to identify subjects to be eliminated from analysis.  Detail is 
provided below for each set. Consolidated tables are also available in Section 13.
5.2.1.
Elimination from Exposed Set (ES)
Code 1030 (Study vaccine not administered at all) and code 900 (invalid informed 
consent or fraud data) will be used for identifying subjects eliminated from ES.
5.2.2.
Safety Set
Code 1150 (Subject did not provide any post-vaccination/post-challenge unsolicited 
safety data) will be used for identifying subjects eliminated from the Unsolicited Safety 
Set.
Code 1160 (Subject did not provide any post-vaccination solicited safety data) will be 
used for identifying subjects eliminated from the Solicited Safety Set.
Subjects with codes 1155 will be eliminated from the Overall Safety Set.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 26 of 57
5.2.3.
Elimination from Full Analysis Set (FAS) for Efficacy 
5.2.3.1.
Excluded subjects
A subject will be excluded from the FAS for Efficacy analysis under the following 
conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered for both doses
3000.a
Did not undergo challenge
3000.c
Missed or incomplete assessment (after challenge)
5.2.4.
Elimination from Per-protocol analysis Set (PPS) for Efficacy
5.2.4.1.
Excluded subjects
A subject will be excluded from the PPS analysis for Efficacy under the following 
conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data:
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered for both doses
1040
Administration of concomitant vaccine(s) forbidden in the protocol*
1050
Randomization failure
1060
Randomization code was broken
1070
Vaccination not according to protocol:
Incomplete treatment course


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 27 of 57
Code
Condition under which the code is used
Route of administration is wrong or unknown
Treatment administered is correct but is not compatible with 
treatment regimen associated to treatment schedule
Wrong replacement or study treatment administered
Study treatment not prepared as per protocol (e.g. reconstitution)
Site of injection for vaccine
1500
Incorrect Volume was given
1500
Study treatment not available at site for administration
1500
Study treatment administered while contraindication
1500
Pregnancy
1080
Vaccine temperature deviation
1090
Expired vaccine administered
2010
Protocol violation (inclusion/exclusion criteria)
2040
Administration of any medication forbidden by the protocol*
2050
medical condition forbidden
2060
infection related to the vaccine
2070
infection not related to the vaccine
2080
Subjects did not comply with vaccination schedule
2130
Subject not planned to be sampled for their all sampling visits:
Testing performed on samples not aligned with ICF
Collection of multiple samples when not required
Subjects bled but not supposed to be bled
Sample discard/destruction not completed as per protocol/SPM/ICF
Sample destroyed and should not have been destroyed
3000.a
Did not undergo challenge
3000.b
Challenge administered out of the window
3000.c
Missed or incomplete assessment (after challenge)
3000.d
Challenge impacted by temperature excursion
3000.e
Challenge not prepared as per protocol (e.g. reconstitution)
3000.f
Challenge administered while contraindication
3000.g
Subject left the inpatient stay during day 5 of inpatient stay or earlier
*See protocol Section 7.6.2 for specific details.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 28 of 57
5.2.5.
Elimination from Full Analysis Set (FAS) for Immunogenicity 
5.2.5.1.
Excluded subjects
A subject will be excluded from the FAS for Immunogenicity analysis under the 
following conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered at all
2100
Serological results not available post-vaccination:
Missed assessment (subject early terminated prior to the visit)
Missed assessment (subject continues participation in the study)
Low volume (not sufficient to perform testing)
No samples collected for subject (and should have been collected)
Mislabeling (sample not tested)
2120
Obvious incoherence or abnormality or error in data (for Antibody 
determination):
Temperature deviations from range defined in protocol and/or SPM –
refrigerator
Temperature deviation from range defined in protocol and/or SPM - -
20Freezer
Temperature deviation from range defined in protocol and/or SPM - -
45 freezer
Temperature deviation from range defined in protocol and/or SPM - -
80 freezer
Central/internal/external lab deviations
Mislabeling (sample tested)
*See protocol Section 5.3.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 29 of 57
5.2.6.
Elimination from Per-protocol analysis Set (PPS) for 
Immunogenicity
5.2.6.1.
Excluded subjects
A subject will be excluded from the PPS analysis for Immunogenicity under the 
following conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered 
1040
Administration of concomitant vaccine(s) forbidden in the protocol*
1050
Randomization failure
1060
Randomization code was broken 
1070
Vaccination not according to protocol:
Incomplete treatment course
Route of administration is wrong or unknown
Treatment administered is correct but is not compatible with 
treatment regimen associated to treatment schedule
Wrong replacement or study treatment administered
Study treatment not prepared as per protocol (e.g. reconstitution)
Site of injection for vaccine
1500
Incorrect Volume was given
1500
Study treatment not available at site for administration
1500
Study treatment administered while contraindication
1500
Pregnancy
1080
Vaccine temperature deviation
1090
Expired vaccine administered
2010
Protocol violation (inclusion/exclusion criteria)**
2040
Administration of any medication forbidden by the protocol*


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 30 of 57
Code
Condition under which the code is used
2050
medical condition forbidden
2060
infection related to the vaccine
2070
infection not related to the vaccine
2080
Subjects did not comply with vaccination schedule
2090
Subjects did not comply with blood sample schedule
2100
Serological results not available post-vaccination:
Missed assessment (subject early terminated prior to the visit)
Missed assessment (subject continues participation in the study)
Low volume (not sufficient to perform testing)
No samples collected for subject (and should have been collected)
mislabeling (sample not tested)
2120
Obvious incoherence or abnormality or error in data (for Antibody 
determination):
Temperature deviations from range defined in protocol and/or SPM –
refrigerator
Temperature deviation from range defined in protocol and/or SPM - -
20Freezer
Temperature deviation from range defined in protocol and/or SPM - -
45 freezer
Temperature deviation from range defined in protocol and/or SPM - -
80 freezer
Central/internal/external lab deviations
Mislabeling (sample tested)
2130
Subject not planned to be sampled:
Testing performed on samples not aligned with ICF
Collection of multiple samples when not required
Subjects bled but not supposed to be bled
Sample discard/destruction not completed as per protocol/SPM/ICF
Sample destroyed and should not have been destroyed
*See protocol Section 7.6.2 for specific details.
**See protocol Section 5.3.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 31 of 57
5.3.
Important protocol deviation not leading to elimination from 
per-protocol analysis set 
Important protocol deviations not leading to elimination from PPS and FAS will be
defined in the Protocol Deviation Management Plan.
6.
STATISTICAL ANALYSES
Note that standard data derivation rule and stat methods are described in Section 12
Annex 1 and will not be repeated below.
6.1.
Demography
6.1.1.
Analysis of demographics/baseline characteristics planned in the 
protocol
Descriptive statistics (mean, standard deviation (SD), median, minimum and maximum) 
for age, height and weight at enrolment will be calculated overall and by vaccine/placebo 
group.
Distributions of subjects by gender and geographic ancestry will be summarized for the 
Exposed Set.
6.1.2.
Additional considerations
Demography data will be tabulated also for the Efficacy Per Protocol Set, Efficacy Full 
Analysis Set, Immunogenicity Per Protocol Post-Vaccination Set, Immunogenicity Per 
Protocol Post-Challenge Set, and All Enrolled Set.
6.2.
Exposure
6.2.1.
Analysis of exposure planned in the protocol
Not applicable.
6.2.2.
Additional considerations
The frequencies and percentages of subjects with vaccination will be summarized overall 
and by vaccine/placebo group. Data will be tabulated for the All Exposed Set.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 32 of 57
6.3.
Efficacy/Effectiveness
6.3.1.
Analysis of efficacy planned in the protocol
VE will be evaluated at the end of study period. VE will be estimated as 1-RR where RR 
is the risk ratio (proportion of subjects reporting the disease in the vaccinated group over 
the proportion in the placebo group) together with 90% CIs.
Subjects with missing values of efficacy endpoints will be excluded from analyses (i.e. 
complete-case analysis) since they are considered missing completely at random, i.e. not 
informative and with no impact on inferences.
6.3.2.
Additional considerations
All the efficacy objectives (i.e. primary and secondary) will be evaluated in the PPS.
For the primary efficacy endpoint, VE will be assessed as 1-RR, where RR is the ratio of 
proportion of subjects with shigellosis in the vaccinated group on the proportion of 
subjects with shigellosis in the placebo group. As per protocol definition, vaccine 
efficacy in reduction of shigellosis will be demonstrated if the lower limit of the 90% CI 
of VE estimated with Miettinen-Nurminen method is above zero (see Section 12.1 for 
methods of calculation of the 90% CI for VE).
This information will be complemented with Barnard test [Barnard, 1945, 1947, 1949] 
(BARNARD option of the EXACT statement in SAS FREQ procedure): the lower limit 
of the 90% Confidence Interval for VE calculated with Miettinen-Nurminen method will 
be above zero if the p-value of the one-sided Barnard test is below 5%.
A subset of specific efficacy objectives will be analyzed also using 85% CI, see more 
details in Second Line Analysis below.
The following calculation will be performed for all secondary efficacy endpoints,
according to the nature of the data:

In case of endpoints measured as proportion (endpoints from a. to g., k., and l. sub-
endpoints in Section 4.3), VE and 90% CI will be calculated as described above in 
the primary endpoint.

For count endpoint (i.e. total number of grade 3-5 stools) the RR will be estimated as 
the rate of grade 3-5 stools in vaccinated subjects divided by the rate of grade 3-5 
stools in placebo. 90% CI for this rate ratio will be calculated from an unadjusted 
negative binomial model, to take into account possible over-dispersion of data 
(DIST=NB in GENMOD SAS procedure); unadjusted P-value from the associated 
two-tailed Wald will be reported.

Continuous endpoints (i.e. weight of grade 3-5 stools per subjects, weight of grade 3-
5 stools per subject in those with at least a grade 3-5 stools, and weight of grade 3-5 
stools accumulated from challenge to discharge per subject) will be compared using 
unequal variance two-sample t-test in case of normality of data, unequal variance 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 33 of 57
two-sample t-test on the log values in case log-values are normally distributed, or by 
Wilcoxon 2-sample test otherwise. In case of comparison via log-values, the 
geometric mean will be calculated as well as the arithmetic mean and associated 90% 
CI. Unadjusted P-values from two-tailed test will be considered reported.

Time to event endpoint (i.e. days from challenge administration to onset of 
shigellosis) will be visually depicted by a Kaplan-Meier cumulative incidence 
curves, and compared using the Log-rank test. Unadjusted P-value will be reported. 
Day of challenge administration will be considered as Day 1.
Sensitivity analysis
The analysis of the primary objective will be repeated using FAS, instead of PPS.
The analysis for the following objectives will be repeated using FAS, instead of PPS, 
only in case the difference between FAS and PPS is greater than 10%:

secondary efficacy objective of Shigellosis, as defined by CHIM expert working 
groups

secondary efficacy objective of Shigellosis, as defined in Section 4.3

secondary efficacy objective of More Severe Shigellosis, as defined in Section 
4.3

secondary efficacy objective of More Severe Diarrhea
Second line Analysis
The analysis for the following objectives will be repeated using a confidence level of 
85% in the PPS:

primary efficacy objective (i.e. assessing reduction of shigellosis)

secondary efficacy objective of Shigellosis, as defined by CHIM expert working 
groups

secondary efficacy objective of Shigellosis, as defined in Section 4.3

secondary efficacy objective of More Severe Shigellosis, as defined in Section 
4.3

secondary efficacy objective of More Severe Diarrhea
Subgroup analysis
The analysis for primary efficacy objective will be repeated for the two subgroups of 
subjects who were responders or non-responders at the pre-challenge visit 
immunogenicity assessment.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 34 of 57
6.3.3.
Definition of shigellosis according to CHIM Expert Working 
Group
After protocol approval, a specific definition of shigellosis proposed by the CHIM Expert 
Working Group consensus meeting, different from the one defined as primary efficacy 
objective, was explicitly requested by the Bill and Melissa Gates Foundation (BMGF)
and therefore added among the secondary efficacy objectives/endpoints.
BMGF shigellosis definition is the following:

Moderate diarrhea OR severe diarrhea OR dysentery
With moderate diarrhea, severe diarrhea, and dysentery specifically defined as per Table 
6.
Table 6
CHIM Expert Working Group Diarrhea and Dysentery definitions
Primary Endpoint
Definition
Severe Diarrhea
≥6 loose stools* in 24 hours 
OR >800 grams loose stools* in 24 hours
Moderate Diarrhea
[4-5 loose stools* in 24 hours 
OR 400-800 grams loose stools* in 24 hours] 
AND 
[oral temperature ≥38.0˚C 
OR ≥1 moderate constitutional/enteric symptom‡ 
OR ≥2 episodes of vomiting in 24 hours]
Dysentery
≥2 loose stools* with gross blood (hemoccult positive) in 24 hours 
AND 
[oral temperature ≥38.0˚C 
OR ≥1 moderate constitutional/enteric symptom 
OR ≥2 episodes of vomiting in 24 hours]
* grade 3 to 5 stools
‡Nausea, abdominal pain/cramping, myalgia/arthralgia, malaise
6.4.
Immunogenicity
6.4.1.
Analysis of immunogenicity planned in the protocol
Analysis of binary variables:
The number and percentages of subjects will be summarized. Two-sided 95% CIs for the 
percentages will be computed.
Missing values of immunogenicity will be excluded from analyses (i.e. complete-case 
analysis) since they are considered missing completely at random, i.e. not informative 
and with no impact on inferences.
Analysis of continuous variables:
Antibody concentration below the limit of quantification (i.e. 22 EU/ml for ELISA and
IC50 of 100 for L-SBA) in the respective assay will be set to half the limit for the 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 35 of 57
purposes of analysis. The limit will be calculated as the average limit of quantification for 
the assays done on Day 1 sera. The antibody concentrations/titers will be logarithmically 
transformed (base10) to fulfil the normal distribution assumption. GMC/GMTs will be 
calculated, with their associated two-sided 95% CIs, by exponentiating the corresponding 
log-transformed means and their 95% CI.
Additionally, within-subject geometric mean ratios (GMRs) will be computed for 
geometric mean concentrations at each time point after vaccination versus baseline (Day 
1) and after challenge versus pre-challenge (Day 57). The GMRs and 95% CIs will be 
constructed by exponentiating the mean within-subject differences in log-transformed 
titers and the corresponding 95% CIs. GMR will be calculated only for subjects with 
valid baseline or pre-challenge valid immunogenicity results.
6.4.2.
Additional considerations
The PPS will be the primary analysis set for the immunogenicity objectives; however, 
immunogenicity objectives will be evaluated also in the FAS, only in case the difference 
between FAS and PPS is greater than 10%.
The percentage of subjects with seroresponse by titer at baseline and with post 
vaccination antibody level ≥ 121 IgG units and associated two-sided 95% Clopper-
Pearson CIs will be computed by vaccine group at each visit.
Unadjusted GMC/GMT s and associated two-sided 95% CIs will be computed for each 
group (i.e. vaccine and placebo) at each visit (i.e. Visit 1-Day 1, Visit 2-Day 8, Visit 3-
Day 29, Visit 4-Day 36, Visit 5-Day 57, End of inpatient stay-Day 64, and Visit 6-Day 
85). For each group, unadjusted GMC/GMTs and their 95% CIs will be obtained by 
exponentiating (base 10) the means and the lower and upper limits of the 95% CIs of the 
log-transformed concentrations (base 10). Additionally, within-subject unadjusted GMRs 
and associated two-sided 95% CIs will be computed for Day 8, Day 29, Day 36, and Day 
57, respectively versus baseline and for Day 64 and Day 85 respectively versus Day 57 
(pre-challenge).
For further details on standard business rule for GMC/GMT/GMR computation, see 
Section 12 Annex 1 standard data derivation rule and statistical methods.
Reverse Cumulative Distribution Curves
The distribution of antibody concentrations will be displayed using Reverse Cumulative 
Distribution Curves (RCDC) by visit (Day 1, Day 8, Day 29, Day 38, Day 57, Day 64, 
and Day 85) for groups of subjects receiving vaccine and placebo [i.e. a plot for each of 
the 7 time-point reporting two curves, one for vaccine group and one for placebo group].
RCDC will be produced to display also the cumulative weight of grade 3-5 stools and the 
number of grade 3-5 stools accumulated from challenge to discharge.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 36 of 57
Derivation of immunogenicity data
a.
Screening (anti S. sonnei LPS IgG Screening-ELISA)

The cut-off value for the anti S. sonnei LPS IgG Screening-ELISA is defined by 
the local laboratory.

A seronegative subject is a subject whose titer is below the cut-off value.

A seropositive subject is a subject whose titer is greater than or equal to the cut-
off value.
b.
Immunogenicity (anti S. sonnei LPS IgG-ELISA):

The cut-off value for the anti S. sonnei LPS IgG-ELISA is defined by the GVGH 
laboratory.

Subjects will be grouped in the following groups:
o
Subjects with antibodies at baseline below Lower Limit of 
Quantification (i.e. with antibodies at baseline ≥ Lower Limit of 
quantification, LLOQ (i.e. 22 EU/ml for ELISA and IC50 of 100 for L-
SBA))
o
Subjects without antibodies at baseline below Lower Limit of 
Quantification (i.e. with antibodies at baseline < LLOQ)
Please note the following difference: seronegative at baseline is evaluated at the 
screening visit by the center lab and it is a reason for exclusion; while antibodies 
above/below LLOQ at baseline are evaluated by GVGH lab, and will determine 
subgroups to be analyzed.
All the immunogenicity analyses (ELISA and L-SBA) will be stratified by the above 
subgroups (i.e. presented overall, for subjects above LLOQ at baseline, and for subjects 
below above LLOQ at baseline).
Seroresponse is aimed to define a significant increase in anti S. sonnei LPS IgG 
concentration in post-vaccination samples; it is defined in this study as follows:

If the baseline value is greater than 50 EU/mL then an increase of at least 50% in the 
post-vaccination sample as compared to baseline [i.e. ((Post-vac minus 
baseline)/baseline)100% ≥ 50%].

If the baseline value is less or equal to 50 EU/mL then an increase of at least 
25 EU/mL in the post-vaccination sample as compared to baseline [i.e. (Post-vac 
minus baseline) ≥ 25 EU].
Note: Threshold values/increases given in the definition of seroresponse might be subject 
to change during the course of the study (e.g., in case of 
optimization/qualification/validation of the anti S. sonnei LPS-IgG-ELISA).
Additionally, all the analysis above described for immunogenicity by ELISA, will be 
repeated by subgroups defined by subjects who did or did not develop shigellosis 
(primary endpoint), and Shigellosis as defined by CHIM (secondary endpoint a.).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 37 of 57
6.5.
Analysis of safety
6.5.1.
Analysis of safety planned in the protocol
The primary analysis will be performed on the All Exposed Set.
Analysis of solicited local and systemic adverse events and other reactions
Solicited AEs will be summarized according to defined severity grading scales.
Frequencies and percentages of subjects experiencing each AE will be presented for each 
symptom severity. Summary tables showing the occurrence of any local or systemic AE 
overall and at each time point, and at each day will also be presented.
Post-vaccination/challenge solicited AE reported from Day 1 to 7 days post-
vaccination/challenge will be summarized by maximal severity and by vaccine/placebo 
group. The severity of solicited local AE erythema and induration will be summarized 
according to categories based on linear measurement.
Injection site pain and systemic reactions occurring up to 7 days after each vaccination 
will be summarized according to “mild”, “moderate” or “severe”.
Each solicited local and systemic AE will also be further summarized as “none” versus 
“any”; same summary will be reported for all local together, all systemic together, and 
local and systemic.
Analysis of unsolicited AEs
All the AEs occurring during the study, judged either as probably related, possibly 
related, or not related to vaccination/challenge by the investigator, will be recorded.
The original verbatim terms used by investigators to identify AEs in the eCRFs will be 
mapped to preferred terms using the Medical Dictionary for Regulatory Activities
(MedDRA) dictionary. The AEs will then be grouped by MedDRA preferred terms into 
frequency tables according to system organ class and PT. All reported AEs, as well as 
AEs judged by the investigator as at least possibly related to study vaccine/placebo or 
challenge agent, will be summarized according to system organ class and preferred term 
within system organ class. These summaries will be presented by vaccination group. 
When an AE occurs more than once for a subject, the maximal severity and strongest 
relationship to the vaccine/placebo group will be counted.
Separate summaries will be produced for the following categories:
a.
SAEs
b.
AESIs
c.
AEs that are possibly or probably related to vaccine/placebo or challenge agent.
d.
AEs leading to withdrawal from the study.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 38 of 57
e.
All AEs occurring within 28 days following administration of vaccination or
challenge
Data listings of all AEs will be provided by subject.
In addition, AEs in the categories above will be provided as listed data.
6.5.2.
Additional considerations
Standard data derivation procedures for safety is available in Section 12.2.5.
6.5.2.1.
Exclusion of implausible solicited Adverse Event
Some local and systemic adverse events will be directly measured by the subject and will 
not be subject to a reconciliation process, even if they are biologically implausible. 
Therefore, these implausible measurements will be removed from the analysis but 
included in listings. Implausible measurements are summarized in the Table 7. 
Table 7
Implausible Solicited Adverse Events
Parameter
Implausible measurements
Body temperature
≤ 33°C or ≥ 42°C
Erythema
≥ 900 mm
Measurements < 0 mm
Induration
≥ 500 mm
Measurements < 0 mm
6.5.2.2.
Solicited Adverse Events
All analyses will be based on the ‘as treated’ Solicited Safety Set (see Section 12.2.5). 
Post-vaccination Solicited Adverse Events will be reported from 30 minutes until 7 days 
after vaccination using structured diary cards. The analyses of solicited adverse events 
will be done separately for 30 minutes, for the remaining day, and after that, for each day 
between day 2 until day 7 included. In addition solicited adverse events ongoing after day 
7 will be presented as unsolicited AE.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 39 of 57
The list of Solicited Local and Systemic adverse events is reported in the Table 8.
Table 8
List of Local and Systemic solicited adverse events
Local adverse events
Pain at injection site
Erythema at injection site
Induration at injection site
Systemic adverse events
Arthralgia
Chills
Fatigue
Malaise
Myalgia
Fever
Headache
The maximum intensity of local injection site erythema/induration/fever will be scored at 
GSK Biologicals as in Table 9 and Table 10.
Table 9
Intensity grade for Erythema/Induration
Erythema/Induration
0:
< 25 mm
1:
25 - 50 mm
2:
> 50 -100 mm
3:
> 100 mm
Table 10
Intensity grade for fever
Fever
Grade 0
Absent
Grade 1
Mild
Grade 2
Moderate
Grade 3
Severe
< 38.0°C
38.0°C – < 39.0°C
39.0°C – <40.0°C
40.0°C
A list of Solicited AE be assessed after vaccination or after challenge agent 
administration with associated intensity is reported in the Table 11. Note that the AEs 
marked with # will be evaluated after both vaccination and challenge.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 40 of 57
Table 11
Intensity scales for solicited symptoms
Adverse Event
Intensity 
grade
Parameter
After vaccine/placebo administration
Pain at injection site
0
Absent
1
Easily tolerated.
2
Interferes with normal activity
3
Prevents normal activity.
Erythema at injection site
Record greatest surface diameter in mm
Induration at injection site
Record greatest surface diameter in mm
Fever#*
Record temperature in °C/°F
Headache#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Fatigue#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Arthralgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Malaise#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Myalgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Chills
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
After challenge agent administration
Nausea
0
Absent
1
Mild or transient; maintains reasonable intake
2
Moderate discomfort; intake decreased significantly; some activity limited
3
No significant intake and requires medical intervention
4
Hospitalization required
Abdominal cramping
0
Absent
1
No interference with daily activities
2
Some interference with daily activities not requiring medical intervention
3
Prevents daily activities and requires medical intervention
4
ER visit or hospitalization
Abdominal pain
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Gas
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 41 of 57
Adverse Event
Intensity 
grade
Parameter
Anorexia
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Vomiting
0
Absent
1
One episode within a 24-hour period
2
2 episodes within a 24-hour period
3
>2 episodes within a 24-hour period or requires medical intervention
4
ER visit or hospitalization for hypotensive shock
Diarrhea**
0
Absent
1
2-3 Grade 3-5 stools (loose or watery) or <400 g/Grade 3-5 (loose or watery) 
stools per 24 hours
2
4-5 Grade 3-5 stools (loose or watery) or 400-800 g/ (loose or watery) Grade 3-5 
stools per 24 hours
3
6 or more Grade 3-5 stools (loose or watery) or >800 g/Grade 3-5 (loose or 
watery) stools per 24 hours or requires medical intervention
4
≥ 10 loose stools (Grade 3 to 5) or 1000 grams of Grade 3 to 5 stools within 24 
hours
#Same grading is used for events present both post-vaccination and post-challenge.
*Fever is defined as temperature 38.0°C / 100.4°F. The preferred location for measuring temperature in this study 
will be the oral cavity.
**The end of a diarrheal episode occurs when a volunteer does not pass any Grade 3-5 stool within 24 hours.
ER: emergency room.
Body temperature will be broken down by route of measurement according to the 
recommendations of the Brighton collaboration and will be summarized according to the 
3 schemes described below:

by 0.5 °C increments: <36.0, 36.0 - 36.4, 36.5 - 36.9, 37.0 - 37.4, 37.5 - 37.9, 38.0 -
38.4, 38.5 - 38.9, 39.0 - 39.4, 39.5 - 39.9, ≥40.0°C

by 1.0 °C increments: <36.0, ≥36.0-<37.0, ≥37.0-<38.0, ≥ 38.0-<39.0, ≥39.0-<40, 
≥40°C
Fever, defined as a body temperature of ≥38°C irrespective of route of measurement, will 
be integrated to the summaries as a systemic adverse event.
The analyses will encompass summaries of the data on five levels:
1.
Daily reports of subjects with solicited adverse events.
2.
Time of first onset of solicited adverse events.
3.
Solicited adverse events, maximum event severity by event and interval from 30 
Min, and specifically for each day between day 2 through Day 7.
4.
Solicited adverse events and indicators of solicited adverse events, occurrence of at 
least one event by category (local, systemic) and interval from 30 Min through Day 
7.
For each of the time points or time intervals presented in the summaries, only subjects 
with at least one plausible observation (i.e., any non-missing values but excluding “Not 
done/unknown” and implausible values) for the solicited adverse events in the interval of 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 42 of 57
interest will be considered. Subjects without plausible data (i.e. missing values or 
reported as “Not done/unknown” and implausible values) will be removed from the 
denominator to prevent a downward bias (towards zero).
Level 1: Daily reports of solicited adverse event
For each of the time points only subjects with at least one plausible observation (i.e., any 
non-missing values but excluding “Not done/unknown” and implausible values) for the 
solicited adverse event in the interval of interest will be considered. Subjects without 
plausible data (i.e. missing values or reported as “Not done/unknown” and implausible 
values) will be removed from the denominator in order to prevent a downward bias 
(towards zero). Data collected will be summarized (frequencies and percentages of 
subjects) by vaccine group, solicited adverse event, vaccination number and time point. 
Level 2: Time of first onset of solicited adverse events
The time of first onset is defined, for each subject, for each solicited adverse event, as the 
time point at which the respective solicited adverse event first occurred. For erythema 
and induration the following threshold will be used: ≥25 mm. The summary will provide 
the frequencies and percentages of subjects with first onset of each solicited adverse 
events by vaccine group and by each time point. 
Level 3: Solicited adverse events, maximum event severity by event and interval
The maximum event severity will be defined if there is at least one plausible non-
missing observation (excluding “Not done/unknown” and implausible values) within this 
time interval, Each subject’s data will be aggregated across the time points of the interval 
and summarized according to the maximal severity observed for each adverse event, 
followed by a summary across subjects for each vaccine. Subjects without any solicited 
adverse events in the interval, i.e., missing values at each of the requested time points, 
will be removed from the denominator. 
Level 4: Number of days with solicited adverse events
The number of days with the adverse event is defined irrespective of severity. This means 
at least ‘mild’ solicited adverse event that are assessed qualitatively and ≥ 25 mm for 
erythema and induration. If a solicited adverse event continues beyond day 7 the period 
after day 7 is added.
Level 5: Solicited adverse events, occurrence of at least one event by category (local, 
systemic) and interval.
The occurrence of at least one solicited adverse event is defined as “any” (≥ 25 mm for 
erythema and induration) for a subject if he/she reports greater than “none” for the 
respective event and “none” otherwise. The occurrence of at least one solicited adverse
event (i.e., none versus any) will be summarized by category (i.e., local, systemic, any), 
by vaccine group, by vaccination (after each vaccination and after any vaccination) and 
by time interval.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 43 of 57
Medications to treat or prevent pain or fever will be summarized by frequencies and 
percentages of subjects reporting use of the medications from 30 min to day 7.
6.5.2.3.
Unsolicited Adverse Events
All the unsolicited adverse events occurring within 28 days following administration of 
each vaccination or occurring within 28 days following challenge administration, judged 
either as probably related, possibly related, or not related to vaccination by the 
investigator, will be recorded. The original verbatim terms used by investigators to 
identify adverse events in the CRFs will be mapped to preferred terms using the 
MedDRA dictionary. The unsolicited adverse events will then be grouped by MedDRA 
preferred terms into frequency tables according to system organ class and PT. Adverse 
events judged by the investigator as at least possibly related to study vaccine will be 
summarized by vaccine group, according to system organ class and preferred term within 
system organ class. When an unsolicited adverse event occurs more than once for a 
subject, the maximal severity and strongest relationship to the vaccine group will be 
counted.
Only vaccine-emergent adverse events (see section 9.1.4 of protocol for definition) will 
be analyzed, i.e., excluding those after a subject has given informed consent but before 
vaccination: those events will be listed with an appropriate flag.
The summaries will be presented by period of onset and will include frequency 
distributions of the different adverse events:

Onset between first vaccination and second vaccination.

Onset between second vaccination and challenge administration.
The analysis of unsolicited adverse events comprises the following categories:

Any unsolicited adverse event.

Possibly or probably related unsolicited adverse events.

Unsolicited adverse events leading to death.

Serious adverse events.

Possibly or probably related serious adverse event.

Unsolicited adverse events leading to premature withdrawal from study.

Unsolicited adverse events leading to hospitalization.

Solicited adverse events continuing beyond day 7 will be coded by MedDRA and 
combined with the respective unsolicited adverse events. 
During the course of this study, symptomatic neutropenia will be considered as AESIs.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 44 of 57
Table 12
List of potential AESI to be followed during the study
Blood disorders

Symptomatic neutropenia (all Grades)
Neutropenia is defined as decrease of neutrophil count asymptomatically or 
symptomatically. Available local laboratory ranges will be used to define neutropenia. 
This is completely diagnosed by laboratory testing for complete blood count. However 
only symptomatic neutropenia cases will be considered as AESI and reported as such.
The following grading will be used to classify neutropenia:

Grade 1: 1800-1500 cells/μL.

Grade 2: 1499-1000 cells/μL.

Grade 3: 999-500 cells/μL.

Grade 4: < 500 cells/μL.
In performing their assessment of symptomatic neutropenia cases, investigators are 
strongly advised to use Table 13 below.
Table 13
Evaluation of symptomatic neutropenia
Common presenting symptoms of neutropenia
Physical findings on examination of a subject with 
neutropenia
Low-grade fever
Fever
Sore mouth
Stomatitis
Odynophagia
Periodontal infection
Gingival pain and swelling
Cervical lymphadenopathy
Skin abscesses
Skin infection: The skin examination focuses on rashes, 
ulcers, or abscesses
Recurrent sinusitis and otitis
Splenomegaly
Symptoms of pneumonia (e.g., cough, dyspnea)
Associated petechial bleeding
Perirectal pain and irritation
Perirectal infection
Neutropenic sepsis
Other according to Investigator’s opinion
Neutropenic infection
Neutropenic colitis
Other according to Investigator’s opinion
In order to facilitate the documentation of AESI in the eCRF, a list of MedDRA preferred 
terms (PTs) and PT codes corresponding to the above diagnoses will be available to 
investigators at study start.
When there is enough evidence to make any of the above diagnoses, the AE must be 
reported as AESI. Symptoms, signs or conditions which might (or might not) represent 
the above diagnoses, should be recorded and reported as AEs but not as AESI until the 
final or definitive diagnosis has been determined, and alternative diagnoses have been 
eliminated or shown to be less likely.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 45 of 57
6.5.2.4.
Combined Solicited and Unsolicited Adverse Events
A summary of subjects with all combined solicited (regardless of their duration) and 
unsolicited adverse events will be provided. Solicited adverse events will be coded by 
MedDRA as per the following codes:
Solicited symptom
Local/Systemic 
symptom
Lower level term 
code
Corresponding Lower level term decode 
Erythema at injection 
site
local
10015150
Erythema
Induration at injection 
site
local
10060708
Induration
Pain at injection site
local
10022086
Injection site pain
Arthralgia
systemic
10003239
Arthralgia
Chills
systemic
10008531
Chills
Fatigue
systemic
10016256
Fatigue
Fever
systemic
10016558
Fever
Headache
systemic
10019211
Headache
Malaise
systemic
10025482
Malaise
Myalgia
systemic
10028411
Myalgia
For clintrial.gov and EudraCT posting purposes, a summary of combined solicited and 
unsolicited non-serious adverse events will be produced by System Organ Class and 
preferred terms and according to occurrence of each event. 
6.5.2.5.
Clinical Safety Laboratory Investigations
The investigator must assess all safety laboratory results (see Section 9.1.4 of the study 
protocol). Clinically significant modifications in hematology test values will be assessed 
by medical judgment based on interpretation of deviations from the institution’s normal 
values. Abnormal laboratory findings (e.g., clinical chemistry, hematology, urinalysis) or 
other abnormal assessments that are judged by the investigator to be clinically significant 
will be recorded as AE or SAE if they meet the definition of an AE or SAE (refer to 
Sections 9.1.1 and 9.1.2 of the Study Protocol).
Clinically significant abnormal laboratory findings or other abnormal assessments that 
are present at baseline and significantly worsen following the start of the study will also 
be reported as AEs or SAEs.
The investigator will exercise his or her medical and scientific judgement in deciding 
whether an abnormal laboratory finding or other abnormal assessment is clinically 
significant. Clinically significant modifications in hematology will be assessed by 
medical judgment based on interpretation of deviations from institution’s normal values 
and recommendations from CBER (FDA Center for Biologics Evaluation and Research) 
FDA GUIDANCE FOR INDUSTRY: Toxicity Grading Scale for Healthy Adults and 
Adolescent Volunteers Enrolled in Preventive Vaccine Clinical Trials and predefined list 
of sign and symptoms related to neutropenia.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 46 of 57
The frequencies of subjects with clinical laboratory values below, within, or above 
normal ranges will be tabulated for each clinical laboratory variable by vaccine-group 
and time-point of assessment (4 x 3 shift tables, including missing at baseline as a 
category).
Laboratory values that are outside the normal range will also be flagged in the data 
listings, along with corresponding normal ranges and assessment of clinical significance.
For subjects presenting at least one clinically significant value, an additional listing will 
be provided of all laboratory results by vaccine group, by subject, and by relevant 
parameter. Clinical significance assessed by the investigator will be presented.
6.5.2.6.
Concomitant Medication
Medications will be coded using the GSKDRUG dictionary. 
The frequencies and percentages of subjects starting/reporting concomitant 
medications/products/vaccination during all study period will be tabulated by vaccine 
group for each study dose and across doses. See Section 7.6.1 of the Study Protocol for 
the list of medications/products/vaccination recorded in the eCRF.
An overview of the protocol-required reporting periods for AEs, SAEs, and pregnancies 
is given below.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 47 of 57
Table 14
Reporting periods for collecting safety information
Timepoints
Scr
D1
D8
D29
D36
D57
D57-D64
D85
D237 (M8)
Solicited local and systemic AEs
Unsolicited AEs
AEs/SAEs leading to withdrawal from the 
study
AESI
SAEs
Pregnancies
SAEs related to study participation or 
concurrent GSK medication/vaccine
Scr: Screening
D: Day
M: Month


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 48 of 57
7.
ANALYSIS INTERPRETATION
Except for analyses on objectives with a pre-defined success criterion and an appropriate 
type I error control (see Section 3.1), comparative analyses will be descriptive with the 
aim to characterize the difference in reactogenicity and immunogenicity efficacy between 
groups. These descriptive analyses should not be interpreted.
8.
CONDUCT OF ANALYSES
8.1.
Sequence of analyses
Description
Analysis 
ID 
Disclosure 
Purpose
(CTRS=public 
posting, 
SR=study 
report, internal)
Dry run 
review 
needed (Y/N)
Study Headline 
Summary 
(SHS)requiring 
expedited 
communication to 
upper 
management 
(Yes/No)
Reference for TFL 
Interim Efficacy 
Analysis
E1_01
Efficacy results to 
BMGF for funding 
Shigella 4-C.
Yes
Yes
Section 2 of TFL 
TOC. 
Interim 
Immunogenicity
Analysis
E1_06
Immunogenicity 
results to BMGF
Yes
No
Section 3 of TFL 
TOC.
Final Analysis
E1_02
SR, CTSR
Yes
No
Section 4 of TFL 
TOC.
The analysis for the Independent Data Monitoring Committee (IDMC) is planned to be 
performed by an Independent Data Analysis Center (IDAC). This analysis is planned as 
per IDMC Charter and will be provided three times, once after each of the first three 
cohorts (36 subjects expected) have completed the challenge phase of the trial.
One Interim Efficacy Analysis is planned after the last subject of the last cohort had been 
discharged and will include all post-challenge efficacy objectives on all subjects. Tables
with efficacy results will be produced by unblinded vaccine and placebo groups, but no 
listings will be provided. Interim Efficacy Analysis will be integrated at the end of the 
study with unblinded safety listings and with Efficacy Analysis stratified by antibody 
concentration below the limit of quantification at baseline visit and by seroresponse at 
pre-challenge.
One Interim Immunogenicity Analysis is planned after latest immunogenicity lab results 
(ELISA and L-SBA) had been released. This analysis will include all secondary 
immunogenicity data (i.e. ELISA) plus SBA tertiary immunogenicity data of all subjects 
(all 4 cohorts). Tables with immunogenicity results will be produced by unblinded 
vaccine and placebo groups, but no listings will be provided. Interim ELISA 
immunogenicity analyses will be also repeated by subgroups defined by subject who did 
or did not develop shigellosis (primary endpoint), and Shigellosis as defined by CHIM 
(secondary endpoint a.).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 49 of 57
An integrated clinical study report containing all Statistical Analysis Results will be 
written and made available to the investigators after the final analysis.
If the data for tertiary endpoints become available at a later stage, (an) additional 
analysis/analyses will be performed. These data will be documented in annex(es) to the 
study report and will be made available to the investigators at that time.
8.2.
Statistical considerations for interim analyses
No statistical adjustment will be made for the interim analyses. The need of the interim 
analysis on efficacy is that it serves as Go/No Go decision for start of the 4-component 
Shigella vaccine trial.
9.
CHANGES FROM PLANNED ANALYSES
To complement the immunogenicity profile, the following timepoints were added to the
immunogenicity analysis:

Seroresponse and concentration ≥ 121 EU at 7 days after each vaccination.

Concentration ≥ 121 EU at 7 and 28 days after challenge.
To complement the immunogenicity profile, the immunogenicity analyses were repeated 
in the following subgroups:

In subject who did and did not developed shigellosis (primary endpoint)

In subject who did and did not developed shigellosis as defined by CHIM (secondary 
endpoint a.)
10.
NON-STANDARD DATA DERIVATION RULES AND 
STATISTICAL METHODS
The following sections describe additional derivation rules and statistical methods which 
are not presented in section 12.1.
10.1.
Data derivation
Specific data derivation will be put in place to derive the primary and the secondary 
efficacy endpoints before Database freeze. Details are reported in Section 12.2.7.
10.2.
Statistical Method
The Confidence Interval for Vaccine Efficacy estimated with Miettinen-Nurminen 
method for the primary objective will be complemented with Barnard test [Barnard,1945,
Barnard,1947, Barnard,1949] (BARNARD option of the EXACT statement in SAS 
FREQ procedure).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 50 of 57
The lower limit of the 90% Confidence Interval for VE calculated with Miettinen-
Nurminen method will be above zero if the p-value of the one-sided Barnard test is below 
5%.
11.
LIST OF FINAL REPORT TABLES, LISTINGS AND 
FIGURES
The TFL TOC including the mock-up tables can be found in eTMF folder Section 11.1.1.
12.
ANNEX 1 STANDARD DATA DERIVATION RULE AND 
STATISTICAL METHODS
12.1.
Statistical Method References
The 90% CIs for RRs calculated in the efficacy analyses (and the correspondent 90% CI 
for VE, defined as 1-RR) will be calculated using the Miettinen-Nurminen method 
[Miettinen, 1985].
The exact two-sided 95% CIs for a proportion within a group will be the Clopper-Pearson 
exact CI [Clopper, 1934].
12.2.
Standard data derivation
The v15 GSK standard data derivation will be adopted. However, custom programming 
will be implemented if needed.
12.2.1.
Date derivation

SAS date of birth derived from a character date:  In case day is missing, 15 is used.   
In case day & month are missing, 30June is used. This is also applicable to start date 
of Ae and medication.

Onset day for an event (ae, medication, vaccination, …): The onset day is the 
number of days between the last study vaccination & the onset/start date of the event.   
This is 1 for an event starting on the same day as a vaccination.    See SAS date 
derived in case the start date of the event is incomplete.

Duration: Duration of an event is expressed in days.   It is the number of days 
between the start & the stop dates + 1.   Therefore duration is 1 day for an event 
starting & ending on the same day.

Association of an event to the specific epoch: An adverse event belongs to Epoch 
002, if the onset date is before and excluding Visit 5 or the last contact date
(assuming last contact date is before Visit 5), whichever is coming first. An adverse 
event belongs to Epoch 003, if the onset date is subsequent to and including Visit 5 
or the last contact date (assuming last contact date is at Visit 5 or at a subsequent 
date), whichever is coming first.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 51 of 57
12.2.2.
Dose number

The study dose number is defined in reference to the number of study visits at which 
vaccination occurred.  More specifically dose 1 refers to all vaccines administered at 
the first vaccination visit while dose 2 corresponds to all vaccinations administered 
at the second vaccination visit even if this is the first time a product is administered 
to the subject. 

Relative dose: the relative dose for an event (AE, medication, vaccination) is the 
most recent study dose given before an event. In case the event takes place on the 
day a study dose is given, the related dose will be that of the study dose, even if the 
event actually took place before vaccination. Otherwise, if the event actually took 
place the same day of vaccination and before vaccination, the related dose will be 
that of the previously administered dose.   

The number of doses for a product is the number of times the product was 
administered to a subject. 

The incidence per dose is the number of vaccination visits at which an event was 
reported among all vaccination visits.  
12.2.3.
Demography

Age: Age at the reference activity, computed as the number of days between the date 
of birth and the reference activity and converted in months (= days *12 /365.25) 
(keeping 1 decimal digit).

Conversion of weight to kg
The following conversion rule is used:  

Weight in Kilogram= weight in Pounds / 2.2

Weight in Kilogram =weight in onces / 35.2
The result is rounded to 2 decimals.

Conversion of height to cm
The following conversion rule is used:  

Height in Centimetres = Height in Feet * 30.48

Height in Centimetres = Height in Inch * 2.54
The result is rounded to the unit (ie no decimal).

Conversion of temperature to °C
The following conversion rule is used:  

Temperature in °Celsius  = ((Temperature in °Fahrenheit -32) *5)/9
The result is rounded to 1 decimal.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 52 of 57
12.2.4.
Immunogenicity

For a given subject and given immunogenicity measurement, missing or non-
evaluable measurements will not be replaced. Therefore, an analysis will exclude 
subjects with missing or non-evaluable measurements.

The Geometric Mean Concentrations (GMC) calculations are performed by taking 
the anti-log of the mean of the log titre transformations. Antibody titres below the 
cut-off of the assay will be given an arbitrary value of half the cut-off of the assay for 
the purpose of GMC calculation. Refer to Section 6.4.2 for details regarding cut-off 
definition and calculations.

All CI computed will be two-sided 95% CI.
12.2.5.
Safety

For the analysis of solicited symptoms, missing or non-evaluable measurements will 
not be replaced. Therefore, the analysis of the solicited symptoms based on the 
Exposed Set will include only vaccinated subjects for doses with documented safety 
data (i.e., symptom screen completed). This corresponds to the Solicited Safety Set 
defined in the protocol (Section 11.5.3.1). More specifically the following rules will 
be used: 

Subjects who documented the absence of a solicited symptom after each of 
vaccine dose will be considered not having that symptom after that dose.

Subjects who documented the presence of a solicited symptom and fully or 
partially recorded daily measurement over the solicited period will be included 
in the summaries at that dose and classified according to their maximum 
observed daily recording over the solicited period.

Subjects who documented the presence of a solicited symptom after one dose 
without having recorded any daily measurement will be assigned to the lowest 
intensity category at that dose (i.e., 38.0°C for fever or grade 1 for other 
symptoms).

Doses without symptom sheets documented will be excluded.

For analysis of unsolicited adverse events, such as serious adverse events or adverse 
events by primary MedDRA term, and for the analysis of concomitant medications, 
all vaccinated subjects will be considered. Subjects who did not report the event or 
the concomitant medication will be considered as subjects without the event or the 
concomitant medication respectively. This corresponds to the Solicited Safety Set 
defined in the protocol (Section 11.5.3.2).
Note that for all tables described in this section, the way the percentage of subjects will 
be derived will depend on the event analyzed (see table below for details). As a result, the 
N value will differ from one table to another.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 53 of 57
Event
N used for deriving % per subject for 
Vaccination phase
N used for deriving % per dose for 
Vaccination phase
Concomitant 
vaccination
All subjects with study vaccine 
administered
All study visits with study vaccine 
administered
Solicited general 
symptom
All subjects with at least one solicited 
general symptom documented as either 
present or absent (i.e., symptom screen 
completed)
All study visits with study vaccine 
administered and with at least one solicited 
general symptom documented as either 
present or absent (i.e., symptom screen 
completed)
Solicited local 
symptom
All subjects with at least one solicited local 
symptom documented as either present or 
absent (i.e., symptom screen completed)
All study visits with study vaccine 
administered and with at least one solicited 
local symptom documented as either
present or absent (i.e., symptom screen 
completed)
Unsolicited symptom
All subjects with study vaccine 
administered 
All study visits with study vaccine 
administered
Concomitant 
medication
All subjects with study vaccine 
administered 
All study visits with study vaccine 
administered
12.2.6.
Number of decimals displayed:
The following decimal description from the decision rules will be used for the 
demography, efficacy, immunogenicity and safety/reactogenicity.
Display Table
Parameters
Number of decimal 
digits
Demographic characteristics
Mean, median age
1
Demographic characteristics
SD (age)
1
Immunogenicity
Ratio of GMT/C
2
Reactogenicity
Mean, Min, Q1, Median, Q3, Max for duration
1
All summaries
% of count, including LL & UL of CI
1
All summaries
% of difference, including LL & UL of CI
2
All summaries
p-value
3
12.2.7.
Efficacy
Specific data derivation will be put in place to derive the primary and the secondary 
efficacy endpoints before Database freeze.
An overview of the algorithms to be used to derive all efficacy endpoints is reported in 
Table 15.
Table 15
Derivation of efficacy endpoints
Endpoint
Definition / Derivation
Primary Efficacy
Shigellosis
[Shedding of S. sonnei strain 53G] AND
[(Moderate diarrhea) OR
(Severe diarrhea) OR
(oral temperature ≥ 38.5°C)] 
Derivation of Shigellosis
Moderate diarrhea
[4 to 5 stools1 within 24 hours] OR


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 54 of 57
Endpoint
Definition / Derivation
[400 to 800 grams of stools1 within 24 hours]
Severe diarrhea
[≥ 6 stools1 within 24 hours] OR
[> 800 grams of stools1 within 24 hours] OR
[intravenous fluids administration, i.e. ATC B05XA in concomitant medication] OR
[anticipation of antibiotic treatment before the 5th day after challenge]
Secondary Efficacy
a. Shigellosis as per 
CHIM definition
[Moderate diarrhea] OR
[Severe diarrhea] OR
[Dysentery] 
Derivation of Shigellosis as per CHIM definition
Moderate diarrhea
[(4 to 5 stools1 within 24 hours) OR
(400 to 800 grams of stools1 within 24 hours)]
AND2
[(oral temperature ≥ 38.0˚C) OR
(≥1 constitutional/enteric symptom3 graded ≥2) OR
[≥2 episodes of vomiting within 24 hours])
Severe diarrhea
[≥6 stools1 within 24 hours] OR
[800 grams loose stools1 within 24 hours]
Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
AND2
[oral temperature ≥38.0˚C OR
(≥1 constitutional/enteric symptom3 graded ≥2) OR
(≥2 episodes of vomiting in 24 hours)]
b. Shigellosis as defined by any one of the three following possible endpoints:
[Severe diarrhea] OR
[Moderate diarrhea AND (oral temperature ≥38.0oC OR ≥1 at least moderate 
constitutional/enteric symptom4)] OR
[Dysentery]
Derivation of Severe diarrhea
[≥ 6 stools1 within 24 hours] OR
[> 800 grams of stools1 within 24 hours]
Derivation of Moderate diarrhea AND (oral temperature ≥38.0oC OR ≥1 at least moderate constitutional/enteric 
symptom4)
(
[4 to 5 stools1 within 24 hours] OR
[400 to 800 grams of stools1 within 24 hours]
)
AND2
(
(oral temperature ≥ 38.0˚C) OR
>=1 at least moderate (i.e. >=grade 2) constitutional/enteric symptom4)


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 55 of 57
Endpoint
Definition / Derivation
)
Derivation of Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
AND2
(>=1 at least mild (i.e. >=grade 1) constitutional/enteric symptom4)
c. More Severe Shigellosis as defined by any one of the two following possible endpoints:
[(Moderate OR Severe diarrhea) AND (oral temperature ≥38.0oC OR ≥1 severe 
constitutional/enteric symptom)] OR
[Dysentery AND (oral temperature ≥38.0oC OR ≥1 severe constitutional/enteric 
symptom4)]
Derivation of Severe diarrhea
[≥ 6 stools1 within 24 hours] OR
[> 800 grams of stools1 within 24 hours]
Derivation of Moderate diarrhea
[4 to 5 stools1 within 24 hours] OR
[400 to 800 grams of stools1 within 24 hours]
Derivation of oral temperature ≥38.0oC
(oral temperature ≥ 38.0˚C)
Derivation of ≥1 severe constitutional/enteric symptom)
>=1 at least severe (i.e. >=grade 3) constitutional/enteric symptom4)
Derivation of Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
d. Shedding of S. sonnei 
strain 53G
At least one stool1 sample positive to S. sonnei strain 53G either by culture or qPCR
e. Severe diarrhea
Severe diarrhea as defined under primary endpoint
f. More severe diarrhea
[≥ 10 stools1 within 24 hours] OR
[≥ 1000 grams of stools1 within 24 hours]
g. Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
AND2
(≥1 constitutional/enteric symptom5 at least mild (i.e. >=grade 1))
h. weight of grade 3-5 
stools
weight of each stool1 during follow-up
i. weight of grade 3-5 
stools accumulated from 
challenge to discharge
For each subject sum the weight of each stool1 accumulated from challenge to 
discharge
j. number of grade 3-5 
stools
For each subject count the number of stools1 accumulated from challenge to discharge
k.
[At least one stool1 sample positive to S. sonnei strain 53G either by culture or qPCR]
AND2
[(Moderate diarrhea) OR
(Severe diarrhea) OR
(Dysentery as defined in g.) OR
(oral temperature ≥ 38.5°C) OR
(≥1 intestinal symptom6 graded ≥3)]


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 56 of 57
Endpoint
Definition / Derivation
l. 
1
[At least one stool (whichever is the grading)]
AND2 NOT
[(Moderate diarrhea) OR
(Severe diarrhea) OR
2
≥1 abdominal pain graded ≥1
3
≥1 abdominal cramps graded ≥1
4
≥1 abdominal gas graded ≥1
5
≥1 abdominal anorexia graded ≥1
6
≥1 abdominal nausea graded ≥1
7
≥1 abdominal headache graded ≥1
8
≥1 abdominal myalgia graded ≥1
9
≥1 abdominal malaise graded ≥1
10
≥1 abdominal arthralgia graded ≥1
11
≥1 oral temperature ≥ 38.5°C 
12
≥1 vomit graded ≥1
13
≥1 IV fluid administration
m. Time to onset of 
Shigellosis during the 
post-challenge period
Shigellosis is defined as in primary objective. The day associated to the first shigellosis6
is the time of onset of Shigellosis.
1Considering only stools graded 3-5
2Where AND combines conditions occurring in the 8-day post-challenge inpatient period 
3Where constitutional/enteric symptoms [symptoms list 1] are: nausea, abdominal pain, abdominal cramping, myalgia, 
arthralgia, malaise
4Where constitutional/enteric symptoms [symptoms list 2] are: headache, fatigue, arthralgia, malaise, myalgia, chills, 
nausea, abdominal cramping, abdominal pain, gas, anorexia, vomiting
5Where constitutional/enteric symptoms [symptoms list 3] are: headache, fatigue, arthralgia, malaise, myalgia, chills, 
nausea, abdominal cramping, abdominal pain, gas, anorexia, vomiting, and fever
6Where intestinal symptoms [symptoms list 4] are: abdominal pain, abdominal cramping, gas, nausea, vomiting, 
anorexia
If the conditions defining shigellosis are verified in 2 different days (e.g. shedding at day 1 and Severe Diarrhea at day 
3), the day of onset of Shigellosis is defined as the day when the latest condition is met is (e.g. day 3).
If a 24-hour period where Shigellosis definition is fulfilled covers 2 subsequent days (e.g. start day is day 2 and end 
day is day 3) the day associated to onset of shigellosis will be the one associated to start day.
13.
ANNEX 2: SUMMARY ON ELIMINATION CODES
Please refer to the exclusion matrix stored in LSAF for a comprehensive list of exclusion 
codes among all the analysis sets. 
14.
ANNEX 3: STUDY SPECIFIC MOCK TFL
Please refer to TFL TOC word file in eTMF folder Section 11.1.1 for the study specific 
mocks.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Amendment 1
03-SEP-2019
Page 57 of 57
The data display, title and footnote are for illustration purpose and will be adapted to the 
study specificity as indicated in the TFL TOC. Note that there may be few changes 
between the study specific SAP mock TFL and the final TFLs as editorial/minor changes 
do not require a SAP amendment
15.
REFERENCES
Barnard,1945 G. A., “A New Test for 2x2 Tables,” Nature, 156, 177.
Barnard,1947 G. A., “Significance Tests for 2x2 Tables,” Biometrika, 34, 123–138.
Barnard,1949 G. A , “Statistical Inference,” Journal of the Royal Statistical Society, 
Series B, 11, 115–139.
Clopper, 1934 CJ, Pearson E. The Use of Confidence or Fiducial Limits Illustrated in the 
case of the Binomial. Biometrika.;26:404-13.
Miettinen, 1985 O. S. and Nurminen, M. Comparative analysis of two rates. Statistics in 
Medicine;4,213-226.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 1 of 53
Statistical Analysis Plan
Detailed Title:
A phase IIb, randomized, placebo-controlled, single 
center, observer-blind, human-challenge study to 
evaluate the efficacy, safety and immunogenicity of 2 
vaccinations with GVGH Shigella sonnei vaccine 
(1790GAHB) administered by intramuscular route in 
healthy non-immune adult population.
eTrack study number and 
Abbreviated Title
205626 (S SONNEI MONO GMMA SBVGH-003 
[H03_03TP])
Scope:
All primary and secondary objectives pertaining to the 
above study. The Analysis Plan for the tertiary 
objectives is part of a separate SAP.
Date of Statistical Analysis 
Plan
Final: 09-Aug-2018
Co-ordinating author:
 (GVGH Expert Biostatistician)
Reviewed by:
 (GVGH Head of Clinical 
Development and Regulatory Affairs)
 (GVGH Project 
Physician)
 (Lead statistician)
 (Lead statistical Analyst)
 (Public disclosure representative)
Approved by:
 (GVGH Head of Clinical 
Development and Regulatory Affairs)
 (Lead statistician)
 (Lead statistical Analyst)
 (Lead Scientific Writer)
APP 9000058193 Statistical Analysis Plan Template ( Effective date: 14 April 2017)
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD
PPD


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 2 of 53
TABLE OF CONTENTS
PAGE
LIST OF ABBREVIATIONS.............................................................................................6
1.
DOCUMENT HISTORY............................................................................................8
2.
STUDY DESIGN ......................................................................................................8
3.
OBJECTIVES.........................................................................................................15
3.1.
Primary objective ........................................................................................15
3.2.
Secondary objectives..................................................................................15
3.3.
Tertiary objectives.......................................................................................16
4.
ENDPOINTS ..........................................................................................................17
4.1.
Case Definitions..........................................................................................17
4.2.
Primary endpoint.........................................................................................18
4.3.
Secondary endpoints ..................................................................................18
4.4.
Tertiary endpoints.......................................................................................21
5.
ANALYSIS SETS ...................................................................................................21
5.1.
Definition.....................................................................................................21
5.1.1.
All Enrolled Set ............................................................................21
5.1.2.
All Exposed Set ...........................................................................21
5.1.3.
Safety Set....................................................................................22
5.1.3.1.
Solicited Safety Set (solicited local and 
systemic adverse events and other solicited 
adverse events)..........................................................22
5.1.3.2.
Unsolicited Safety Set (unsolicited adverse 
events) .......................................................................22
5.1.3.3.
Overall Safety Set ......................................................22
5.1.4.
Full Analysis Set (FAS) for Efficacy/Immunogenicity....................22
5.1.4.1.
Full Analysis Set for Efficacy ......................................22
5.1.4.2.
Full Analysis Set for Immunogenicity..........................22
5.1.5.
Per-Protocol Set (PPS) for Efficacy/Immunogenicity....................22
5.2.
Criteria for eliminating data from Analysis Sets...........................................23
5.2.1.
Elimination from Exposed Set (ES)..............................................23
5.2.2.
Safety Set....................................................................................23
5.2.3.
Elimination from Full Analysis Set (FAS) for Efficacy ...................23
5.2.3.1.
Excluded subjects ......................................................23
5.2.4.
Elimination from Per-protocol analysis Set (PPS) for 
Efficacy........................................................................................24
5.2.4.1.
Excluded subjects ......................................................24
5.2.5.
Elimination from Full Analysis Set (FAS) for 
Immunogenicity............................................................................26
5.2.5.1.
Excluded subjects ......................................................26
5.2.6.
Elimination from Per-protocol analysis Set (PPS) for 
Immunogenicity............................................................................27
5.2.6.1.
Excluded subjects ......................................................27
5.3.
Important protocol deviation not leading to elimination from per-
protocol analysis set ...................................................................................29


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 3 of 53
6.
STATISTICAL ANALYSES.....................................................................................29
6.1.
Demography...............................................................................................29
6.1.1.
Analysis of demographics/baseline characteristics planned 
in the protocol..............................................................................29
6.1.2.
Additional considerations.............................................................29
6.2.
Exposure ....................................................................................................29
6.2.1.
Analysis of exposure planned in the protocol...............................29
6.2.2.
Additional considerations.............................................................29
6.3.
Efficacy/Effectiveness.................................................................................29
6.3.1.
Analysis of efficacy planned in the protocol..................................29
6.3.2.
Additional considerations.............................................................30
6.3.3.
Definition of shigellosis according to BMGF.................................31
6.4.
Immunogenicity...........................................................................................32
6.4.1.
Analysis of immunogenicity planned in the protocol.....................32
6.4.2.
Additional considerations.............................................................32
6.5.
Analysis of safety........................................................................................34
6.5.1.
Analysis of safety planned in the protocol ....................................34
6.5.2.
Additional considerations.............................................................35
6.5.2.1.
Exclusion of implausible solicited Adverse
Event..........................................................................35
6.5.2.2.
Solicited Adverse Events............................................35
6.5.2.3.
Unsolicited Adverse Events........................................40
6.5.2.4.
Combined Solicited and Unsolicited Adverse 
Events ........................................................................42
6.5.2.5.
Clinical Safety Laboratory Investigations ....................42
6.5.2.6.
Concomitant Medication .............................................43
7.
ANALYSIS INTERPRETATION..............................................................................45
8.
CONDUCT OF ANALYSES....................................................................................45
8.1.
Sequence of analyses.................................................................................45
8.2.
Statistical considerations for interim analyses.............................................46
9.
CHANGES FROM PLANNED ANALYSES.............................................................46
10. LIST OF FINAL REPORT TABLES, LISTINGS AND FIGURES .............................47
11. ANNEX 1 STANDARD DATA DERIVATION RULE AND STATISTICAL 
METHODS .............................................................................................................47
11.1.
Statistical Method References ....................................................................47
11.2.
Standard data derivation.............................................................................47
11.2.1.
Date derivation ............................................................................48
11.2.2.
Dose number...............................................................................48
11.2.3.
Demography................................................................................49
11.2.4.
Immunogenicity............................................................................49
11.2.5.
Safety ..........................................................................................50
11.2.6.
Number of decimals displayed:....................................................51
11.2.7.
Efficacy........................................................................................51
12. ANNEX 2: SUMMARY ON ELIMINATION CODES ................................................53
13. ANNEX 3: STUDY SPECIFIC MOCK TFL..............................................................53


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 4 of 53
LIST OF TABLES
PAGE
Table 1
Study groups and epochs foreseen in the study.......................................9
Table 2
Study groups and treatment foreseen in the study ...................................9
Table 3
Blinding of study epochs ..........................................................................9
Table 4
List of study procedures (Amended: 08 February 2018).........................12
Table 5
Intervals between study visits.................................................................14
Table 6
BMGF Diarrhea and Dysentery definitions .............................................31
Table 7
Implausible Solicited Adverse Events.....................................................35
Table 8
List of Local and Systemic solicited adverse events...............................36
Table 9
Intensity grade for Erythema/Induration..................................................36
Table 10
Intensity grade for fever..........................................................................36
Table 11
Intensity scales for solicited symptoms...................................................37
Table 12
List of potential AESI to be followed during the study .............................41
Table 13
Evaluation of symptomatic neutropenia..................................................41
Table 14
Reporting periods for collecting safety information .................................44
Table 15
Derivation of efficacy endpoints..............................................................51


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 5 of 53
LIST OF FIGURES
PAGE
Figure 1
Study Design..........................................................................................11


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 6 of 53
LIST OF ABBREVIATIONS
AE
Adverse Event
AESI
Adverse Events of Special Interest
BMGF
Bill and Melissa Gates Foundation
CBER
FDA Center for Biologics Evaluation and Research
CHIM
Controlled Human Infection Model
CI
Confidence Interval
CTRS
Clinical Trial Registry Summary
eCRF
electronic Case Report Form
ELISA
Enzyme-linked immunosorbent assay
EoS:
End of Study
ER
Emergency Room
ES
Exposed Set
EU/ml
ELISA unit per milliliter
FAS
Full Analysis Set
Fc
Fragment crystallisable
FDA
Food and Drug Administration, United States of America
GMC
Geometric mean antibody concentration
GMMA
Generalized Modules for Membrane Antigens
GMR
Geometric Mean Ratio
GSK
GlaxoSmithKline
GVGH
GSK Vaccines Institute for Global Health
HBV
Hepatitis B Virus
HCV
Hepatitis C Virus
HIV
Human Immunodeficiency Virus
HLA
Human Leukocyte Antigen
ICF
Informed Consent Form
IDAC
Independent Data Analysis Center
IDMC
Independent Data Monitoring Committee
IgG
Immunoglobulin G
IM
Intramuscular
LL
Lower Limit of the confidence interval
LPS
Lipopolysaccharide


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 7 of 53
MedDRA
Medical Dictionary for Regulatory Activities
MSD
Moderate to Severe Diarrhea
OAg
O antigen
PBMC
Peripheral Blood Mononuclear Cells
PCD
Primary Completion Date
PD
Protocol Deviation
PPS
Per Protocol Set
qPCR
quantitative Polymerase Chain Reaction
RCDC
Reverse Cumulative Distribution Curve
RR
Risk Ratio
S. sonnei
Shigella sonnei
SAE
Serious adverse event
SAP
Statistical Analysis Plan
SBA
Serum Bactericidal Assay
SBIR
GSK Biological’s Internet Randomization System
SD
Standard Deviation
sIgA
Secretory Immunoglobulin A
TFL
Tables Figures and Listings 
TOC
Table of Content
UL
Upper Limit of the confidence interval
Vacc
Vaccination
VE
Vaccine Efficacy


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 8 of 53
1.
DOCUMENT HISTORY
Date
Description
Protocol Version
09-AUG-2018
Final Version
22-JUN-2018
Amendment 2 Final
2.
STUDY DESIGN
This is a randomized, placebo-controlled, single center, observer-blind, phase 2b human 
challenge trial. The study includes a screening visit (performed between study Days -45 
to -1), 2 clinical visits with vaccination (performed at study Day 1 and Day 29), 2 clinical 
visits 7 days after each vaccination (performed at study Day 8 and Day 36), 1 clinical 
visit with challenge administration 28 days after second vaccination (performed at study 
Day 57), and 3 visits after challenge, 28 days (study Day 85), 56 days (study Day 113) 
and 6 months (study Day 237) after challenge.
This study will evaluate the efficacy, safety and immunogenicity of the 1790GAHB 
vaccine administered via intramuscular (IM) route to adults (18-50 years of age at 
enrolment). The objectives will be assessed through the conduct of the study in two 
phases: a vaccination phase with 1790GAHB vaccine or placebo followed by a challenge 
phase with S. sonnei strain 53G.
A total of 72 subjects will be divided in 4 cohorts of 18 subjects each. The vaccination 
and challenge will be done in overlapping cohorts and randomization will ensure there is 
the same number of vaccinees and controls in each cohort. However if for any reason, a 
cohort did not reach the planned 18 subjects, additional subjects can be added to the 
following cohorts. The maximum number of subjects must not be more than 20 
(maximum number of beds) in each cohort.

Experimental design: Phase IIB, observer-blind, randomized, placebo control, 
mono-centric study with two parallel groups (S. sonnei group and placebo group).

Duration of the study: Each subject will be followed up for approximately 6 months 
after challenge with the pathogenic S. sonnei strain 53G, with a total study duration 
of approximately 32 weeks (i.e., 8 months) for each study subject.

Epoch 001: Starting at Screening Visit (Day -45 to Day -1) and ending before 
Visit 1 (Day 1).

Epoch 002: Starting the day of randomization and first vaccination (Visit 1) and 
ending before the receipt of the challenge agent, 28 days after second vaccination 
(Visit 5).

Epoch 003: Starting with the receipt of the challenge agent at 28 days after 
second vaccination (Visit 5) and ending 6 months after challenge (Visit 8).

Primary completion date (PCD): Visit 8 (6 months after challenge).
Refer to Glossary Section of the protocol for the definition of PCD.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 9 of 53

End of Study (EoS): Last testing results released of samples collected for primary 
and secondary objectives at Visit 8.
Refer to Glossary Section of the protocol for the definition of EoS.

Study groups:
Table 1
Study groups and epochs foreseen in the study
Study 
groups
Number of 
subjects
Age (Min - Max)
Epochs
Epoch 001
Epoch 002
Epoch 003
Screening
1st and 2nd vaccination
Challenge
S. sonnei
36
18 years – 50 years
x
x
x
Placebo
36
18 years – 50 years
x
x
x
Table 2
Study groups and treatment foreseen in the study
Treatment name
Vaccine/ placebo/
challenge agent name
Study Groups
S. sonnei
Placebo
S. sonnei
1790GAHB
x
Placebo
GAHB-Placebo
x
Challenge
S. sonnei 53G strain
x
x

Control: Placebo control with GAHB-Placebo with the same composition as the 
vaccine except the active ingredient. GAHB-Placebo will also be used as diluent for 
bed-side mixing of the vaccine.

Vaccination schedule: Subjects will receive 2 doses of either the study vaccine or 
placebo 28 days apart. At 28 days after the second dose, all subjects will receive the 
challenge dose.

Treatment allocation: Following the screening period before the first vaccination 
(Day -45 to Day -1), subjects will be randomized in a 1:1 ratio to receive either the 
study vaccine or the placebo.

Blinding: The study will be observer-blind.
Table 3
Blinding of study epochs
Study Epochs
Blinding
Screening (Epoch 001)
N/A
1st and 2nd vaccination (Epoch 002)
observer-blind
Challenge (Epoch 003)
observer-blind


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 10 of 53
An overview of the study design is given in Figure 1 and a list of study procedures is 
reported in Table 4. For further details please refer to Section 3 of the protocol.
Randomization
After obtaining the signed and dated ICF from the subject and having checked the 
eligibility of the subject, the site staff in charge of the vaccine administration will access 
GSK Biological’s Internet Randomization System (SBIR). Upon providing the subject 
identification number, the randomization system will determine the study group and will 
provide the treatment number to be used for each dose.
The number of each administered treatment must be recorded in the eCRF (electronic 
Case Report Form) on the Vaccine Administration screen.
The target will be to enroll approximately 72 eligible subjects (36 per treatment group) 
who will be randomly assigned to two study groups in a (1: 1) ratio. The randomization 
algorithm will use a minimization procedure accounting for study. The block size used
for the material randomization list is 6.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 11 of 53
Figure 1
Study Design
Scr: Screening
N: Number of subjects
B: Blood sampling
S: Stool sampling
U: Urine sampling


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 12 of 53
Table 4
List of study procedures (Amended: 08 February 2018)
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient stay Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to 
Day -1
Day 1
Day 3 and 
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to 
Day 65 8
Day 
85
Day 
113
Day 237
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9 Inpatient stay
Post-challenge
Informed consent
●
Check inclusion/exclusion criteria
●
●
●
Collect demographic data
●
Measure/record height and weight
●
Medical history
●
History directed physical examination
O
O
O
O
O
O
Physical examination
●
●
●
●
Urine pregnancy test 1
●
●
●
●
●
Check contraindications to vaccination
O
O
O
Pre-vaccination/placebo/challenge agent 
administration body temperature
●
●
●
Vaccine/placebo/challenge agent administration
Study group and treatment number 
allocation
●
Recording of administered treatment 
number
●
●
Vaccine/placebo administration
●
●
Challenge with S. sonnei 53G
●
Laboratory assays
Blood sampling for antibody response 
(~20 mL)
●2, 3
●
●2
●
●2, 3
●4
●
Blood sampling for PBMC isolation (α4β7 
plasmablasts response and 
transcriptomics) (~50 mL)
●
●
●
●4
Blood sampling for hematology (~5 mL) 5
●
●
●
●
●
●
Blood sampling for biochemical analysis 
(~5 mL)
●


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 13 of 53
Epoch
Screening
Vaccination
Challenge
Type of contact
Screening 
visit
Visit 1
Phone Call
Visit 2
Visit 3
Phone call
Visit 4
Visit 5
Inpatient stay Visit 6 Visit 7
Visit 8
Timepoints (days)
Day -45 to 
Day -1
Day 1
Day 3 and 
Day 7
Day 8
Day 29
Day 31 and 
Day 35
Day 36
Day 57
Day 57 to 
Day 65 8
Day 
85
Day 
113
Day 237
(Month 8)
Sampling timepoints
Screening
Pre-vacc 1
Post-
vacc 1
Pre-vacc 2
Post-
vacc 2
Pre-
challenge9 Inpatient stay
Post-challenge
Serology for virology: HIV, HBV, HCV 
(~10 mL)
●
Blood test for HLA-B27 and local anti S. 
sonnei LPS IgG (Screening-ELISA) (~15 
mL)
●
Urine sampling for urinalysis 6
●
●
Stool sample for sIgA
●
●
●
●4
Stool sample for microbiome testing 7
●
●
Stool assessment: weight, consistency, 
blood and S. sonnei by culture and qPCR
●
Safety assessment
Record any concomitant 
medications/vaccinations
●
●
●
●
●
●
●
●
●
Distribution of diary cards
O
O
Return of diary cards
●
●
Diary card transcription by investigator
●
●
Recording of solicited adverse events (1–
7 days post-vaccination)
●
●
Recording of non-serious adverse events 
within 28 days post-vaccination
●
●
●
●
Recording of AESI, SAEs and 
pregnancies
●
●
●
●
●
●
●
●
●
●
Recording of SAEs related to study 
participation, or to a concurrent GSK 
medication/vaccine
●
●
●
●
●
●
●
●
●
●
Study Conclusion
●
V: Visit, D: Day, Vacc: Vaccination; HIV: Human Immunodeficiency Virus, HCV: Hepatitis C Virus, HBV: Hepatitis B Virus, ELISA: Enzyme-linked immunosorbent assay, AESI: 
Adverse Events of Specific Interest, SAEs: Serious Adverse Events.
● is used to indicate a study procedure that requires documentation in the individual eCRF.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 14 of 53
O is used to indicate a study procedure that does not require documentation in the individual eCRF.
1Female subjects will be randomized and study vaccine/placebo or challenge agent may only be administered if the pregnancy test is negative.
2Serum bactericidal assay will be performed at these visits in addition to the S. sonnei LPS IgG antibody response.
3Fc glycosylation test on leftover serum samples will be performed at these visits in addition to the S. sonnei LPS IgG antibody response and serum bactericidal assay.
4Sampling to be done 7 days after challenge agent administration (i.e., Day 64).
5Additionally, hematology is repeated weekly until resolution if neutropenia occurs. On the day of vaccination/challenge, sampling will be done before vaccination/challenge
6Urine dipstick to be done for all subjects and, in case of abnormal results, a urine culture is to be performed (urinalysis).
7Before vaccination/challenge (Day 1/Day 57 sample can be collected by the subject at most a week before and stored in a freezer).
8Sampling to be done daily during inpatient stay and if subject is still shedding 7 days post-challenge administration (Day 64). However, all subjects even if not shedding anymore will 
remain in the inpatient stay until 7 days post-challenge and will be discharged on Day 65.
9 Samples collection can be performed between Day 56 and Day 57.
Whenever possible, the investigator should arrange study visits within the interval described in Table 5.
Table 5
Intervals between study visits
Interval
Optimal length of interval
Allowed interval
Screening visit Visit 1
-7 days
-45 days – -1 days
Visit 1 Phone Call
3 days
2 days - 6 days
Visit 1 Visit 2
7 days
7 days - 10 days
Visit 1 Visit 3
28 days
26 days - 33 days
Visit 3 Phone call
3 days
2 days - 6 days
Visit 3 Visit 4
7 days
7 days - 10 days
Visit 3 Visit 5
28 days
26 days - 33 days
Visit 5 Inpatient stay
9 days
9 days - as needed
Visit 5 Visit 6
28 days
28 days - 35 days
Visit 5 Visit 7
56 days
56 days - 70 days
Visit 5 Visit 8
180 days
166 days - 194 days


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 15 of 53
3.
OBJECTIVES
3.1.
Primary objective
Efficacy
To demonstrate the efficacy of two vaccinations with 25 µg of 1790GAHB vaccine in 
healthy adults compared to placebo in reducing shigellosis, fulfilling the primary protocol 
case definition, after challenge with S. sonnei strain 53G.
Criterion:
Vaccine efficacy (VE) of 1790GAHB vaccine will be shown if the lower limit (LL) of the 
90% confidence interval (CI) of VE will be above zero.
Refer to Section 4.1 below for the protocol case definition of shigellosis and to Section 
4.2 for the definition of the primary endpoint.
3.2.
Secondary objectives
Efficacy

To determine the efficacy of the 1790GAHB vaccine compared to placebo against:

Shigellosis, as per definition requested by the Controlled Human Infection Model
(CHIM) expert working group (see Section 6.3.3).

Shedding of S. sonnei strain 53G

Severe diarrhea.

More severe diarrhea.

Dysentery.

Weight of all grade 3-5 stools.

The total number of grade 3-5 stools.

Confirmed S. sonnei 53G shedding AND [moderate or severe diarrhea OR 
dysentery OR presence of fever 38.5°C OR presence of one or more severe 
intestinal symptoms (abdominal pain, cramping, nausea, vomiting …)].

Disease not fulfilling the protocol primary case definition for shigellosis 
associated or not with mild to moderate symptoms including: passing loose stool 
(not meeting the protocol definition of moderate or severe diarrhea), abdominal 
pain, abdominal cramps, gas, anorexia, nausea, headache, myalgia, malaise, 
arthralgia, fever, vomiting and IV fluid administration.

Time to onset of shigellosis after challenge


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 16 of 53
Safety

To assess the safety and reactogenicity of the 1790GAHB vaccine in terms of 
solicited symptoms, unsolicited symptoms, serious adverse events (SAEs), adverse 
events of special interest (AESI) and laboratory parameters.

To assess safety after challenge in terms of SAEs, AESI and laboratory parameters.
Immunogenicity

To evaluate the IgG ELISA (Enzyme-linked immunosorbent assay) immunogenicity 
profile of the 1790GAHB vaccine at 7, and 28 days after the first and second 
vaccination (IgG ELISA coated with O antigen (OAg) containing Lipopolysaccharide 
(LPS)).

To evaluate the immunogenicity profile of the 1790GAHB vaccine at pre-challenge 
and at 7 and 28 days after challenge (IgG ELISA coated with OAg containing LPS).

To assess seroresponse for anti-S. sonnei LPS at 7, and 28 days after first and second 
vaccination.

To assess post vaccination concentration ≥ 121 EU/ml for anti-LPS S. sonnei at 28 
days after first and second vaccination
Refer to Section 4.3 for the definition of the secondary endpoints.
3.3.
Tertiary objectives
The following tertiary objectives which are part of the study exploratory objectives may 
be evaluated in addition to the primary and secondary objectives and will complement 
assessment of the vaccine immunogenicity profile:

Evaluate Secretory Immunoglobulin A (sIgA) in stool at Day 1 and 7 days after first 
and second vaccination and 7 days after challenge (Day 64).

Evaluate presence and migration of α4β7 plasmablast at Day 1 and 7 days after first 
and second vaccination and 7 days after challenge (Day 64).

Evaluate serum bactericidal activity against S. sonnei at Day 1 and 28 days after first 
and second vaccination.

Evaluate correlation between serum anti-S. sonnei LPS IgG level, serum bactericidal 
activity titer, shigellosis, shedding, mild, moderate, severe or more severe diarrhea, 
and dysentery after challenge.

Evaluate glycosylation of fragment crystallisable (Fc) portion of IgG antibodies at 
Day 1 and 28 days after second vaccination and association with clinical protection 
and/or serological endpoints.

Evaluate gene expression signatures at Day 1 and 7 days after first and second 
vaccination and 7 days after challenge (Day 64).

Investigate gut microbiome at Day 1 and 28 days after second vaccination and its 
potential association with protection and immune response.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 17 of 53
These last two tertiary objectives involve pharmacogenomics testing. Refer to the
Glossary of the protocol for the definition of Pharmacogenomics.
Refer to Section 4.4 for the definition of the tertiary endpoints. Details for the analysis of 
the tertiary objective will be reported in a please refer to a subsequent SAP.
4.
ENDPOINTS
4.1.
Case Definitions
Stools
Stools will be graded as follows:

Grade 1: firm formed;

Grade 2: soft formed;

Grade 3: viscous opaque liquid or semi-liquid which assumes the shape of the bowl;

Grade 4: watery opaque liquid;

Grade 5: clear watery or mucoid liquid.
Diarrhea
For the purpose of this study, diarrhea is defined as:

Moderate diarrhea: 4 to 5 loose or watery (Grade 3 to 5) stools or 400 to 800 grams of 
Grade 3 to 5 stools within 24 hours.

Severe diarrhea: 6 or more loose or watery (Grade 3 to 5) stools or > 800 grams of 
Grades 3 to 5 stools within 24 hours or required medical intervention.

More severe diarrhea: 10 loose or watery (Grade 3 to 5) stools or 1000 grams of 
Grade 3 to 5 stools within 24 hours or required medical intervention.

Note: Diarrhea severity classes are not mutually exclusive, as more severe diarrhea is 
a subset of severe diarrhea.

In case of severe diarrhea, medical intervention is defined as intravenous (IV) fluids 
administration or anticipation of antibiotic treatment before the 5th day after 
challenge.

In case of more severe diarrhea, medical intervention is defined as ER visit or 
hospitalization for hypotensive shock. 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 18 of 53
Dysentery
For the purpose of this study, dysentery is defined as:

A Grade 3, 4, or 5 stool with gross blood on at least 2 occasions within 24 hours AND 
presence of constitutional symptoms (i.e. fever, headache, fatigue,  arthralgia, 
malaise, myalgia, chills, nausea, abdominal cramping, abdominal pain,   gas, 
anorexia, vomiting).
Shigellosis
For the challenge phase of the study, the protocol primary case definition for shigellosis 
is:

Shedding of S.sonnei 53G accompanied by moderate or severe diarrhea OR shedding 
with an oral temperature ≥ 38.5°C.
4.2.
Primary endpoint
Primary Efficacy endpoint
Vaccine efficacy (VE) will be evaluated in the 7-day post-challenge inpatient period after 
visit 5 (i.e. from challenge to discharge) by:

Attack Rate of shigellosis (fulfilling the protocol case definition) occurring within a 
period starting with the challenge visit and lasting up to the end of the inpatient stay, 
in all subjects. The attack rate of shigellosis is expressed as proportion of subjects per 
group with at least one episode of shigellosis after challenge.
4.3.
Secondary endpoints
Secondary Efficacy endpoints
All the secondary endpoints will be assessed in the 7-day post-challenge inpatient period
after visit 5 (i.e. from challenge to discharge).
All subjects receiving the 1790GAHB vaccine vs. placebo will be compared according to 
the following endpoints:
a.
Attack rate of shigellosis, with shigellosis defined by CHIM expert working group
(see Section 6.3.3)
b. Proportion of subjects with shedding of S. sonnei strain 53G.
Shedding of S. sonnei strain 53G is defined as positivity of at least one stool sample 
either by culture or quantitative Polymerase Chain Reaction (qPCR).
c.
Proportion of subjects with at least one episode of severe diarrhea.
d. Proportion of subjects with at least one episode of more severe diarrhea.
e.
Proportion of subjects with at least one episode of dysentery.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 19 of 53
f.
Mean (arithmetic or geometric, according to distribution of the data) weight of grade 
3-5 stools per subject, for all subjects and for subjects with at least one grade 3-5 
stool (i.e. grade 3-5 stool).
g. Mean weight per subject of all grade 3-5 stools accumulated from challenge to 
discharge
h. Mean number of grade 3-5 stools per subject from challenge to discharge.
i.
Proportion of subjects with confirmed S. sonnei 53G shedding AND [moderate or 
severe diarrhea, OR dysentery, OR presence of fever (oral temperature ≥ 38.5°C), OR 
presence of at least one intestinal symptom (abdominal pain, abdominal cramping, 
gas, nausea, vomiting, anorexia) graded as severe].
j.
Disease not fulfilling the protocol case definition for shigellosis associated or not with 
mild to moderate symptoms including: 
1.
Proportion of subjects with at least one stool (not meeting the protocol definition 
of moderate or severe or more severe diarrhea), 
2.
Proportion of subjects with at least one episode of abdominal pain, 
3.
Proportion of subjects with at least one episode of abdominal cramps, 
4.
Proportion of subjects with at least one episode of gas, 
5.
Proportion of subjects with at least one episode of anorexia, 
6.
Proportion of subjects with at least one episode of nausea, 
7.
Proportion of subjects with at least one episode of headache, 
8.
Proportion of subjects with at least one episode of myalgia, 
9.
Proportion of subjects with at least one episode of malaise, 
10. Proportion of subjects with at least one episode of arthralgia, 
11. Proportion of subjects with at least one episode of fever (oral temperature ≥ 
38.5°C), 
12. Proportion of subjects with at least one episode of vomiting, and 
13. Proportion of subjects with at least one IV fluid administration.
k. Time to onset of Shigellosis during the post-challenge period
All endpoints are measured from challenge to discharge.
Note that in the primary and secondary efficacy endpoints, fever is defined as oral 
temperature ≥ 38.5°C, in agreement with challenge model set up at Cincinnati. However, 
fever as solicited event will be defined as a body temperature of ≥38°C irrespective of 
route of measurement, in agreement with latest GSK standards and Brighton 
collaboration rules (see Section 6.5.2.2).
For derivation of the primary and secondary endpoints refer to Section 11.2.7.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 20 of 53
Secondary Safety endpoints
The measures of safety will include:

Number of subjects with solicited local and systemic reactions during 7 days 
following each vaccination. Solicited local reactions include injection site erythema, 
injection site induration and injection site pain; solicited systemic reactions include 
headache, arthralgia, chills, fatigue, malaise, myalgia, and fever (as measured orally).

Number of subjects with reported unsolicited adverse events (of any nature and 
severity) during 28 days following vaccination and challenge, i.e. up to second 
vaccination visit (when evaluating after first vaccination) whichever comes first, and 
up to challenge visit (when evaluating after second vaccination) whichever comes
first, and up to 28th day after challenge.

Number of subjects with reported SAEs throughout the study duration.

Number of subjects with reported AESI (i.e., symptomatic neutropenia) throughout 
the study duration.

Number of subjects with deviations from normal values (i.e. reference range and/or 
clinically significant value, according to local ranges) of hematological tests at 7 days 
after first and second vaccination (Visit 2 and Visit 4) and at last study visit (Visit 8).
Secondary Immunogenicity endpoints
The measures of immunogenicity, against the LPS of S. sonnei, will include:

IgG geometric mean concentrations (GMCs) pre-vaccination (Day 1), 7 days after 
first vaccination (Day 8), 28 days after first vaccination (Day 29), 7 days after 
second vaccination (Day 36), and 28 days after second vaccination (Day 57) overall 
and by antibody concentration at baseline (i.e., above vs. below the assay detection 
limit), as determined by anti-S. sonnei LPS IgG ELISA and applicable within-subject 
geometric mean ratios (GMRs) between post vaccination and baseline samples
(D8/D1, D29/D1, D36/D1 and D57/D1).

IgG GMC pre-challenge (Day 57), 7 and 28 days after challenge (Day 64 and Day 
85) as determined by anti-S. sonnei LPS IgG ELISA and applicable within-subject 
geometric mean ratios (GMRs) between post-challenge and pre-challenge samples 
(D64/D57, and D85/D57).

Number and percentage of seroresponders for anti-S. sonnei LPS at 28 days after 
first and second vaccination. Seroresponse is aimed to define a significant increase in 
anti S. sonnei LPS IgG concentration in post-vaccination samples and relies on the 
definition already used in a previous phase II study in Kenyan population. See 
Section 6.4.2 for definition of seroresponders.

Number and percentage of subjects with titers post vaccination concentration ≥ 121 
EU/ml for anti-LPS S. sonnei at 28 days after first and second vaccination 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 21 of 53
4.4.
Tertiary endpoints

Specific anti-S. sonnei LPS IgA antibody concentration in stool samples at Day 1, 7 
days after first and second vaccination and 7 days after challenge (Day 64).

Frequency of S. sonnei LPS specific IgG α4β7+ antibody secreting cells per 10^6 
Peripheral Blood Mononuclear Cells (PBMC) plasmablast at Day 1 and 7 days after 
first and second vaccination and 7 days after challenge (Day 8, Day 36 and Day 64).

Glycosylation profiles of IgG antibodies at Day 1 and 28 days after second 
vaccination (Day 57).

Correlation between serum anti-S. sonnei LPS IgG concentration, Serum 
Bactericidal Assay (SBA) titer, shigellosis, shedding, Moderate to Severe Diarrhea 
(MSD), dysentery and mild diarrhea after challenge.

The number of differential expressed genes 7 days after first and second vaccination 
and 7 days after challenge by comparing the relative abundance of mRNA sequences 
compared to Day 1 (pre-vaccination baseline).

Diversity and frequency of microbiome components (taxa and/or genes according to 
technology) at Day 1 prior to vaccination and 28 days after second vaccination (Day 
57).
Exploratory analysis for hypotheses generation will include the evaluation of the 
association of the microbiome components with efficacy and immunogenicity described 
above.
Additionally exploratory endpoints might be evaluated as per ICF. A further SAP will be 
provided for the analysis of the tertiary endpoints and reported in an Annex to the 
Clinical Study Report.
5.
ANALYSIS SETS
5.1.
Definition
5.1.1.
All Enrolled Set
All screened subjects who provide informed consent, and provide demographic and/or 
baseline screening assessments and received a Subject ID, regardless of the subject’s 
randomization and treatment status in the study.
5.1.2.
All Exposed Set
All subjects in the enrolled set who receive a study vaccination. Please note that 
throughout Section 5, vaccine/study vaccination refer to study vaccine or placebo.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 22 of 53
5.1.3.
Safety Set
5.1.3.1.
Solicited Safety Set (solicited local and systemic adverse events and 
other solicited adverse events)
All subjects in the All Exposed Set with any valid data on solicited AEs.
5.1.3.2.
Unsolicited Safety Set (unsolicited adverse events)
All subjects in the Exposed Set that do not withdraw early and are lost to follow-up on a 
vaccination visit.
5.1.3.3.
Overall Safety Set
All subjects who are in the Solicited Safety Set and/or Unsolicited Safety Set.
5.1.4.
Full Analysis Set (FAS) for Efficacy/Immunogenicity
5.1.4.1.
Full Analysis Set for Efficacy 
All subjects in the All Enrolled Set who are randomized, receive a study vaccination and 
provide efficacy data.
5.1.4.2.
Full Analysis Set for Immunogenicity
All subjects in the All Enrolled Set who are randomized, receive at least one study 
vaccination and provide post vaccination immunogenicity data at the relevant timepoints.
In case of vaccination error, subjects in the FAS sets will be analyzed “as randomized” 
(i.e. according to the vaccine a subject was designated to receive, which may be different 
from the vaccine the subject actually received).
5.1.5.
Per-Protocol Set (PPS) for Efficacy/Immunogenicity
All subjects in the FAS for Efficacy/Immunogenicity who:

Correctly receive the vaccines (i.e., receive the vaccine to which the subjects is 
randomized and at the scheduled timepoints).
Have no protocol deviations leading to exclusion as defined prior to unblinding / analysis.
Are not excluded due to other reasons defined prior to unblinding or analysis.
PPS are subsets of FAS and should be always defined even if the objectives do not 
require it.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 23 of 53
Examples for subjects excluded due to other reasons than protocol deviations are:

Subjects who withdrew informed consent.
The primary analysis will be based on the PPS for efficacy and immunogenicity. 
However, selected efficacy and immunogenicity secondary analyses will be performed on 
both FAS and PPS sets (more details in Section 6).
5.2.
Criteria for eliminating data from Analysis Sets
Elimination codes are used to identify subjects to be eliminated from analysis.  Detail is 
provided below for each set. Consolidated tables are also available in Section 12.
5.2.1.
Elimination from Exposed Set (ES)
Code 1030 (Study vaccine not administered at all) and code 900 (invalid informed 
consent or fraud data) will be used for identifying subjects eliminated from ES.
5.2.2.
Safety Set
Code 1150 (Subject did not provide any post-vaccination/post-challenge unsolicited 
safety data) will be used for identifying subjects eliminated from the Unsolicited Safety 
Set.
Code 1160 (Subject did not provide any post-vaccination solicited safety data) will be 
used for identifying subjects eliminated from the Solicited Safety Set.
Subjects with codes 2155 will be eliminated from the Overall Safety Set.
5.2.3.
Elimination from Full Analysis Set (FAS) for Efficacy 
5.2.3.1.
Excluded subjects
A subject will be excluded from the FAS for Efficacy analysis under the following 
conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered for both doses


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 24 of 53
3000.a
Did not undergo challenge
3000.c
Missed or incomplete assessment (after challenge)
5.2.4.
Elimination from Per-protocol analysis Set (PPS) for Efficacy
5.2.4.1.
Excluded subjects
A subject will be excluded from the PPS analysis for Efficacy under the following 
conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data:
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered for both doses
1040
Administration of concomitant vaccine(s) forbidden in the protocol*
1050
Randomization failure
1060
Randomization code was broken
1070
Vaccination not according to protocol:
Incomplete treatment course
Route of administration is wrong or unknown
Treatment administered is correct but is not compatible with 
treatment regimen associated to treatment schedule
Wrong replacement or study treatment administered
Study treatment not prepared as per protocol (e.g. reconstitution)
Site of injection for vaccine
1500
Incorrect Volume was given
1500
Study treatment not available at site for administration
1500
Study treatment administered while contraindication
1500
Pregnancy
1080
Vaccine temperature deviation
1090
Expired vaccine administered


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 25 of 53
2010
Protocol violation (inclusion/exclusion criteria)
2040
Administration of any medication forbidden by the protocol*
2050
medical condition forbidden
2060
infection related to the vaccine
2070
infection not related to the vaccine
2080
Subjects did not comply with vaccination schedule
2130
Subject not planned to be sampled for their all sampling visits:
Testing performed on samples not aligned with ICF
Collection of multiple samples when not required
Subjects bled but not supposed to be bled
Sample discard/destruction not completed as per protocol/SPM/ICF
Sample destroyed and should not have been destroyed
3000.a
Did not undergo challenge
3000.b
Challenge administered out of the window
3000.c
Missed or incomplete assessment (after challenge)
3000.d
Challenge impacted by temperature excursion
3000.e
Challenge not prepared as per protocol (e.g. reconstitution)
3000.f
Challenge administered while contraindication
*See protocol Section 7.6.2 for specific details.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 26 of 53
5.2.5.
Elimination from Full Analysis Set (FAS) for Immunogenicity 
5.2.5.1.
Excluded subjects
A subject will be excluded from the FAS for Immunogenicity analysis under the 
following conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered at all
2100
Serological results not available post-vaccination:
Missed assessment (subject early terminated prior to the visit)
Missed assessment (subject continues participation in the study)
Low volume (not sufficient to perform testing)
No samples collected for subject (and should have been collected)
Mislabeling (sample not tested)
2120
Obvious incoherence or abnormality or error in data  (for Antibody 
determination):
Temperature deviations from range defined in protocol and/or SPM –
refrigerator
Temperature deviation from range defined in protocol and/or SPM - -
20Freezer
Temperature deviation from range defined in protocol and/or SPM - -
45 freezer
Temperature deviation from range defined in protocol and/or SPM - -
80 freezer
Central/internal/external lab deviations
Mislabeling (sample tested)
*See protocol Section 5.3.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 27 of 53
5.2.6.
Elimination from Per-protocol analysis Set (PPS) for 
Immunogenicity
5.2.6.1.
Excluded subjects
A subject will be excluded from the PPS analysis for Immunogenicity under the 
following conditions 
Code
Condition under which the code is used
900
Invalid informed consent or fraud data
Signed informed consent not available on site
Informed consent not signed and/or dated by subject
Informed consent not signed prior to any study procedure
Fraudulent Data
1030
Study vaccine not administered 
1040
Administration of concomitant vaccine(s) forbidden in the protocol*
1050
Randomization failure
1060
Randomization code was broken 
1070
Vaccination not according to protocol:
Incomplete treatment course
Route of administration is wrong or unknown
Treatment administered is correct but is not compatible with 
treatment regimen associated to treatment schedule
Wrong replacement or study treatment administered
Study treatment not prepared as per protocol (e.g. reconstitution)
Site of injection for vaccine
1500
Incorrect Volume was given
1500
Study treatment not available at site for administration
1500
Study treatment administered while contraindication
1500
Pregnancy
1080
Vaccine temperature deviation
1090
Expired vaccine administered
2010
Protocol violation (inclusion/exclusion criteria)**
2040
Administration of any medication forbidden by the protocol*


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 28 of 53
2050
medical condition forbidden
2060
infection related to the vaccine
2070
infection not related to the vaccine
2080
Subjects did not comply with vaccination schedule
2090
Subjects did not comply with blood sample schedule
2100
Serological results not available post-vaccination:
Missed assessment (subject early terminated prior to the visit)
Missed assessment (subject continues participation in the study)
Low volume (not sufficient to perform testing)
No samples collected for subject (and should have been collected)
mislabeling (sample not tested)
2120
Obvious incoherence or abnormality or error in data (for Antibody 
determination):
Temperature deviations from range defined in protocol and/or SPM –
refrigerator
Temperature deviation from range defined in protocol and/or SPM - -
20Freezer
Temperature deviation from range defined in protocol and/or SPM - -
45 freezer
Temperature deviation from range defined in protocol and/or SPM - -
80 freezer
Central/internal/external lab deviations
Mislabeling (sample tested)
2130
Subject not planned to be sampled:
Testing performed on samples not aligned with ICF
Collection of multiple samples when not required
Subjects bled but not supposed to be bled
Sample discard/destruction not completed as per protocol/SPM/ICF
Sample destroyed and should not have been destroyed
*See protocol Section 7.6.2 for specific details.
**See protocol Section 5.3.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 29 of 53
5.3.
Important protocol deviation not leading to elimination from 
per-protocol analysis set 
Important protocol deviations not leading to elimination from PPS and FAS will be
defined in the Protocol Deviation Management Plan.
6.
STATISTICAL ANALYSES
Note that standard data derivation rule and stat methods are described in Section 11
Annex 1 and will not be repeated below.
6.1.
Demography
6.1.1.
Analysis of demographics/baseline characteristics planned in the 
protocol
Descriptive statistics (mean, standard deviation (SD), median, minimum and maximum) 
for age, height and weight at enrolment will be calculated overall and by vaccine/placebo 
group.
Distributions of subjects by gender and geographic ancestry will be summarized for the 
Exposed Set.
6.1.2.
Additional considerations
Demography data will be tabulated also for the All Enrolled Set.
6.2.
Exposure
6.2.1.
Analysis of exposure planned in the protocol
Not applicable.
6.2.2.
Additional considerations
The frequencies and percentages of subjects with vaccination will be summarized overall 
and by vaccine/placebo group. Data will be tabulated for the All Exposed Set.
6.3.
Efficacy/Effectiveness
6.3.1.
Analysis of efficacy planned in the protocol
VE will be evaluated at the end of study period. VE will be estimated as 1-RR where RR 
is the risk ratio (proportion of subjects reporting the disease in the vaccinated group over 
the proportion in the placebo group) together with 90% CIs.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 30 of 53
Subjects with missing values of efficacy endpoints will be excluded from analyses (i.e. 
complete-case analysis) since they are considered missing completely at random, i.e. not 
informative and with no impact on inferences.
6.3.2.
Additional considerations
All the efficacy objectives (i.e. primary and secondary) will be evaluated in the PPS.
For the primary efficacy endpoint, VE will be assessed as 1-RR, where RR is the ratio of 
proportion of subjects with shigellosis in the vaccinated group on the proportion of 
subjects with shigellosis in the placebo group. As per protocol definition, vaccine 
efficacy in reduction of shigellosis will be demonstrated if the lower limit of the 90% CI 
of VE is above zero (see Section 11.1 for methods of calculation of the 90% CI for VE).
The following calculation will be performed for all secondary efficacy endpoints,
according to the nature of the data:
In case of endpoints measured as proportion (endpoints from a. to g., k., and l. sub-
endpoints in Section 4.3), VE and 95% CI will be calculated as described above in the 
primary endpoint.
For count endpoint (i.e. total number of grade 3-5 stools) the RR will be estimated as the 
rate of grade 3-5 stools in vaccinated subjects divided by the rate of grade 3-5 stools in 
placebo. 95% CI for this rate ratio will be calculated from an unadjusted negative 
binomial model, in order to take into account possible over-dispersion of data (DIST=NB 
in GENMOD SAS procedure); a P-value from the associated two-tailed Wald will be 
considered statistically significant at alpha level of 0.05.
Continuous endpoint (i.e. weight of grade 3-5 stools per subjects, weight of grade 3-5 
stools per subject in those with at least a grade 3-5 stools, and weight of grade 3-5 stools 
accumulated from challenge to discharge per subject) will be compared using unequal 
variance two-sample t-test in case of normality of data, unequal variance two-sample t-
test on the log values in case log-values are normally distributed, or by Wilcoxon 2-
sample test otherwise. In case of comparison via log-values, the geometric mean will be 
calculated as well as the arithmetic mean and associated 95% CI. In all cases a P-value 
from two-tailed test will be considered statistically significant at alpha level of 0.05.
Time to event endpoint (i.e. hours from challenge administration to onset of shigellosis) 
will be visually depicted by a Kaplan-Meier cumulative incidence curves, and compared 
using the Log-rank test, with P-value considered statistically significant at al alpha level 
of 0.05.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 31 of 53
Sensitivity analysis
As sensitivity analyses, the analysis for primary efficacy objective (i.e. assessing 
reduction of shigellosis) and for secondary efficacy objective a. (i.e. assessing reduction 
of shigellosis, with shigellosis defined by CHIM expert working group consensus 
meeting) will be repeated:
Using FAS, instead of PPS.
Using a confidence level of 95%, instead of 90% on the PPS.
Subgroup analysis
The analysis for primary efficacy objective will be repeated for the two subgroups of 
subjects who were responders or non responders at the pre-challenge visit 
immunogenicity assessment.
6.3.3.
Definition of shigellosis according to BMGF
After protocol approval, a specific definition of shigellosis proposed by the CHIM expert 
working group consensus meeting, different from the one defined as primary efficacy 
objective, was explicitly requested by the Bill and Melissa Gates Foundation (BMGF)
and therefore added among the secondary efficacy objectives/endpoints.
BMGF shigellosis definition is the following:
Moderate diarrhea OR severe diarrhea OR dysentery
With moderate diarrhea, severe diarrhea, and dysentery specifically defined as per Table 
6.
Table 6
BMGF Diarrhea and Dysentery definitions
Primary Endpoint
Definition
Severe Diarrhea
≥6 loose stools* in 24 hours 
OR >800 grams loose stools* in 24 hours
Moderate Diarrhea
[4-5 loose stools* in 24 hours 
OR 400-800 grams loose stools* in 24 hours] 
AND 
[oral temperature ≥38.0˚C 
OR ≥1 moderate constitutional/enteric symptom‡ 
OR ≥2 episodes of vomiting in 24 hours]
Dysentery
≥2 loose stools* with gross blood (hemoccult positive) in 24 hours 
AND 
[oral temperature ≥38.0˚C 
OR ≥1 moderate constitutional/enteric symptom 
OR ≥2 episodes of vomiting in 24 hours]
* grade 3 to 5 stools
‡Nausea, abdominal pain/cramping, myalgia/arthralgia, malaise


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 32 of 53
6.4.
Immunogenicity
6.4.1.
Analysis of immunogenicity planned in the protocol
Analysis of binary variables:
The number and percentages of subjects will be summarized. Two-sided 95% CIs for the 
percentages will be computed.
Missing values of immunogenicity will be excluded from analyses (i.e. complete-case 
analysis) since they are considered missing completely at random, i.e. not informative 
and with no impact on inferences.
Analysis of continuous variables:
Antibody concentration below the limit of detection in the respective assay will be set to 
half the limit for the purposes of analysis. The limit will be calculated as the average limit 
of detection for the assays done on Day 1 sera. The antibody concentrations/titers will be 
logarithmically transformed (base10) to fulfil the normal distribution assumption. GMCs 
will be calculated, with their associated two-sided 95% CIs, by exponentiating the 
corresponding log-transformed means and their 95% CI.
Additionally, within-subject geometric mean ratios (GMRs) will be computed for 
geometric mean concentrations at each time point after vaccination versus baseline (Day 
1) and after challenge versus pre-challenge (Day 57). The GMRs and 95% CIs will be 
constructed by exponentiating the mean within-subject differences in log-transformed 
titers and the corresponding 95% CIs. GMR will be calculated only for subjects with 
valid baseline or pre-challenge valid immunogenicity results.
6.4.2.
Additional considerations
The PPS will be the primary analysis set for the immunogenicity objectives; however, a 
subset of immunogenicity objectives will be evaluated also in the FAS.
The percentage of subjects with seroresponse by titer at baseline and with post 
vaccination antibody level ≥ 121 IgG units and associated two-sided 95% Clopper-
Pearson CIs will be computed by vaccine group at each visit.
Unadjusted GMCs and associated two-sided 95% CIs will be computed for each group 
(i.e. vaccine and placebo) at each visit (i.e. Visit 1-Day 1, Visit 2-Day 8, Visit 3-Day 29, 
Visit 4-Day 36, Visit 5-Day 57, End of inpatient stay-Day 64, and Visit 6-Day 85). For 
each group, unadjusted GMCs and their 95% CIs will be obtained by exponentiating 
(base 10) the means and the lower and upper limits of the 95% CIs of the log-transformed 
concentrations (base 10). Additionally, within-subject unadjusted GMRs and associated 
two-sided 95% CIs will be computed for Day 8, Day 29, Day 36, and Day 57, 
respectively versus baseline and for Day 64 and Day 85 respectively versus Day 57 (pre-
challenge).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 33 of 53
For further details on standard business rule for GMC/GMR computation, see Section 
REF _Ref508290693 \r \h \* MERGEFORMAT 11 Annex 1.Reverse Cumulative
Distribution Curves
The distribution of antibody concentrations will be displayed using Reverse Cumulative 
Distribution Curves (RCDC) by visit (Day 1, Day 8, Day 29, Day 38, Day 57, Day 64, 
and Day 85) for groups of subjects receiving vaccine and placebo [i.e. a plot for each of 
the 7 time-point reporting two curves, one for vaccine group and one for placebo group].
RCDC will be produced to display also the cumulative weight of grade 3-5 stools and the 
number of grade 3-5 stools accumulated from challenge to discharge.
Derivation of immunogenicity data
a.
Screening (anti S. sonnei LPS IgG Screening-ELISA)

The cut-off value for the anti S. sonnei LPS IgG Screening-ELISA is defined by 
the local laboratory.

A seronegative subject is a subject whose titer is below the cut-off value.

A seropositive subject is a subject whose titer is greater than or equal to the cut-
off value.
b. Immunogenicity (anti S. sonnei LPS IgG-ELISA):

The cut-off value for the anti S. sonnei LPS IgG-ELISA is defined by the GVGH 
laboratory.

Subjects will be grouped in the following groups:
o
Subjects with detectable antibodies at baseline (i.e. with antibodies at 
baseline ≥ Lower Limit of quantification, LLOQ)
o
Subjects without detectable antibodies at baseline (i.e. with antibodies at 
baseline < LLOQ)
Please note the following difference: seronegative at baseline is evaluated at the 
screening visit by the center lab and it is a reason for exclusion; while detectable 
antibodies at baseline are evaluated by GVGH lab, and will determine subgroups to be 
analyzed. 
All the immunogenicity analyses will be stratified by the above subgroups (i.e. presented 
overall, for subjects with detectable antibodies at baseline, and for subjects without 
detectable antibodies at baseline).
Seroresponse is aimed to define a significant increase in anti S. sonnei LPS IgG 
concentration in post-vaccination samples; it is defined in this study as follows:

If the baseline value is greater than 50 EU/mL then an increase of at least 50% in the 
post-vaccination sample as compared to baseline [i.e. ((Post-vac minus 
baseline)/baseline)100% ≥ 50%].


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 34 of 53

If the baseline value is less or equal to 50 EU/mL then an increase of at least 
25 EU/mL in the post-vaccination sample as compared to baseline [i.e. (Post-vac 
minus baseline) ≥ 25 EU].
Note: Threshold values/increases given in the definition of seroresponse might be subject 
to change during the course of the study (e.g., in case of 
optimization/qualification/validation of the anti S. sonnei LPS-IgG-ELISA).
6.5.
Analysis of safety
6.5.1.
Analysis of safety planned in the protocol
The primary analysis will be performed on the All Exposed Set.
Analysis of solicited local and systemic adverse events and other reactions
Solicited AEs will be summarized according to defined severity grading scales.
Frequencies and percentages of subjects experiencing each AE will be presented for each 
symptom severity. Summary tables showing the occurrence of any local or systemic AE 
overall and at each time point, and at each day will also be presented.
Post-vaccination/challenge solicited AE reported from Day 1 to 7 days post-
vaccination/challenge will be summarized by maximal severity and by vaccine/placebo 
group. The severity of solicited local AE erythema and induration will be summarized 
according to categories based on linear measurement.
Injection site pain and systemic reactions occurring up to 7 days after each vaccination 
will be summarized according to “mild”, “moderate” or “severe”.
Each solicited local and systemic AE will also be further summarized as “none” versus 
“any”; same summary will be reported for all local together, all systemic together, and 
local and systemic.
Analysis of unsolicited AEs
All the AEs occurring during the study, judged either as probably related, possibly 
related, or not related to vaccination/challenge by the investigator, will be recorded.
The original verbatim terms used by investigators to identify AEs in the eCRFs will be 
mapped to preferred terms using the Medical Dictionary for Regulatory Activities
(MedDRA) dictionary. The AEs will then be grouped by MedDRA preferred terms into 
frequency tables according to system organ class and PT. All reported AEs, as well as 
AEs judged by the investigator as at least possibly related to study vaccine/placebo or 
challenge agent, will be summarized according to system organ class and preferred term 
within system organ class. These summaries will be presented by vaccination group. 
When an AE occurs more than once for a subject, the maximal severity and strongest 
relationship to the vaccine/placebo group will be counted.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 35 of 53
Separate summaries will be produced for the following categories:
a.
SAEs
b. AEs that are possibly or probably related to vaccine/placebo or challenge agent.
c.
AEs leading to withdrawal from the study.
d. All AEs occurring within 28 days following administration of vaccination or
challenge
Data listings of all AEs will be provided by subject.
In addition, AEs in the categories above will be provided as listed data.
6.5.2.
Additional considerations
Standard data derivation procedures for safety is available in Section 11.2.5.
6.5.2.1.
Exclusion of implausible solicited Adverse Event
Some local and systemic adverse events will be directly measured by the subject and will 
not be subject to a reconciliation process, even if they are biologically implausible. 
Therefore these implausible measurements will be removed from the analysis but 
included in listings. Implausible measurements are summarized in the Table 7. 
Table 7
Implausible Solicited Adverse Events
Parameter
Implausible measurements
Body temperature
≤ 33°C or ≥ 42°C
Erythema
≥ 900 mm
Measurements < 0 mm
Induration
≥ 500 mm
Measurements < 0 mm
6.5.2.2.
Solicited Adverse Events
All analyses will be based on the ‘as treated’ Solicited Safety Set (see Section 11.2.5).
Post-vaccination Solicited Adverse Events will be reported from 30 minutes until 7 days 
after vaccination using structured diary cards. The analyses of solicited adverse events 
will be done separately for 30 minutes, 4 hours, 6 hours, and after that, for each day 
between day 2 until day 7 included. In addition solicited adverse events ongoing after day 
7 will be presented as unsolicited AE.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 36 of 53
The list of Solicited Local and Systemic adverse events is reported in the Table 8.
Table 8
List of Local and Systemic solicited adverse events
Local adverse events
Pain at injection site
Erythema at injection site
Induration at injection site
Systemic adverse events
Arthralgia
Chills
Fatigue
Malaise
Myalgia
Fever
Headache
The maximum intensity of local injection site erythema/induration/fever will be scored at 
GSK Biologicals as in Table 9 and Table 10.
Table 9
Intensity grade for Erythema/Induration
Erythema/Induration
0:
< 25 mm
1:
≥25 - 50 mm
2:
> 50 - 100 mm
3:
> 100 mm
Table 10
Intensity grade for fever
Fever
Grade 0
Absent
Grade 1
Mild
Grade 2
Moderate
Grade 3
Severe
< 38.0°C
38.0°C – < 39.0°C
39.0°C – <40.0°C
40.0°C
A list of Solicited AE be assessed after vaccination or after challenge agent 
administration with associated intensity is reported in the Table 11. Note that the AEs 
marked with # will be evaluated after both vaccination and challenge.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 37 of 53
Table 11
Intensity scales for solicited symptoms
Adverse Event
Intensity 
grade
Parameter
After vaccine/placebo administration
Pain at injection site
0
None
1
Mild: Any pain neither interfering with nor preventing normal every day activities.
2
Moderate: Painful when limb is moved and interferes with every day activities
3
Severe: Significant pain at rest. Prevents normal every day activities.
Erythema at injection site
Record greatest surface diameter in mm
Induration at injection site
Record greatest surface diameter in mm
Fever#*
Record temperature in °C/°F
Headache#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
Fatigue#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
Arthralgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
Malaise#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
Myalgia#
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
Chills
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
That prevents normal activity
After challenge agent administration
Nausea
0
Absent
1
Mild or transient; maintains reasonable intake
2
Moderate discomfort; intake decreased significantly; some activity limited
3
No significant intake and requires medical intervention
4
Hospitalization required
Abdominal cramping
0
Absent
1
No interference with daily activities
2
Some interference with daily activities not requiring medical intervention
3
Prevents daily activities and requires medical intervention
4
ER visit or hospitalization
Abdominal pain
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Gas
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 38 of 53
Adverse Event
Intensity 
grade
Parameter
Anorexia
0
Absent
1
Easily tolerated
2
Interferes with normal activity
3
Prevents normal activity
Vomiting
0
Absent
1
One episode within a 24-hour period
2
2 episodes within a 24-hour period
3
>2 episodes within a 24-hour period or requires medical intervention
4
ER visit or hospitalization for hypotensive shock
Diarrhea**
0
Normal
1
2-3 Grade 3-5 stools (loose or watery) or <400 g/Grade 3-5 (loose or watery) 
stools per 24 hours
2
4-5 Grade 3-5 stools (loose or watery) or 400-800 g/ (loose or watery) Grade 3-5 
stools per 24 hours
3
6 or more Grade 3-5 stools (loose or watery) or >800 g/Grade 3-5 (loose or 
watery) stools per 24 hours or requires medical intervention
4
10 loose stools (Grade 3 to 5) or 1000 grams of Grade 3 to 5 stools within 24 
hours or ER visit or hospitalization for hypotensive shock
#Same grading is used for events present both post-vaccination and post-challenge.
*Fever is defined as temperature 38.0°C / 100.4°F. The preferred location for measuring temperature in this study 
will be the oral cavity.
**The end of a diarrheal episode occurs when a volunteer does not pass any Grade 3-5 stool within 24 hours.
ER: emergency room.
Body temperature will be broken down by route of measurement according to the 
recommendations of the Brighton collaboration and will be summarized according to the 
3 schemes described below:

by 0.5 °C increments: <36.0, 36.0 - 36.4, 36.5 - 36.9, 37.0 - 37.4, 37.5 - 37.9, 38.0 -
38.4, 38.5 - 38.9, 39.0 - 39.4, 39.5 - 39.9, ≥40.0°C

by 1.0 °C increments: <36.0, ≥36.0-<37.0, ≥37.0-<38.0, ≥ 38.0-<39.0, ≥39.0-<40, 
≥40°C
Fever, defined as a body temperature of ≥38°C irrespective of route of measurement, will 
be integrated to the summaries as a systemic adverse event.
The analyses will encompass summaries of the data on five levels:
1.
Daily reports of subjects with solicited adverse events.
2.
Time of first onset of solicited adverse events.
3.
Solicited adverse events, maximum event severity by event and interval from 30 
Min, 4 hours, 6 hours, and specifically for each day between day 2 through Day 7.
4.
Solicited adverse events and indicators of solicited adverse events, occurrence of at 
least one event by category (local, systemic) and interval from 30 Min through Day 
7.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 39 of 53
For each of the time points or time intervals presented in the summaries, only subjects 
with at least one plausible observation (i.e., any non-missing values but excluding “Not 
done/unknown” and implausible values) for the solicited adverse events in the interval of 
interest will be considered. Subjects without plausible data (i.e. missing values or 
reported as “Not done/unknown” and implausible values) will be removed from the 
denominator to prevent a downward bias (towards zero).
Level 1: Daily reports of solicited adverse event
For each of the time points only subjects with at least one plausible observation (i.e., any 
non-missing values but excluding “Not done/unknown” and implausible values) for the 
solicited adverse event in the interval of interest will be considered. Subjects without 
plausible data (i.e. missing values or reported as “Not done/unknown” and implausible 
values) will be removed from the denominator in order to prevent a downward bias 
(towards zero). Data collected will be summarized (frequencies and percentages of 
subjects) by vaccine group, solicited adverse event, vaccination number and time point. 
Level 2: Time of first onset of solicited adverse events
The time of first onset is defined, for each subject, for each solicited adverse event, as the 
time point at which the respective solicited adverse event first occurred. For erythema 
and induration the following threshold will be used: ≥ 25 mm. The summary will provide 
the frequencies and percentages of subjects with first onset of each solicited adverse 
events by vaccine group and by each time point. 
Level 3: Solicited adverse events, maximum event severity by event and interval
The maximum event severity will be defined if there is at least one plausible non-
missing observation (excluding “Not done/unknown” and implausible values) within this 
time interval, Each subject’s data will be aggregated across the time points of the interval 
and summarized according to the maximal severity observed for each adverse event, 
followed by a summary across subjects for each vaccine. Subjects without any solicited 
adverse events in the interval, i.e., missing values at each of the requested time points, 
will be removed from the denominator. 
Level 4: Number of days with solicited adverse events
The number of days with the adverse event is defined irrespective of severity. This means 
at least ‘mild’ solicited adverse event that are assessed qualitatively and ≥ 25 mm for 
erythema and induration. If a solicited adverse event continues beyond day 7 the period 
after day 7 is added.
Level 5: Solicited adverse events, occurrence of at least one event by category (local, 
systemic) and interval.
The occurrence of at least one solicited adverse event is defined as “any” (≥ 25 mm for 
erythema and induration) for a subject if he/she reports greater than “none” for the 
respective event and “none” otherwise. The occurrence of at least one solicited adverse 
event (i.e., none versus any) will be summarized by category (i.e., local, systemic, any), 


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 40 of 53
by vaccine group, by vaccination (after each vaccination and after any vaccination) and 
by time interval.
Medications to treat or prevent pain or fever will be summarized by frequencies and 
percentages of subjects reporting use of the medications from 30 min to day 7.
6.5.2.3.
Unsolicited Adverse Events
All the unsolicited adverse events occurring within 28 days following administration of 
each vaccination or occurring within 28 days following challenge administration, judged 
either as probably related, possibly related, or not related to vaccination by the 
investigator, will be recorded. The original verbatim terms used by investigators to 
identify adverse events in the CRFs will be mapped to preferred terms using the 
MedDRA dictionary. The unsolicited adverse events will then be grouped by MedDRA 
preferred terms into frequency tables according to system organ class and PT. Adverse 
events judged by the investigator as at least possibly related to study vaccine will be 
summarized by vaccine group, according to system organ class and preferred term within 
system organ class. When an unsolicited adverse event occurs more than once for a 
subject, the maximal severity and strongest relationship to the vaccine group will be 
counted.
Only vaccine-emergent adverse events (see section 9.1.4 of protocol for definition) will 
be analyzed, i.e., excluding those after a subject has given informed consent but before 
vaccination: those events will be listed with an appropriate flag.
The summaries will be presented by period of onset and will include frequency 
distributions of the different adverse events:

Onset between first vaccination and second vaccination.

Onset between second vaccination and challenge administration.
The analysis of unsolicited adverse events comprises the following categories:

Any unsolicited adverse event.

Possibly or probably related unsolicited adverse events.

Unsolicited adverse events leading to death.

Serious adverse events.

Possibly or probably related serious adverse event.

Unsolicited adverse events leading to premature withdrawal from study.

Unsolicited adverse events leading to hospitalization.

Solicited adverse events continuing beyond day 7 will be coded by MedDRA and 
combined with the respective unsolicited adverse events. 
During the course of this study, symptomatic neutropenia will be considered as AESIs.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 41 of 53
Table 12
List of potential AESI to be followed during the study
Blood disorders

Symptomatic neutropenia (all Grades)
Neutropenia is defined as decrease of neutrophil count asymptomatically or 
symptomatically. Available local laboratory ranges will be used to define neutropenia. 
This is completely diagnosed by laboratory testing for complete blood count. However 
only symptomatic neutropenia cases will be considered as AESI and reported as such.
The following grading will be used to classify neutropenia:

Grade 1: 1800-1500 cells/mL.

Grade 2: 1499-1000 cells/mL.

Grade 3: 999-500 cells/mL.

Grade 4: < 500 cells/mL.
In performing their assessment of symptomatic neutropenia cases, investigators are 
strongly advised to use Table 13 below.
Table 13
Evaluation of symptomatic neutropenia
Common presenting symptoms of neutropenia
Physical findings on examination of a subject with 
neutropenia
Low-grade fever
Fever
Sore mouth
Stomatitis
Odynophagia
Periodontal infection
Gingival pain and swelling
Cervical lymphadenopathy
Skin abscesses
Skin infection: The skin examination focuses on rashes, 
ulcers, or abscesses
Recurrent sinusitis and otitis
Splenomegaly
Symptoms of pneumonia (e.g., cough, dyspnea)
Associated petechial bleeding
Perirectal pain and irritation
Perirectal infection
Neutropenic sepsis
Other according to Investigator’s opinion
Neutropenic infection
Neutropenic colitis
Other according to Investigator’s opinion
In order to facilitate the documentation of AESI in the eCRF, a list of MedDRA preferred 
terms (PTs) and PT codes corresponding to the above diagnoses will be available to 
investigators at study start.
When there is enough evidence to make any of the above diagnoses, the AE must be 
reported as AESI. Symptoms, signs or conditions which might (or might not) represent 
the above diagnoses, should be recorded and reported as AEs but not as AESI until the 
final or definitive diagnosis has been determined, and alternative diagnoses have been 
eliminated or shown to be less likely.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 42 of 53
6.5.2.4.
Combined Solicited and Unsolicited Adverse Events
A summary of subjects with all combined solicited (regardless of their duration) and 
unsolicited adverse events will be provided. Solicited adverse events will be coded by 
MedDRA as per the following codes:
Solicited symptom
Local/Systemic 
symptom
Lower level term code
Corresponding Lower level term decode 
Erythema at injection site
local
10015150
Erythema
Induration at injection site
local
10060708
Induration
Pain at injection site
local
10022086
Injection site pain
Arthralgia
systemic
10003239
Arthralgia
Chills
systemic
10008531
Chills
Fatigue
systemic
10016256
Fatigue
Fever
systemic
10016558
Fever
Headache
systemic
10019211
Headache
Malaise
systemic
10025482
Malaise
Myalgia
systemic
10028411
Myalgia
For clintrial.gov and EudraCT posting purposes, a summary of combined solicited and 
unsolicited non-serious adverse events will be produced by System Organ Class and 
preferred terms and according to occurrence of each event. 
6.5.2.5.
Clinical Safety Laboratory Investigations
The investigator must assess all safety laboratory results (see Section 9.1.4 of the study 
protocol). Clinically significant modifications in hematology test values will be assessed 
by medical judgment based on interpretation of deviations from the institution’s normal 
values. Abnormal laboratory findings (e.g., clinical chemistry, hematology, urinalysis) or 
other abnormal assessments that are judged by the investigator to be clinically significant 
will be recorded as AE or SAE if they meet the definition of an AE or SAE (refer to 
Sections 9.1.1 and 9.1.2 of the Study Protocol).
Clinically significant abnormal laboratory findings or other abnormal assessments that 
are present at baseline and significantly worsen following the start of the study will also 
be reported as AEs or SAEs.
The investigator will exercise his or her medical and scientific judgement in deciding 
whether an abnormal laboratory finding or other abnormal assessment is clinically 
significant. Clinically significant modifications in hematology will be assessed by 
medical judgment based on interpretation of deviations from institution’s normal values 
and recommendations from CBER (FDA Center for Biologics Evaluation and Research) 
FDA GUIDANCE FOR INDUSTRY: Toxicity Grading Scale for Healthy Adults and 
Adolescent Volunteers Enrolled in Preventive Vaccine Clinical Trials and predefined list 
of sign and symptoms related to neutropenia.
The frequencies of subjects with clinical laboratory values below, within, or above 
normal ranges will be tabulated for each clinical laboratory variable by vaccine-group 
and time-point of assessment (4 x 3 shift tables, including missing at baseline as a 
category).


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 43 of 53
Laboratory values that are outside the normal range will also be flagged in the data 
listings, along with corresponding normal ranges and assessment of clinical significance.
For subjects presenting at least one clinically significant value, an additional listing will 
be provided of all laboratory results by vaccine group, by subject, and by relevant 
parameter. Clinical significance assessed by the investigator will be presented.
6.5.2.6.
Concomitant Medication
Medications will be coded using the GSKDRUG dictionary. 
The frequencies and percentages of subjects starting/reporting concomitant 
medications/products/vaccination during all study period will be tabulated by vaccine 
group for each study dose and across doses. See Section 7.6.1 of the Study Protocol for 
the list of medications/products/vaccination recorded in the eCRF.
An overview of the protocol-required reporting periods for AEs, SAEs, and pregnancies 
is given below.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 44 of 53
Table 14
Reporting periods for collecting safety information
Timepoints
Scr
D1
D8
D29
D36
D57
D57-D64
D85
D237 (M8)
Solicited local and systemic AEs
Unsolicited AEs
AEs/SAEs leading to withdrawal from the 
study
AESI
SAEs
Pregnancies
SAEs related to study participation or 
concurrent GSK medication/vaccine
Scr: Screening
D: Day
M: Month


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 45 of 53
7.
ANALYSIS INTERPRETATION
Except for analyses on objectives with a pre-defined success criterion and an appropriate 
type I error control (see Section 3.1), comparative analyses will be descriptive with the 
aim to characterize the difference in reactogenicity and immunogenicity efficacy between 
groups. These descriptive analyses should not be interpreted.
8.
CONDUCT OF ANALYSES
8.1.
Sequence of analyses
Description
Analysis 
ID 
Disclosure 
Purpose
(CTRS=public 
posting, 
SR=study 
report, internal)
Dry run 
review 
needed (Y/N)
Study Headline 
Summary 
(SHS)requiring 
expedited 
communication to 
upper 
management 
(Yes/No)
Reference for TFL 
Interim Efficacy 
Analysis
E1_01
SR
Y
Yes
Tables 14.4.1.1 to 
14.4.7 from 
205626 (S 
SONNEI MONO 
GMMA SBVGH-
003 [H03_03TP]) 
TOC
Final Analysis
E1_02
SR, CTSR
Y
No
205626 (S 
SONNEI MONO 
GMMA SBVGH-
003 [H03_03TP]) 
TOC
The analysis for the Independent Data Monitoring Committee (IDMC) is planned to be 
performed by an Independent Data Analysis Center (IDAC). This analysis is planned as 
per IDMC Charter and will be provided three times, once after each of the first three 
cohorts (36 subjects expected) have completed the challenge phase of the trial.
One interim analysis is intended after the last subject of the last cohort had been 
discharged and will include all post-challenge efficacy objectives not requiring laboratory 
data on all subjects. In other words, all efficacy endpoints reported in Section 4.2 and 4.3
will be analyzed, but the positivity to shedding of S. sonnei 53G will be assessed only by 
culture results and not by qPCR.    
An integrated clinical study report containing all data will be written and made available 
to the investigators after the final analysis.
If the data for tertiary endpoints become available at a later stage, (an) additional 
analysis/analyses will be performed. These data will be documented in annex(es) to the 
study report and will be made available to the investigators at that time.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 46 of 53
8.2.
Statistical considerations for interim analyses
No statistical adjustment will be made for the interim analyses. The need of the interim 
analysis on efficacy is that it serves as Go/No Go decision for start of the 4-component 
Shigella vaccine trial.
9.
CHANGES FROM PLANNED ANALYSES
Below is reported a list of major changes from protocol Amendment 2 (22-Jun-2018) to 
this SAP. At the moment of SAP finalization, all the below changes are under 
implemented in the Protocol Amendment Form, and will be implemented in the 
upcoming Amendment 3 of the Protocol.
1.
The BMGF requested a new shigellosis definition byCHIM (Controlled Human 
Infection Model) working group after protocol approval. It was added as secondary 
efficacy endpoint.
2.
Additional efficacy endpoints had been added after late revision of the SAP by 
clinical team: 
a.
Weight of grade 3-5 stool, instead of weight of grade 3-5 diarrhea episodes.
b. Total number of grade 3-5 stool, instead of total number of grade 3-5 diarrhea 
episodes.
c.
Time to onset of shigellosis after challenge
3.
Though data were collected, analysis of Immunogenicity at 7 days after each vaccine 
was missing, therefore it was added.
4.
Analysis of percentage of subjects with immunogenicity ≥ 121 EU/ml after 
vaccination was added, as 121 EU is an historical value of a panel of 87 Israeli 
convalescent subjects after natural infection by S. Sonnei.
5.
Medical interventions needed in case of “Severe Diarrhea” and “More Severe 
Diarrhea” had been clarified.
6.
As it is of interest to explore whether the efficacy of vaccine differs in the groups of 
subjects with different pre-challenge antibody titers the following subgroup analysis 
was added:
d. The analysis for the primary endpoints will be repeated for the two subgroups of 
subjects above and below the limit of antibody quantification at the pre-challenge 
visit.
7.
The interim analysis of immunogenicity on a subset of subjects and visits was 
removed, as it is not necessary.
8.
As requested by FDA, unsolicited events, are going to be collected also 28 days after 
challenge.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 47 of 53
10.
LIST OF FINAL REPORT TABLES, LISTINGS AND 
FIGURES
The TFL TOC provides the list of tables/listings and figures needed for the study report. 
It also identifies the tables eligible for each analyses and their role (synopsis, in-text, 
post-text, SHS, CTRS,…).  Note that all TFL aimed to be included as post-text are noted 
as post-text even if these are tabulation of individual data such as listing of SAE.  The 
post-text material contains all source material for the study report and accordingly a post-
text table may be redundant with an in-text table.
!
The TFL TOC is reported in the “205626 (S SONNEI MONO GMMA SBVGH-003 
(H03_03TP)) TOC 09Aug2018”. The latest GSK TOC and mock-up catalogues 
available in SDD were used
 
!
Standard mock-up tables are reported in “205626 (S SONNEI MONO GMMA 
SBVGH-003 [H03_03TP]) Mock-up catalogue 09Aug2018.docx”
!
Specific ad hoc tables not present in the catalogue (i.e. all efficacy tables) are reported 
in “205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP]) Mock-up 
customs 09Aug2018.xlsx”
Please note that the above TOC and mock-up are intended as a draft and will be finalized 
before Database freeze.
11.
ANNEX 1 STANDARD DATA DERIVATION RULE AND 
STATISTICAL METHODS
11.1.
Statistical Method References
The 90% CIs for RRs calculated in the efficacy analyses (and the correspondent 90% CI 
for VE, defined as 1-RR) will be calculated using the Miettinen-Nurminen method 
[Miettinen O., Nurminen M. Comparative analysis of two rates. Statistics in Medicine, 4, 
213–226, 1985].
The exact two-sided 95% CIs for a proportion within a group will be the Clopper-Pearson 
exact CI [Clopper CJ, Pearson ES. The use of confidence or fiducial limits illustrated in 
the case of binomial. Biometrika. 1934;26:404-413].
11.2.
Standard data derivation
The v15 GSK standard data derivation will be adopted. However, custom programming 
will be implemented if needed.
PPD


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 48 of 53
11.2.1.
Date derivation

SAS date of birth derived from a character date:  In case day is missing, 15 is used.   
In case day & month are missing, 30June is used. This is also applicable to start date 
of Ae and medication.

Onset day for an event (ae, medication, vaccination, …): The onset day is the number 
of days between the last study vaccination & the onset/start date of the event.   This is 
1 for an event starting on the same day as a vaccination.    See SAS date derived in 
case the start date of the event is incomplete.

Duration: Duration of an event is expressed in days.   It is the number of days 
between the start & the stop dates + 1.   Therefore duration is 1 day for an event 
starting & ending on the same day.

Association of an event to the specific epoch: An adverse event belongs to Epoch 
002, if the onset date is before and excluding Visit 5 or the last contact date
(assuming last contact date is before Visit 5), whichever is coming first. An adverse 
event belongs to Epoch 003, if the onset date is subsequent to and including Visit 5 or 
the last contact date (assuming last contact date is at Visit 5 or at a subsequent date), 
whichever is coming first.
11.2.2.
Dose number

The study dose number is defined in reference to the number of study visits at which 
vaccination occurred.  More specifically dose 1 refers to all vaccines administered at 
the first vaccination visit while dose 2 corresponds to all vaccinations administered at 
the second vaccination visit even if this is the first time a product is administered to 
the subject. 

Relative dose: the relative dose for an event (AE, medication, vaccination) is the most 
recent study dose given before an event. In case the event takes place on the day a 
study dose is given, the related dose will be that of the study dose, even if the event 
actually took place before vaccination,. Otherwise, if the event actually took place the 
same day of vaccination and before vaccination, the related dose will be that of the 
previously administered dose.   

The number of doses for a product is the number of times the product was 
administered to a subject. 

The incidence per dose is the number of vaccination visits at which an event was 
reported among all vaccination visits.  


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 49 of 53
11.2.3.
Demography

Age: Age at the reference activity, computed as the number of days between the date 
of birth and the reference activity and converted in months (= days *12 /365.25) 
(keeping 1 decimal digit).

Conversion of weight to kg
The following conversion rule is used:  

Weight in Kilogram= weight in Pounds / 2.2

Weight in Kilogram =weight in onces / 35.2
The result is rounded to 2 decimals.

Conversion of height to cm
The following conversion rule is used:  

Height in Centimetres = Height in Feet * 30.48

Height in Centimetres = Height in Inch * 2.54
The result is rounded to the unit (ie no decimal).

Conversion of temperature to °C
The following conversion rule is used:  

Temperature in °Celsius  = ((Temperature in °Fahrenheit -32) *5)/9
The result is rounded to 1 decimal.
11.2.4.
Immunogenicity

For a given subject and given immunogenicity measurement, missing or non-
evaluable measurements will not be replaced. Therefore, an analysis will exclude 
subjects with missing or non-evaluable measurements.

The Geometric Mean Concentrations (GMC) calculations are performed by taking the 
anti-log of the mean of the log titre transformations. Antibody titres below the cut-off 
of the assay will be given an arbitrary value of half the cut-off of the assay for the 
purpose of GMC calculation. Refer to Section 6.4.2 for details regarding cut-off 
definition and calculations.

All CI computed will be two-sided 95% CI.


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 50 of 53
11.2.5.
Safety

For the analysis of solicited symptoms, missing or non-evaluable measurements will 
not be replaced. Therefore the analysis of the solicited symptoms based on the 
Exposed Set will include only vaccinated subjects for doses with documented safety 
data (i.e., symptom screen completed). This corresponds to the Solicited Safety Set 
defined in the protocol (Section 11.5.3.1). More specifically the following rules will 
be used: 

Subjects who documented the absence of a solicited symptom after each of 
vaccine dose will be considered not having that symptom after that dose.

Subjects who documented the presence of a solicited symptom and fully or 
partially recorded daily measurement over the solicited period will be included in 
the summaries at that dose and classified according to their maximum observed 
daily recording over the solicited period.

Subjects who documented the presence of a solicited symptom after one dose 
without having recorded any daily measurement will be assigned to the lowest 
intensity category at that dose (i.e., 38.0°C for fever or grade 1 for other 
symptoms).

Doses without symptom sheets documented will be excluded.

For analysis of unsolicited adverse events, such as serious adverse events or adverse 
events by primary MedDRA term, and for the analysis of concomitant medications, 
all vaccinated subjects will be considered. Subjects who did not report the event or 
the concomitant medication will be considered as subjects without the event or the 
concomitant medication respectively. This corresponds to the Solicited Safety Set 
defined in the protocol (Section 11.5.3.2).
Note that for all tables described in this section, the way the percentage of subjects will 
be derived will depend on the event analyzed (see table below for details). As a result, the 
N value will differ from one table to another.
Event
N used for deriving % per subject for 
Vaccination phase
N used for deriving % per dose for 
Vaccination phase
Concomitant 
vaccination
All subjects with study vaccine administered
All study visits with study vaccine 
administered
Solicited general 
symptom
All subjects with at least one solicited 
general symptom documented as either 
present or absent (i.e., symptom screen 
completed)
All study visits with study vaccine 
administered and with at least one solicited 
general symptom documented as either 
present or absent (i.e., symptom screen 
completed)
Solicited local symptom
All subjects with at least one solicited local 
symptom documented as either present or 
absent (i.e., symptom screen completed)
All study visits with study vaccine 
administered and with at least one solicited 
local symptom documented as either present 
or absent (i.e., symptom screen completed)
Unsolicited symptom
All subjects with study vaccine administered 
All study visits with study vaccine 
administered
Concomitant 
medication
All subjects with study vaccine administered 
All study visits with study vaccine 
administered


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 51 of 53
11.2.6.
Number of decimals displayed:
The following decimal description from the decision rules will be used for the 
demography, efficacy, immunogenicity and safety/reactogenicity.
Display Table
Parameters
Number of decimal 
digits
Demographic characteristics
Mean, median age
1
Demographic characteristics
SD (age)
1
Immunogenicity
Ratio of GMT/C
2
Reactogenicity
Mean, Min, Q1, Median, Q3, Max for duration
1
All summaries
% of count, including LL & UL of CI
1
All summaries
% of difference, including LL & UL of CI
2
All summaries
p-value
3
11.2.7.
Efficacy
Specific data derivation will be put in place to derive the primary and the secondary 
efficacy endpoints before Database freeze.
Stool sample assessment will be combined with solicited events after challenge to derive 
diarrhea and dysentery as defined in the protocol and as defined by BMGF after protocol 
was approved.
An overview of the algorithms to be used to derive all efficacy endpoints is reported in 
Table 15.
Table 15
Derivation of efficacy endpoints
Endpoint
Definition / Derivation
Primary Efficacy
Shigellosis
[Shedding of S. sonnei strain 53G] AND
[(Moderate diarrhea) OR
(Severe diarrhea) OR
(oral temperature ≥ 38.5°C)] 
Derivation of Shigellosis
Moderate diarrhea
[4 to 5 stools1 within 24 hours] OR
[400 to 800 grams of stools1 within 24 hours] OR
[intravenous (IV) fluids administration] OR
[anticipation of antibiotic treatment before the 5th day after challenge]
Severe diarrhea
[≥ 6 stools1 within 24 hours] OR
[> 800 grams of stools1 within 24 hours] OR
[ER visit or emergency care for hypotensive shock]
Secondary Efficacy
a. Shigellosis as per 
BMGF definition
[Moderate diarrhea] OR


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 52 of 53
Endpoint
Definition / Derivation
[Severe diarrhea] OR
[Dysentery] 
Derivation of Shigellosis as per BMGF definition
Moderate diarrhea
[(4 to 5 stools1 within 24 hours) OR
(400 to 800 grams of stools1 within 24 hours)]
AND2
[(oral temperature ≥ 38.0˚C) OR
(≥1 constitutional/enteric symptom3 graded ≥2) OR
[≥2 episodes of vomiting within 24 hours])
Severe diarrhea
[≥6 stools1 within 24 hours] OR
[800 grams loose stools1 within 24 hours]
Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
AND2
[oral temperature ≥38.0˚C OR
(≥1 constitutional/enteric symptom3 graded ≥2) OR
(≥2 episodes of vomiting in 24 hours)]
b. Shedding of S. sonnei 
strain 53G
At least one stool1 sample positive to S. sonnei strain 53G either by culture or qPCR
c. Severe diarrhea
Severe diarrhea as defined under primary endpoint
d. More severe diarrhea
[≥ 10 stools1 within 24 hours] OR
[≥ 1000 grams of stools1 within 24 hours]
e. Dysentery
[≥2 stools1 with gross blood (hemoccult positive) in 24 hours]
AND2
(≥1 constitutional symptom4 graded ≥1)
f. weight of grade 3-5 
stools
weight of each stool1 during follow-up
g. weight of grade 3-5 
stools accumulated from 
challenge to discharge
For each subject sum the weight of each stool1 accumulated from challenge to discharge
h. number of grade 3-5 
stools
For each subject count the number of stools1 accumulated from challenge to discharge
i.
[At least one stool1 sample positive to S. sonnei strain 53G either by culture or qPCR]
AND2
[(Moderate diarrhea) OR
(Severe diarrhea) OR
(Dysentery as defined in f.) OR
(oral temperature ≥ 38.5°C) OR
(≥1 intestinal symptom5 graded ≥3)]
j. 
1
[At least one stool (whichever is the grading)]
AND2 NOT


CONFIDENTIAL
205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP])
Statistical Analysis Plan Final
09-AUG-2018
Page 53 of 53
Endpoint
Definition / Derivation
[(Moderate diarrhea) OR
(Severe diarrhea) OR
2
≥1 abdominal pain graded ≥1
3
≥1 abdominal cramps graded ≥1
4
≥1 abdominal gas graded ≥1
5
≥1 abdominal anorexia graded ≥1
6
≥1 abdominal nausea graded ≥1
7
≥1 abdominal headache graded ≥1
8
≥1 abdominal myalgia graded ≥1
9
≥1 abdominal malaise graded ≥1
10
≥1 abdominal arthralgia graded ≥1
11
≥1 oral temperature ≥ 38.5°C 
12
≥1 vomit graded ≥1
13
≥1 IV fluid administration
k. Time to onset of 
Shigellosis during the 
post-challenge period
Shigellosis is defined as in primary objective. The day associated to the first shigellosis (e.g. 
day of the first stool that defined the 24 hours time-window that actually defined shigellosis) is 
the time of onset of Shigellosis.
1Considering only stools graded 3-5
2Where AND combines conditions occurring in the 7-day post-challenge inpatient period 
3Where constitutional/enteric symptom are: Nausea, Abdominal pain/cramping, Myalgia/arthralgia, Malaise
4Where constitutional symptoms are: fever, headache, fatigue,  arthralgia, malaise, myalgia, chills, nausea, abdominal 
cramping, abdominal pain,   gas, anorexia, vomiting
5Where intestinal symptoms are: abdominal pain, abdominal cramping, gas, nausea, vomiting, anorexia
12.
ANNEX 2: SUMMARY ON ELIMINATION CODES
Please refer to the exclusion matrix for a comprehensive list of exclusion codes among all 
the analysis sets. 
13.
ANNEX 3: STUDY SPECIFIC MOCK TFL
Please refer to “205626 (S SONNEI MONO GMMA SBVGH-003 [H03_03TP]) Mock-
up customs 09Aug2018.xlsx” for the study specific mocks.
The data display, title and footnote are for illustration purpose and will be adapted to the 
study specificity as indicated in the TFL TOC. Note that there may be few changes 
between the study specific SAP mock TFL and the final TFLs as editorial/minor changes 
do not require a SAP amendment