Systems Biology of 23 Valent Pneumococcal Polysaccharide Vaccine (PNEUMOVAX®23) and 13-valent Pneumococcal Conjugate Vaccine (PREVNAR 13®)
Phase: NA
Conditions: Pneumococcal Infection
Sponsor: Emory University

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
 
 
PROTOCOL TITLE 
Systems Biology of 23-valent pneumococcal polysaccharide vaccine (PNEUMOVAX®23) and 
13-valent pneumococcal conjugate vaccine (PREVNAR 13®).  
Protocol Number 
HIPC: VAX-003 
 
Principal Investigator 
Investigator: Nadine Rouphael 
 
IRB00047973 
NCT01307449 
 
VERSION 7.0/03.30.2017  
IND # N/A 
 Study Sponsor: DAIT/NIAID 
 
 
 
 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
PRINCIPAL INVESTIGATOR 
Nadine Rouphael, MD 
Hope Clinic, 500 Irvin Court. Suite 200, 
Decatur, GA 30030 
Office: 404-712-1435 
Cell : 404-822-1411 
Pager : 404-686-5500 (PIC 16509) 
Fax : 404-499-9727 
Email:nroupha@emory.edu 
 
 
CO-INVESTIGATORS 
 
Mark J. Mulligan, MD (Clinical Core Direc
Hope Clinic, 500 Irvin Court, Suite 200, 
Decatur, GA 30030 
Office:404-712-9046 
Pager : 404 686 5500 (PIC 13632) 
Fax : 404-499-9727 
Email: mmulli2@emory.edu 
 
Aneesh K. Mehta, MD (co-PI) 
2101 Woodruff Memorial Research 
Building, 101 Woodruff Circle, , Atlanta, 
GA 30322 
Office: 404-727-8435 
Lab: 404-727-5854 
Cell: 678-428-6728 
Pager: 404-686-5500 (PIC 16927) 
Fax: 404-712-2278 
Email aneesh.mehta@emory.edu 
 
CO-INVESTIGATOR(S) 
 
 
Srilatha Edugupanti, MD, MPH 
Hope Clinic, 500 Irvin Court, Suite 200 Decatur, GA 
30030 
Office: 404-712-1434 
Pager : 404-686-5500 (PIC 13721) 
Fax : 404-499-9727 
Email: sedupug@emory.edu 
 
Colleen F. Kelley, MD 
Hope Clinic, 500 Irvin Court, Suite 200, Decatur, GA 30
Office:  404-712-1434 
Fax:  404-499-9727 
Email  colleen.kelley@emory.edu 
 
Allison Beck, PA 
Hope  Clinic, 500 Irvin Court, Suite 200  , Decatur, GA 
30030 
Office: 404-712-1408 
Fax: 404-499-9727 
Email: aabeck@emory.edu 
 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
BIOSTATISTICIAN 
Tianwei Yu, PhD 
Department of Biostatistics and 
Bioinformatics 
Rollins School of Public Health 
1518 Clifton Rd., N.E. 
Atlanta, GA 30322 
Office: 404-727-7671 
Fax: 404-727-1370 
Email: tyu8@emory.edu 
INDEPENDENT  SAFETY MONITOR 
Primary ISM 
Bruce Ribner, MD, MPH 
Emory University Hospital 
1364 Clifton Road, NE Suite B-705, 
Atlanta, GA 30322    
 
Phone: 404-727-1580 
Pager : 404 686 5500 (PIC 15326) 
Fax:404-712-4361 
Email: bribner@emory.edu 
 
Back up ISM 
David Rimland, MD 
VA Medical Center 
1670 Clairmont Rd, Decatur, GA 30033 
Phone: 770-393-8951  
Fax: 404-728-7782 
Email: rimlandmd@gmail.com 
 
NIAID MEDICAL MONITOR: 
 
Alkis Togias, MD 
Branch Chief, Asthma, Allergy and Airway Biology 
Branch, DAIT, NIAID, NIH,  DHHS 
5601 Fishers Lane, Room 6B40, MSC 9827 
Rockville, MD  20852 
Phone:  (240) 627-3587 OR (240) 507-9697 
Fax:  (240) 627-3115 
Email: togiasa@niaid.nih.gov 
  
Confidentiality Statement 
The information contained within this document is not to be disclosed in any way without the prior
permission of the Principal Investigator and the Division of Allergy, Immunology and Transplantat
of the National Institute of Allergy and Infectious Diseases. 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
INVESTIGATOR SIGNATURE PAGE 
Protocol 
Systems Biology of 23-valent pneumococcal 
polysaccharide vaccine (PNEUMOVAX®23) 
and 13-valent pneumococcal conjugate vaccine 
(PREVNAR®13). 
 
Version/Date: 
 7.0/03/30/2017 
IND Number 
N/A 
Principal Investigator: 
Nadine Rouphael, MD 
Short Title:  Systems Biology of PPV23 and PCV 13  
IND Sponsor: N/A 
 
INSTRUCTIONS:  The Principal Investigator will print, sign, and date at the indicated location below. A 
copy should be kept in the investigator’s records and the original signature page sent to the NIAID. 
After signature, please return the original of this form by surface mail to: 
Project Manager:  
Susan Perry, RN 
Division of Allergy, Immunology and Transplantation 
National Institute of Allergy and Infectious Diseases 
5601 Fishers Ln 
Rockville, MD  20892-9827 
Phone:  (240) 669-2865 
E-mail: susan.perry@nih.gov 
 
I confirm that I have read the above protocol in the latest version. I understand it, and I will work 
according to principles of Good Clinical Practice (GCP) as described in the United States Code of Federal 
Regulations (CFR) 45 CFR part 46 and 21 CFR parts 50, 56, and 312 , and the  International 
Conference on Harmonization (ICH) document “Guidance for Industry:  E6 Good Clinical Practice:  
Consolidated Guidance” dated April 19961  and the spirit of the Declaration of Helsinki,  Further, I will 
conduct the study in keeping with local, legal, and regulatory requirements.  
 
As the Principal Investigator, I agree to conduct HIPC: VAX-003:  Systems Biology of 23-valent 
pneumococcal polysaccharide vaccine (PNEUMOVAX®23) and 13-valent pneumococcal conjugate vaccine 
(PREVNAR®13). I agree to carry out the study by the criteria written in the protocol and understand that 
no changes can be made to this protocol without written permission by the NIAID, the local IRB. 
 
 
 
___NADINE ROUPHAEL, MD_______________________________ 
Principal Investigator (Print) 
 
 
 
___________________________________________                                             ____________ 
Principal Investigator (Signature)                                                                              Date 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
Synopsis 
Title 
Systems Biology of 23-valent pneumococcal polysaccharide vaccine 
(PNEUMOVAX®23) and 13-valent pneumococcal conjugate 
vaccine (PREVNAR®13) (HIPC: VAX-003). 
Short Title 
Systems Biology PPV23 and PCV13. 
Rationale 
PCV13 [13-valent pneumococcal conjugate vaccine (Prevnar®13)] 
induces better functional immune responses when compared to 
PPV23 
[23-valent 
pneumococcal 
polysaccharide 
vaccine 
(Pneumovax®23)] in older naïve adults. We hypothesize that this is 
due to intrinsic defects in innate responses that could explain the 
poor immunogenicity of PPV23 when compared to PCV13. 
Therefore, we propose to extensively study innate and adaptive 
immune responses generated after administration of either 
pneumococcal polysaccharide or conjugate vaccines in older adults. 
Clinical Phase 
N/A 
Mechanistic Study 
Yes 
IND Sponsor 
N/A 
Principal Investigator  
Nadine Rouphael, MD (PI-Hope Clinic*)  
Office: 404-712-1435 
Cell: 404-822-1411 
Pager: 404 686 5500 (PIC16509) 
Fax: 404-499-9727 
Email: nroupha@emory.edu 
Mark J. Mulligan, MD, FIDSA (Clinical Core Director-Hope Clinic*
Office:404-712-9046 
Pager: 404-686-5500 (PIC 13632) 
Fax: 404-499-9727 
Email: mmulli2@emory.edu 
Aneesh K. Mehta (co-PI) 
Office: 404-727-8435 
Lab: 404-727-5854 
Cell: 678-428-6728 
Pager: 404-686-5500 (PIC 16927) 
Fax: 404-712-2278 
Email aneesh.mehta@emory.edu 
Participating Site(s) 
The Hope Clinic of the Emory Vaccine Center, 500 Irvin Court, 
Suite 200, Decatur, GA 30030. 
The Hope Clinic is a community-based vaccine research clinic and 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
is the clinical arm of the Emory Vaccine Center at Emory 
University. 
Accrual Objective 
N=88 (22 subjects (ages 25-40) and 66 subjects ( ages 60-89)) 
Primary Study Objective To identify innate immune signatures that correlate with the 
magnitude, quality and persistence of B cell responses after 
vaccination with either PPV23 or PCV13.  
Study Design 
Single center, mechanistic study in which healthy subjects will be 
will be stratified by age in 22 subjects (ages 25-40) and 66 
subjects (ages 60-89) and randomized to receive PPV23 or PCV13 
in 1:1 ratio. Blood samples will be collected on Days D0 (at 
enrollment) and D1, D3, D7, D14, D30, D180 and year 2-3.5 post 
vaccination to study innate and adaptive immune responses. 
 
 Recording and reporting safety data will be as follows: 
 
Any Adverse Event (including – but not only- vaccine 
reactions and local or systemic Reactogenicity Events) of 
grade 3 or higher severity or serious adverse event (SAE) 
occurring after vaccination while the subjects is still at the 
clinical site. 
 
Local REs evaluation of grade 3 or higher severity occurring 
from Day 0 to Day 7 reported over the telephone by the 
participant and/or assessed at the clinic. 
 
AEs of grade 3 or higher severity throughout D180 of the 
study (including -but not only – AEs linked to blood draws). 
 
All SAEs throughout D180.  
Primary Endpoints 
1. Identification of generic innate immune signatures 
 
[Traditional immune parameters measurements + array-based 
gene expression] at days 1, 3 and 7 post vaccination with either 
PPV23 or PCV13 in the elderly. 
2. Measurement 
of 
adaptive 
immune 
responses 
[Opsonophagocytosis assay (OPA) titers] at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
3. Correlation of signatures of generic innate immune responses at 
days 
1, 
3 
and 
7 
with 
adaptive 
immune 
responses 
[Opsonophagocytosis assay OPA titers] at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
Secondary Endpoints 
 
1. Comparison of the serotype-specific IgG levels at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
2. Correlation of signatures of generic innate immune responses at 
days 1, 3 and 7 with serotype specific IgG levels at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
3. Comparison of the serotype-specific avidity indexes in a subset 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
of up to 6 vaccinees per vaccine group at day 180 post 
vaccination with either PPV23 or PCV13 in the elderly. 
4. Correlation of signatures of generic innate immune responses at 
days 1, 3 and 7 with serotype specific avidity indexes in a subset 
of vaccinees at day 180 post vaccination with either PPV23 or 
PCV13 in the elderly. 
5. Comparison 
of 
the 
adaptive 
immune 
responses 
[Opsonophagocytosis assay (OPA) titers] at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
Exploratory Endpoints 
1. Correlation of signatures of generic innate immune 
responses at days 1, 3 and 7 with adaptive immune 
responses 
[Opsonophagocytosis 
assay 
OPA 
titers 
specifically] at day 30 post vaccination with either PPV23 or 
PCV13 among subjects in different age strata.  
2. Comparison of the kinetics and magnitude of select 
serotype specific plasmablasts (days 7, 14, 30(with day 30 on 
a subset of vaccinees only)) and memory B cells (days 30, 
180) post vaccination with either PPV23 or PCV13. 
3. Comparison of the plasmablast repertoire and monoclonal 
antibodies from plasmablasts in a subset of vaccinees per 
vaccine group at day 7 post vaccination with either PPV23 
or PCV13. 
4. 
Comparison of identified innate signature variables 
and correlation signature variables between PPV23 and 
PCV13 recipients. 
5. Correlation of signatures of generic innate immune 
responses at days 1, 3 and 7 with adaptive immune 
responses [Opsonophagocytosis assay OPA titers and 
ELISA] at years 2-3.5 post vaccination with either PPV23 or 
PCV13. 
Note: This will include - but not only - a comparison of 
identified innate signature variables and correlation 
signature variables between elderly (60 to 89 yo) recipients 
of PCV13 and young (25-40yo) recipients of PPV23. 
Inclusion Criteria 
1. Able to understand and give informed consent. 
2. Immunocompetent community dwelling subjects between the 
ages of ages of 25-40 and 60-89 years. 
Exclusion Criteria 
1. Prior vaccination with pneumococcal vaccine. 
2. Receipt of   any of the following products: 
a. Blood products within 3 months prior to study entry or 
expected receipt at any time after study entry*. 
b. Any live virus vaccines within 4 weeks prior to study entry 
or expected receipt within 4 weeks after study entry*. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
c. Any inactivated vaccine within 2 weeks or expected receipt 
within 2 weeks after study entry*. 
 
3. Presence of co-morbidities or immunosuppressive states such 
as: 
o Chronic medical problems including (but not limited to) 
insulin dependent diabetes, severe heart disease, severe lung 
disease, severe liver disease, cerebrospinal fluid leaks, severe 
kidney disease, autoimmune diseases, severe gastrointestinal 
diseases and grade 4 hypertension per CTCAE criteria** .  
o Alcohol, drug abuse or psychiatric conditions that in the 
opinion of the investigator would preclude compliance with 
the trial or interpretation of safety or endpoint data. 
o Impaired immune function or known chronic infections 
including, but not limited, to known HIV,  hepatitis B or C; 
organ transplant; immunosuppression due to cancer; current 
and/or expected receipt of chemotherapy, radiation therapy, 
steroids*** (i.e., more than 20 mg of prednisone given daily 
or on alternative days for 2 weeks or more in the past 90 
days , or high dose inhaled corticosteroids**** or any other 
immunosuppressive therapies (including anti-TNF therapy),  
functional 
or 
anatomic 
asplenia 
and 
congenital 
immunodeficiency. 
4. Conditions that could affect the safety of the volunteers such as: 
o Severe reactions to prior vaccinations. 
o An allergy to any component of the study vaccines (phenol, 
aluminum, CRM197 protein, succinic acid, Polysorbate 80). 
o History of Guillain-Barré syndrome. 
o History of bleeding disorders. 
5. Volunteers with any acute illness* including, but not limited to, - 
fever (> 100.4 F [> 38 C], regardless of the route)  within 3 days 
prior to study entry. 
6. Volunteers with social conditions or occupational conditions or 
any condition that in the opinion of the investigator might 
interfere with compliance with the study and vaccine 
evaluation. 
7. Pregnant or breast feeding or women expected to conceive 
within 30 days after vaccination ***** 
 
* An individual who initially is excluded from study participation 
based on one or more of the time-limited exclusion criteria (e.g., 
acute illness, receipt or expected  receipt of live or inactivated 
vaccines ) may be reconsidered for enrollment once the condition 
has resolved as long as the subject continues to meet all other  
entry criteria. 
** Grade 4 hypertension per CTCAE criteria is defined as Life 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
     threatening consequences(e.g., malignant hypertension,  
     transient or permanent neurologic deficit, hypertensive crisis)   
     urgent intervention indicated. 
***Subjects receiving > 20 mg/day of prednisone or its equivalent 
daily or on alternate days for more than 2 weeks may enter the   
study after therapy has been discontinued for more than 3   
months. 
****High dose ICS is defined as: > 960 mcg/day of beclomethasone  
     dipropionate or equivalent 
***** Women of child-bearing potential (not surgically sterile via 
tubal ligation, bilateral oophorectomy or hysterectomy or who 
are not postmenopausal for ≥1 year) must agree to practice 
adequate contraception that may include, but is not limited to, 
abstinence, 
monogamous 
relationship 
with 
vasectomized 
partner, barrier methods such as condoms, diaphragms, 
spermicides, intrauterine devices, and licensed hormonal 
methods for 30 days before and 30 days after receiving PPV23 or 
PCV13. 
Investigational 
Product(s)/ 
Intervention(s)  
23-valent pneumococcal polysaccharide vaccine (PNEUMOVAX® 
23 or PPV23) (Merck, Whitehouse Station, NJ). 
13-valent pneumococcal conjugate vaccine (PREVNAR®13 or 
PCV13) (Pfizer, New York, NY). 
Study Procedures 
Vaccination, targeted physical examination, phlebotomy, urine 
pregnancy test. 
Statistical 
Considerations 
At the center of this study is the identification of the generic innate 
signatures and the correlation signatures of innate immune 
response.  
The generic innate signatures will be identified from both immune 
parameters measured by FACS/Luminex assays and array-based 
gene expression will be measured by microarray experiments. The 
generic innate signatures will be identified for the treatment groups 
separately.  
The traditional immune parameters and array-based gene 
expression that change after immunization are considered generic 
innate signatures.  
After vaccination, the innate signatures that are correlated with the 
adaptive immune responses (day 30 OPA titers, day 30 IgG levels, 
day 180 serotype specific avidity indexes, plasmasblasts) are 
considered correlation signatures of the innate immune responses. 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
Table of Contents 
1. 
BACKGROUND AND RATIONALE ................................................................ 17 
1.1 
BACKGROUND .................................................................................................................. 17 
1.2 
RATIONALE FOR SELECTION OF STUDY POPULATION ...................................... 19 
1.3 
INVESTIGATIONAL PRODUCT(S)/INTERVENTION(S) .......................................... 20 
1.4 
RATIONALE FOR SELECTION OF INVESTIGATIONAL 
PRODUCT(S)/INTERVENTION(S) AND REGIMEN .................................................. 20 
1.5 
IMMUNE RESPONSE AGAINST PNEUMOCOCCUS AND SYSTEMS BIOLOGY 
EXPERIENCE ...................................................................................................................... 20 
1.6 
RISKS .................................................................................................................................... 22 
1.6.1 
Risks of Investigational Product(s)/Intervention(s) ...................................................... 22 
1.6.2 
Risk of Study Procedures ................................................................................................... 25 
1.6.3 
Risk of Concomitant Medications, Prophylactic Medications and Rescue Medications
 
…………………………………………………………………………………………...26 
1.7 
BENEFITS ............................................................................................................................. 26 
1.7.1 
Benefits of Investigational Product(s)/Intervention(s).................................................. 26 
1.7.2 
Benefits of Study Procedure(s) .......................................................................................... 26 
2. 
OBJECTIVES .......................................................................................................... 27 
2.1 
PRIMARY OBJECTIVE(S) .................................................................................................. 27 
2.2 
SECONDARY OBJECTIVE(S) ........................................................................................... 27 
2.3 
EXPLORATORY OBJECTIVE(S) ....................................................................................... 27 
3. 
STUDY DESIGN .................................................................................................... 28 
3.1 
STUDY ENDPOINTS ......................................................................................................... 28 
3.1.1 
Primary Endpoint(s) ........................................................................................................... 28 
3.1.2 
Secondary Endpoint(s) ....................................................................................................... 28 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
3.1.3 
Exploratory Endpoint(s) .................................................................................................... 29 
3.2 
STUDY COMPLETION ...................................................................................................... 29 
4. 
SELECTION AND WITHDRAWAL OF PARTICIPANTS ............................ 31 
4.1 
INCLUSION CRITERIA ..................................................................................................... 31 
4.2 
EXCLUSION CRITERIA .................................................................................................... 31 
4.3 
EARLY STUDY TERMINATION ..................................................................................... 32 
5. 
INVESTIGATIONAL PRODUCT(S)/INTERVENTION MATERIAL(S), 
OTHER STUDY PRODUCTS (CONTROLS/PLACEBOS) ............................ 35 
5.1 
INVESTIGATIONAL PRODUCT(S)/INTERVENTION(S) .......................................... 35 
5.2 
FORMULATION, PACKAGING, AND LABELING ..................................................... 35 
5.3 
PREPARATION, ADMINISTRATION, AND DOSAGE ............................................... 36 
5.4 
ACCOUNTABILITY OF INVESTIGATIONAL PRODUCT(S)/INTERVENTION(S)37 
5.5 
ASSESSMENT OF COMPLIANCE WITH INVESTIGATIONAL 
PRODUCT(S)/INTERVENTION MATERIAL(S) .......................................................... 37 
5.6 
MODIFICATION OR DISCONTINUATION OF INVESTIGATIONAL 
PRODUCT(S)/INTERVENTION MATERIAL(S) .......................................................... 37 
5.6.1 
Modification of Investigational Product(s)/Intervention(s) ......................................... 37 
5.6.2 
Premature Discontinuation of Investigational Product(s)/Intervention(s) ................ 37 
6. 
OTHER MEDICATIONS ............................................................................................. 39 
6.1 
CONCOMITANT MEDICATIONS .................................................................................. 39 
6.2 
PROPHYLACTIC MEDICATIONS .................................................................................. 39 
6.3 
RESCUE MEDICATIONS .................................................................................................. 39 
6.4 
PROHIBITED MEDICATIONS ......................................................................................... 40 
7. 
STUDY VISITS AND PROCEDURES ............................................................... 40 
7.1 
ENROLLMENT AND RANDOMIZATION ................................................................... 40 
7.2 
SCREENING VISIT(S) ........................................................................................................ 40 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
7.3 
BASELINE VISIT(S) ............................................................................................................ 40 
7.4 
MAIN STUDY VISIT(S) ...................................................................................................... 41 
7.5 
FOLLOW-UP VISIT(S) (IF APPLICABLE) ....................................................................... 43 
7.6 
VISIT WINDOWS ............................................................................................................... 43 
7.7 
STUDY PROCEDURES ...................................................................................................... 44 
7.8 
STUDY ARM ASSIGNMENT PROCEDURES ................................................................ 44 
7.8.1 
Blinding and Randomization ............................................................................................ 44 
7.8.2 
Securing Blinding and Randomization Information ...................................................... 44 
7.8.3 
Requirements for Unblinding ........................................................................................... 44 
7.8.4 
Documenting an Unblinding............................................................................................. 44 
8. 
SAFETY PROCEDURES ....................................................................................... 45 
8.1 
STOPPING RULES ............................................................................................................. 45 
8.1.1 
Study Stopping Rules ......................................................................................................... 45 
8.1.2 
Individual Stopping Rules ................................................................................................. 45 
8.1.3 
Follow-up after early study termination ......................................................................... 45 
8.1.4 
Participant Replacement .................................................................................................... 45 
8.2 
ADVERSE EVENTS ............................................................................................................ 46 
8.2.1 
Definitions ............................................................................................................................ 46 
8.2.1.1 Adverse Events ...................................................................................................................... 46 
8.2.1.2 Adverse Events Associated with Study Vaccines and Study Procedures ............................. 46 
8.2.2 Serious Adverse Event (SAE) ................................................................................................ 46 
8.2.3 Unexpected Adverse Event or Adverse Reaction .............................................................. 46 
8.2.4 
Independent Safety Monitor ............................................................................................. 48 
8.2.5 
Collecting, Recording and Managing Adverse Events .................................................. 48 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
8.2.5.1 Collecting and Reporting Adverse Events ............................................................................. 48 
8.2.5.2 Managing Adverse Events .................................................................................................... 49 
8.2.6 
Grading and Attribution .................................................................................................... 50 
8.2.6.1 Grading criteria ..................................................................................................................... 50 
8.2.6.2 Definition of Attribution ....................................................................................................... 50 
8.2.7 
SAE Reporting Criteria and Procedures .......................................................................... 52 
8.2.7.1 Notifying the Independent Safety Monitor and the NIAID Medical Officer of SAEs and 
pregnancy .............................................................................................................................. 52 
8.2.7.2 Notifying the FDA ................................................................................................................. 53 
8.2.7.3 Notifying the Institutional Review Board ............................................................................. 53 
8.3 
PROTOCOL DEVIATIONS ............................................................................................... 53 
9. 
SAMPLE SIZE CALCULATIONS AND STATISTICAL PLAN .................... 55 
9.1 
SAMPLE SIZE AND POWER CALCULATIONS .......................................................... 55 
9.2 
DATA ANALYSIS............................................................................................................... 57 
9.2.1 
General considerations ....................................................................................................... 57 
9.2.2 
Patient populations ............................................................................................................. 62 
9.2.3     Study Participant Baseline Characteristics and Demographics ................................... 63 
9.2.4     Status of Study Subjects ..................................................................................................... 61 
9.3 
INTERIM ANALYSES ........................................................................................................ 63 
9.4 
DEVIATIONS FROM STATISTICAL PLAN................................................................... 63 
10. 
IDENTIFICATION AND ACCESS TO SOURCE DATA ............................... 64 
10.1 
IDENTIFYING SOURCE DATA ....................................................................................... 64 
10.2 
UPDATING SOURCE DOCUMENTATION .................................................................. 64 
10.3 
PERMITTING ACCESS TO SOURCE DATA ................................................................. 64 
11. 
QUALITY CONTROL AND QUALITY ASSURANCE .................................. 66 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
12. 
ETHICAL CONSIDERATIONS AND COMPLIANCE WITH GOOD 
CLINICAL PRACTICE .......................................................................................... 67 
12.1  
STATEMENT OF COMPLIANCE .................................................................................... 67 
12.2  
INFORMED CONSENT AND ASSENT .......................................................................... 67 
12.3 
PRIVACY AND CONFIDENTIALITY ............................................................................. 68 
13. 
PUBLICATIONS .......................................................................................................... 69 
14. 
REFERENCES ......................................................................................................... 70 
List of Appendices  
Appendix 1  Schedule of Events.......................................................................................................... 75 
Appendix 2 Definitions….………………………………….…………………………….................77 
 
Appendix 3 Severity Scale for Local Vaccine Reactions (local reactogenicity events)………………78 
 
Appendix 4 Severity Scale for Generalized Vaccine Reactions (systemic reactogenicity events)…..79 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
Glossary of Abbreviations 
ACIP 
Advisory Committee on Immunization Practices 
AADCRC 
Asthma and Allergic Diseases Cooperative Research Center 
AE 
Adverse Event 
CFR 
Code of Federal Regulations 
CRF 
Case Report Form 
CTCAE 
Common Terminology Criteria for Adverse Events 
DAIT 
Division of Allergy, Immunology, and Transplantation 
DC 
Dendritic Cell 
ELISA 
Enzyme-Linked ImmunoSorbent Assay 
cGCP 
Current Good Clinical Practice 
GLP 
Good Laboratory Practice 
ICH 
International Conference on Harmonization 
IDE 
Investigational Device Exemption 
IL 
InterLeukin 
IM 
IntraMuscular 
ISM 
Independent Safety Monitor (Physician who is independent from the 
study site and will, at minimum, review all SAEs to assess for 
possible changes to the overall risk of the study). 
IND 
Investigational New Drug 
IRB 
Institutional Review Board 
IPD 
Invasive Pneumococcal Disease 
MCP1 
Monocyte Chemoattractant Protein 1 
MOP 
Manual of Procedures 
NCI 
National Cancer Institute 
NIAID 
National Institute of Allergy and Infectious Diseases 
NSAIDs 
NonSteroidal Anti-Inflammatory Drugs 
OPA 
OpsonoPhagocytic Assay 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
PCV13 
13-valent pneumococcal conjugate vaccine (Prevnar13®) 
PI 
Principal Investigator 
PPV23 
23-valent pneumococcal polysaccharide vaccine (Pneumovax®) 
SAE 
Serious Adverse Event 
SAP 
Statistical Analysis Plan 
SOP 
Standard Operating Procedure. 
TLR 
Toll-Like Receptor 
TNF 
Tumor Necrosis Factor 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
BACKGROUND AND RATIONALE 
1.1 
Background 
Pneumococcal diseases are a major public health problem, globally. According to the World 
Health Organization, invasive pneumococcal diseases (IPD) are responsible for 1.6 million 
deaths per year globally2. In the United States alone, there are four million cases of pneumonia 
each year and the pneumococcus is the most common agent leading to hospitalization3. 
Although all age groups may be affected, the highest rate of pneumococcal disease occurs in 
young children and in the elderly population. In addition, persons suffering from a wide range 
of chronic conditions and immune deficiencies are at increased risk. 
Vaccination is the most effective way of preventing pneumococcal infections. Until  
December 2011, only one vaccine was licensed in the United States for adults: 
PNEUMOVAX®23, the 23-valent pneumococcal polysaccharide (PPV23) based on the 23 most 
common serotypes. With its wide serotype coverage, PPV23 is recommended for elderly and 
younger adults at high risk for pneumococcal infections4. The 23-valent vaccine accounts for at 
least 90% of pneumococcal blood isolates and at least 85% of all pneumococcal isolates from 
sites which are generally sterile as determined by ongoing surveillance of U.S. data. Despite the 
high valency of the vaccine and the good vaccine uptake in the US (>70%) among adults, they 
are still 24,000 cases per year of IPD leading to 4,500 deaths among adults>50 years5. Also 
PPV23 does not appear to reduce the much larger burden of nonbacteremic pneumococcal 
pneumonia with 364,000 cases each year among adults ≥ 65 years of age in the United States4. 
This is explained in part by the decrease in functionality (OPA activity and avidity) of 
antibodies in the elderly after PPV236.  
The 7 and 13-valent pneumococcal conjugate vaccines (PCV7, PREVNAR®7 and PCV13, 
PREVNAR®13, respectively) have been licensed for use in the US for children since 2000 and 
2010 respectively. The 7-valent conjugate vaccine has led to a marked reduction (~84 to 90%)  in 
disease burden events linked to the 7 vaccine serotypes  even in adults due to a “herd 
immunity” effect from universal vaccination in children <2 years old 5,7. Since December 2011, 
PREVNAR®13 (PCV13) is licensed for adults 50 years and older. When PCV13 is given to older 
adults (age 60-64) who have never received PPV23, it induces opsonophagocytic antibody 
(OPA) titers to shared serotypes in both vaccines, and for most of those serotypes the immune 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
responses to PCV13 are significantly greater than those induced by PPV238. A Phase IV trial, the 
Community Acquired Pneumonia Immunization Trial in Adults (CAPITA) is currently 
underway to evaluate the efficacy of PCV13 against vaccine type nonbacteremic pneumococcal 
pneumonia in adults ≥ 65 years of age who have never received pneumococcal vaccines in the 
past9. The trial enrolled approximately 85,000 adults in the Netherlands and efficacy results are 
expected in 2013. 
A better understanding of the innate and adaptive immunologic mechanisms by which the 
elderly respond to both pneumococcal vaccines could determine the best vaccination strategies 
necessary to decrease the burden of disease associated with increase age. Defining the generic 
innate immune signatures of existing pneumococcal vaccines will allow more rapid and reliable 
evaluation of new vaccine candidates more suitable to populations at high risk for 
pneumococcal diseases particularly the elderly. Therefore additional early surrogates of 
protection are required to more accurately and rapidly evaluate and predict immune response 
after vaccination in the elderly. 
 In this context, systems biology approaches offer a new approach to compare the global 
architecture of the immune response between PPV23 and PCV13. Systems biology is a biology-
based inter-disciplinary study field that focuses on complex interactions in biological systems, 
using a new holistic perspective. Systems biology offers several so-called “Omic” technologies 
that can provide unbiased and rich information on the physiological state of organisms through 
their molecular profiles. These systems biology approaches are likely to be of value in 
identifying molecular signatures that are induced rapidly after vaccination and that correlate 
with, and predict, the later development of protective immune responses. Such a strategy 
would be particularly useful when evaluating the efficacy or immunogenicity of suboptimal 
vaccines, or in identifying individuals who are likely to respond sub-optimally to vaccination, 
such as the elderly receiving PPV23 in particular. Furthermore, the predictive signatures would 
highlight new correlates of protective immunity and stimulate the formulation and validation 
of new hypotheses on the biological mechanisms by which such molecular signatures modulate 
vaccine-induced immunity and protection. Despite this promise in identifying molecular 
signatures, they have only recently been applied to vaccinology10, 11. 
Accordingly, a key goal of the present proposal is to identify molecular signatures that predict 
the sub-optimal immunogenicity of PPV23 when compared to PCV13 in the elderly. One of the 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
key systems biology technologies that will be employed are microarray analyses. Essentially, 
blood samples will be isolated at baseline (day 0 prior to vaccination), and at days 1, 3, 7, 14 post 
vaccination, and the RNA from the peripheral blood mononuclear cells isolated and analyzed 
for the expression of mRNAs. The microarray platform will be Affymetrix Human Genome 
U133 Plus 2.0 Array, similar to what we had used previously10. In our previous work on yellow 
fever vaccine10, we identified a gene signature that correlates with and predicted YF-17D CD8+ 
T cell responses with up to 90% accuracy in an independent, trial. A distinct signature, 
including B cell growth factor TNFRS17, predicted then neutralizing antibody response with up 
to 100% accuracy. These findings highlight the utility of system biology approaches in 
predicting vaccine efficacy. 
In summary the proposed study offers an unprecedented opportunity to capture the global 
architecture of immune responses to PPV23 versus PCV13 in the elderly. This is likely to have a 
major impact in two areas: (i) the elucidation of unique signatures of innate immune response 
that predict vaccine immunogenicity, and will thus be relevant from a public health perspective; 
(ii) such unique signatures of innate immune response may illuminate the immunologic defects 
responsible for sub-optimal immunity in the elderly population when using a polysaccharide 
vaccine when compared to a conjugate vaccine. 
1.2 
Rationale for Selection of Study Population 
To be able to probe the immune system and better understand the innate and adaptive immune 
responses in older adults to pneumococcal vaccines, 88 healthy volunteers between the ages of 
25-40 and 60-89 years will be randomized to receive either PPV23 or PCV13 in a 1:1 ratio. Both 
vaccines are approved for persons 50 and above. However, we elected to study older subjects 
(60 years and above) because functional antibodies decrease markedly with more advanced age. 
The younger group will include 22 subjects between the ages of 25-40 and will help understand 
the potential effect of age on immune responses to PCV13 and PPV23. Subjects will be recruited 
from the general population of metro Atlanta and enrolled at the Hope Clinic, located in 
Decatur, GA. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
1.3 
Investigational Product(s)/Intervention(s) 
The vaccines used in the study will be PNEUMOVAX®23 manufactured by Merck (Whitehouse 
Station, NJ) and PREVNAR®13 manufactured by Pfizer (New York, NY). Subjects in the study 
will be administered 1 dose per label of PNEUMOVAX®23 or PREVNAR®13. Study vaccines 
will be purchased from the manufacturers or their distributors. 
1.4 
Rationale for Selection of Investigational 
Product(s)/Intervention(s) and Regimen 
Both vaccines will be tested and compared to better understand the innate and adaptive 
immune responses of polysaccharide and conjugate pneumococcal vaccines in the elderly.  
1.5 
IMMUNE RESPONSE AGAINST PNEUMOCOCCUS AND 
SYSTEMS BIOLOGY EXPERIENCE 
Immunity following pneumococcal disease is directed primarily against the capsular 
polysaccharide of the bacteria serotype involved. Protective immunity is mainly dependent 
upon type-specific, anti-capsular antibodies, although serological correlates of immunity are 
poorly defined. Capsular polysaccharides when incorporated alone into vaccines are recognized 
by the immune system as “T-cell independent antigens”. The “T-cell independent” responses 
do not develop in children until 2 years of age. Although adequate IgG levels are obtained, the 
humoral response is characterized by a short-lived initial IgM response and the absence of a 
memory response12. In elderly, these “T-cell independent” responses elicit an adequate 
quantitative response (by ELISA) but a suboptimal qualitative response (measured by OPA and 
avidity) in vaccine recipients6. Thus, capsular polysaccharides alone are poorly immunogenic in 
the young and the elderly13, 6. 
The limited response to capsular polysaccharides has been overcome by coupling the 
polysaccharide to an immunogenic protein carrier, which can present the antigen as a T-cell 
dependent epitope. The glycoconjugate vaccines are “T-cell dependent antigens” and induce 
antibodies with good avidity 14 (47 to 76% of antibodies remaining bound to the antigen coated-
ELISA well after addition of 0.05M sodium thiocyanate), maturation, isotype switching, as well 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
as memory formation 15. Other major effects of these vaccines are prolonged mucosal antibody 
expression, interference with bacterial transmission, and herd immunity 5, 7  
Antibody mediated killing of Streptococcus pneumoniae (pneumococcus) by phagocytes is an 
important mechanism of protection of the human host against pneumococcal infections. It is 
thought that opsonophagocytic antibodies reflect in vivo mechanisms of defense against 
pneumococcal infection. Measurement of opsonophagocytic antibodies (functional antibody 
assay) using a standardized opsonophagocytic assay (OPA) is important for the evaluation of 
candidate vaccines4 and a requirement for the licensure of new pneumococcal conjugate vaccine 
formulations in infant populations. The measurement of functional antibodies has been shown 
to better correlate with protection in infant populations and it is also likely to be a better 
indicator for elderly populations than the measurement of antibodies specific to the capsular 
polysaccharides by ELISA (antibody binding assay). 
Although vaccination with PPV23 provides some protection against invasive pneumococcal 
disease in a healthy elderly population, there is evidence that vaccine efficacy declines with age 
16, and with associated co-morbidities4. The decrease in efficacy could be associated with the 
impairment in the functional quality of the response. Even with advanced age, individuals seem 
to retain the ability to quantitatively respond to PPV (measured by ELISA). However, the ability 
to elicit a functional antibody response (measured by opsonophagocytic assay (OPA) is reduced 
with advanced age 6, 17. 
In a randomized study comparing PCV13 to PPV23 in pneumococcal vaccine naïve subjects 
between the ages of 60 to 64 years, the GMTs for 10 of the 12 serotypes common to both 
vaccines were higher in the PCV13 group, and were statistically significant higher for 8 of the 12 
serotypes8. In a previous randomized study comparing PCV7 to PPV23 in pneumococcal 
vaccine naïve subjects ≥70 years of age, OPA GMTs were significantly higher in the PCV7 group 
for 5 of the 7 common serotypes18.  
Data on innate immunity to PCV13 and to PPV23 are limited. Sen et al.19 have shown that 
PPV23 contains both TLR2 and TLR4 ligands. Our preliminary in vitro data show that PPV23 
signals via TLR2 and TLR9 and activates human CD11c+ myeloid DC precursors to secrete 
several cytokines and chemokines, including IL-6, IL-12p40, TNF and IL-8. Interestingly MCP-1, 
a chemokine involved in recruitment of many inflammatory cells including monocytes, was not 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
induced. In contrast, monocytes only produced IL-8 to PPV23. These results suggest that PPV23 
induces distinct cytokine profiles from different subsets of antigen presenting cells.  
A better knowledge of the innate immunity is crucial to understand the immunologic 
mechanisms of response to PPV23 and PCV13 vaccines.  
1.5.1 Preclinical studies 
N/A 
 
1.5.2. Clinical studies 
N/A 
1.6 
Risks 
1.6.1 
Risks of Investigational Product(s)/Intervention(s) 
Pneumococcal polysaccharide vaccine is recommended for all adults aged ≥65 years and those 
adults aged 19-64 years with underlying medical conditions that put them at greater risk for 
serious pneumococcal infection 20. The Advisory Committee on Immunization Practices (ACIP) 
will continue to review evidence as it becomes available to guide development of a 
recommendation regarding routine use of PCV13 in adults aged 50 years and older21 . Eleven 
immunocompetent subjects between the ages of 25-40 will receive PPV23 without an indication. 
Safety concerns in this group are not anticipated on the basis of previous safety data generated 
in young adults vaccinated with pneumococcal vaccines with lower valency (6 and 12) which 
was used to support the licensure of PPV2321a .Additionally, the safety profile is not expected to 
differ between young adults without co-morbidities and adults with a medical indication to 
receive PPV23. 
PNEUMOVAX®23, manufactured by Merck (Whitehouse Station, NJ), is indicated for 
vaccination against pneumococcal disease caused by those pneumococcal types included in the 
vaccine. The most common adverse experiences reported in >10% of subjects vaccinated with 
PNEUMOVAX®23 in clinical trials were: local reaction at injection site including 
pain/soreness/tenderness, erythema, swelling/induration and systemic reaction, mostly with 
asthenia/fatigue, myalgia and headache.  
  

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
Other Adverse reactions identified during post approval use of PNEUMOVAX 23 include:  
Guillain-Barré syndrome,  radiculoneuropathy, seizure, angioneurotic edema, cellulitis, nausea, 
vomiting, arthralgia, arthritis, limb mobility decreased, paresthesia, weakness, anaphylactoid 
reaction, lymphadenitis, serum sickness. Because these reactions are reported voluntarily from a 
population of uncertain size, it is not always possible to reliably estimate their frequency or 
their causal relationship to product exposure. 22. 
PREVNAR®13, manufactured by Pfizer (New York, NY), is indicated in adults (50 years or 
older) for prevention of pneumonia and invasive disease caused by those pneumococcal types 
included in the vaccine. In adults aged 50 years and older solicited adverse reactions reported in 
>10% of subjects vaccinated with PREVNAR®13 were: pain at the injection site (>50%), fatigue 
(>30%), headache (>20%), muscle pain (>20%), joint pain (>10%), decreased appetite (>10%), 
injection site redness (>10%), injection site swelling (>10%) and  limitation of arm movement 
(>10%)23. In one randomized study comparing safety of PCV13 to PPV23 in 60-64 years old 
previously unvaccinated, the frequency of local reactions was not statistically significant in both 
arms except for pain (more frequent in the PCV13 arm). Also the frequency of systemic 
reactions was not statistically different in both arms except for decrease in appetite, joint and 
muscle pains (more frequent in the PPV23 arm) 23. In 6 studies comparing the safety of PCV13 to 
PPV23, SAE were similar among both groups (around 6% at 6 months post vaccination) 23.  
Eleven immunocompetent subjects between the ages of 25-40 will receive PCV13 without an 
indication. The safety profile of PREVNAR13®  in immunocompetent healthy adults aged 25-40 
years -including both systemic and injection-site adverse events- is not expected to be different 
than in subjects ≥ 50 years old. Safety concerns in this group are not anticipated on the basis of 
previous safety data generated in young adults vaccinated with pneumococcal conjugate 
vaccines with lower valency (7). Multiple studies have been published on the use of 
PREVNAR7® in immunocompromised hosts in transplant recipients23a and HIV infected 
subjects 23b with acceptable safety profile. In one study with 25 young adults non HIV infected 
between the ages of 29-46, side effects with PREVNAR7® were mild (98%) mostly involving 
local tenderness, malaise, and myalgia. These side effects occurred within 7 days after 
vaccination and none were severe or life-threatening 23b.  
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
Revaccination with PPV23 is recommended by the ACIP for subjects with functional or 
anatomic asplenia and for persons with immunocompromising conditions20, although, this 
population is not eligible for the current study. However, the ACIP recommends that those who 
received PPV23 before age 65 years for any indication should receive another dose of the 
vaccine at age 65 years or later if at least 5 years have passed since their previous dose.  
Persons aged >65 years should be administered a second dose of vaccine if they received the 
vaccine >65 years previously and were aged <65 years at the time of primary vaccination. 
Revaccination with PNEUMOVAX®23 is considered safe although for subjects aged > 65 years 
the overall injection-site adverse experiences rate was higher following revaccination (79.3%) 
than following primary vaccination (52.9%). The rate of vaccine-related systemic adverse 
experiences was also higher following revaccination (33.1%) than following primary vaccination 
(21.7%) in subjects > 65 years of age22. With revaccination there is a potential risk of 
hyporesponsiveness with certain serotypes 24, 25. In both of these longitudinal studies, patients 
were, of course, older at the time of revaccination than at first vaccination and so it is possible 
that some of the differences in the immune response to revaccination were due to an age-effect, 
rather than to an effect of prior receipt of pneumococcal polysaccharide vaccine. 
Ortqvist et al. also show how the responses in the elderly are serotype specific, with some 
serotypes eliciting poorer responses than others26. A recent study by Manoff et al., show that 
both IgG antibodies and functional antibodies persist in persons older than 65 year above 
baseline concentrations five year after primary vaccination and revaccination27. Although the 
responses were slightly lower after revaccination there was no blunting of the responses to a 
second dose of the polysaccharide vaccine. Responses are markedly different in the elderly if 
the polysaccharide vaccine is given after the conjugate vaccine, where there is clear evidence of 
the lack of booster response and possible hyporesponsiveness regardless of the dose of 
conjugate vaccine used for priming 28, 29. In contrast, immunologic hyporesponsiveness is not 
seen with PCVs, and repeated doses of PCVs can be given to without diminishment of the 
immune response 28, 30.  
However, it should be noted that because the quantity of antibodies that correlate with 
protection against pneumococcal disease has not been clearly defined, it is unknown if the 
lower antibody levels seen on revaccination correlate with inferior protection. There is also the 
added advantage of increased serotype coverage by the PPV23.  Currently, there are no 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
published recommendations from the ACIP regarding the subsequent use of PCV13 in 
immunocompetent adults previously vaccinated with PCV13.  
1.6.2 
Risk of Study Procedures 
The discomforts of this study include having blood drawn, intramuscular (IM) injection, and 
possible allergic reactions to the components the pneumococcal vaccines administered in the 
study. 
Drawing blood causes transient discomfort and may cause fainting. Bruising at the blood draw 
site may occur but can be prevented or lessened by applying pressure to the draw site for 
several minutes. Intramuscular injection also may cause transient discomfort. The use of aseptic 
technique will make infection at the site where blood will be drawn or where the vaccination is 
given extremely unlikely. Vaccines used in the study will be a single vial dose preventing the 
risk of over or under dosing and the potential risk of contamination when compared to multi-
dose vials. 
In the clinical trials of PNEUMOVAX® 23 22, the most common local adverse events at the site of 
injection were pain/tenderness/soreness (60.0%), swelling/induration (20.3%), and erythema. 
The most common systemic adverse experiences were headache (17.6%), asthenia/fatigue 
(13.2%), and myalgia (11.9%).  All of these adverse reactions were reported at a rate lower than 
10% after receiving a placebo injection.  
In the post-marketing experience of PNEUMOVAX®23, the following additional adverse 
reactions have been identified: Cellulitis, Malaise, Fever (>102°F), Warmth at the injection site, 
Decreased limb mobility, Peripheral edema in the injected extremity, Nausea, Vomiting, 
Lymphadenitis, Lymphadenopathy, Thrombocytopenia in patients with stabilized idiopathic 
thrombocytopenic purpura, Hemolytic anemia in patients who have had other hematologic 
disorders, Leukocytosis, Anaphylactoid reactions, Serum Sickness, Angioneurotic edema, 
Arthralgia, Arthritis, Paresthesia, Radiculoneuropathy, Guillain-Barré syndrome, Febrile 
convulsion, Rash, Urticaria, Cellulitis-like reactions, and Increased serum C-reactive protein. In 
the clinical trials of PREVNAR® 13 23, the most common solicited local reactions were pain (69-
88%), limitation of arm movement (24-41%), swelling (10-22%), and redness (12-20%).  The most 
common systemic adverse experiences were generalized new muscle pain (47-62%), generalized 
aggravated muscle pain (16-32%), generalized new joint pain (16-32%), generalized aggravated 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
joint pain (14-26%), decreased appetite (15-25%), chills (20-24%), headache (50-66%), fatigue (51-
63%). 
1.6.3 
Risk of Concomitant Medications, Prophylactic Medications and 
Rescue Medications 
We do not anticipate the use of any other medication; however should anaphylactic or 
hypersensitivity reactions occur, an epinephrine (1:1000) and diphenhydramine injections are 
readily available at the Hope Clinic during vaccine use. Epinephrine injection can be associated 
with high blood pressure, arrhythmia, lightheadedness, nervousness, restlessness, tremor, 
shortness of breath and diaphoresis. The frequency of these side effects is not defined. 
Diphenhydramine injection can be associated with low blood pressure, arrhythmia, confusion, 
dizziness, sedation, restlessness, diarrhea, nausea and urinary retention. The frequency of these 
side effects is also not defined. 
Subjects are allowed to use acetaminophen or NSAIDs if they experience a moderate to severe 
local or systemic side effects after vaccine administration. 
1.7 
Benefits 
1.7.1 
Benefits of Investigational Product(s)/Intervention(s) 
Participants will have the benefit of receiving a licensed pneumococcal vaccine which may offer 
protection against pneumococcal disease. Also the knowledge gained from this study could 
facilitate the design of more effective pneumococcal vaccines for the geriatric population. 
1.7.2 
Benefits of Study Procedure(s) 
None 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
2. 
OBJECTIVES 
PCV13 induces better functional immune responses when compared to PPV23 in older naïve 
adults. We hypothesize that this is due to intrinsic defects in innate responses that could explain 
the poor immunogenicity of PPV23 when compared to PCV13. Therefore, we propose to 
extensively study innate and adaptive immune responses generated after administration of 
either pneumococcal polysaccharide or conjugate vaccines in older adults. 
2.1 
Primary Objective(s) 
To analyze the generic innate immune signatures that correlate with  the magnitude of the 
adaptive immune responses (opsonophagocytosis [OPA] titers)  at day 30 in order to identify 
the correlation signatures of the innate immune responses to PPV23 and PCV13. 
2.2 
 Secondary Objective(s) 
To analyze the generic innate immune signatures that correlate with the persistence and the 
quality of the adaptive immune responses determined by serological assays to PPV23 and 
PCV13. 
2.3 
Exploratory Objective(s) 
To compare the generic innate immune signatures that correlate with the magnitude of the 
adaptive immune responses (opsonophagocytosis [OPA] titers) in elderly and the young in the 
different age strata. 
To compare the generic innate immune signatures that correlate with the persistence and the 
quality of the adaptive immune responses as determined by memory B cells, plasmablasts and 
monoclonal antibodies to PPV23 and PCV13. 
 
 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
3. 
STUDY DESIGN 
This is a single center, mechanistic study in which 88 healthy subjects will be stratified by age 
with 22 subjects (ages 25-40) and 66 subjects (ages 60-89). and randomized to receive PPV23 or 
PCV13 in a 1:1 ratio. 
Study volunteers will be recruited from the general population of metropolitan Atlanta. The 
study will be conducted at the Hope Clinic of the Emory Vaccine Center (Decatur, GA). The 
expected duration of subject participation is 6 months. An additional optional blood draw will 
be offered 2-3.5 years after enrollment. 
3.1 
Study Endpoints 
3.1.1 
Primary Endpoint(s) 
3.1.1.1 Identification of generic innate immune signatures [Traditional immune parameters 
measurements + array-based gene expression] at days 1, 3 and 7 post vaccination with 
either PPV23 or PCV13 in the elderly. 
3.1.1.2. Measurement of adaptive immune responses [Opsonophagocytosis assay (OPA) titers] 
at day 30 post vaccination with either PPV23 or PCV13 in the elderly. 
3.1.1.3. Correlation of signatures of generic innate immune  responses at days 1, 3 and 7 with 
adaptive immune responses [Opsonophagocytosis assay OPA titers] at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
3.1.2 
Secondary Endpoint(s) 
3.1.2.1. Comparison of serotype specific IgG levels at day 30 post vaccination with either PPV23 
or PCV13 in the elderly. 
3.1.2.2. Correlation of signatures of generic innate immune responses at days 1, 3 and 7 that 
correlate to serotype specific IgG levels at day 30 post vaccination with either PPV23 or 
PCV13 in the elderly. 
3.1.2.3. Comparison of the serotype specific avidity indexes in a subset of up to 6 vaccinees per 
vaccine group at day180 post vaccination with either PPV23 or PCV13 in the elderly. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
3.1.2.4. Correlation signatures of generic innate immune responses at days 1, 3 and 7 that 
correlate to serotype specific avidity indexes in a subset of up to 6 vaccinees per vaccine 
group at day 180 post vaccination with either PPV23 or PCV13 in the elderly. 
3.1.2.5. Comparison of the adaptive immune responses [Opsonophagocytosis assay (OPA) 
titers] at day 30 post vaccination with either PPV23 or PCV13 in the elderly. 
3.1.3 
Exploratory Endpoint(s) 
3.1.3.1. Identification of correlation signatures of generic innate immune  responses at days 1, 3 
and 7 that correlate to adaptive immune responses [Opsonophagocytosis assay OPA titers 
specifically] at day 30 post vaccination among subjects in different age strata. 
3.1.3.2. Comparison of the kinetics and magnitude of select serotype specific plasmablasts (days 
7, 14, 30(with day 30 on a subset of vaccinees only)) and memory B cells (days 30, 180) post 
vaccination with either PPV23 or PCV13. 
3.1.3.3. Comparison of the repertoire and monoclonal antibodies from plasmablasts in a subset 
of vaccinees per vaccine group at day 7 post vaccination with either PPV23 or PCV13. 
3.1.3.4. Comparison of identified innate signature variables and correlation signature variables 
between PPV23 and PCV13 recipients. 
3.1.3.5. Comparison of generic innate immune responses at days 1, 3 and 7 with adaptive 
immune responses [Opsonophagocytosis assay OPA titers and ELISA] at years 2-3.5 post 
vaccination with either PPV23 or PCV13. 
 
Note: This will include - but not only - a comparison of identified innate signature variables and 
correlation signature variables between elderly (60 to 89 yo) recipients of PCV13 and young (25-
40yo) recipients of PPV23. 
3.2 
Study Completion 
This study will be considered “completed” when the primary and secondary objectives have 
been met. This includes the analysis of all the data required to meet the study objectives 
described above. 
After the study is completed, the Principal Investigator (or co-PI) or Data Center will compile an 
abbreviated study reports. The study report will be reviewed by the ISM and submitted to the 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
local IRB and DAIT/NIAID. Alternatively, the publication of the study could be used for the 
purposes of this requirement. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
4. 
SELECTION OF STUDY PARTICIPANTS 
4.1 
Inclusion Criteria 
1. Able to understand and give informed consent. 
2. Immunocompetent community dwelling subjects between the ages of 25-40 and 60-89 
years. 
4.2 
Exclusion Criteria 
1. Prior vaccination with pneumococcal vaccine. 
2. Receipt of immune products 
a. Subjects received blood products within 3 months*. 
b. Subjects received of any live virus vaccines within 4 weeks prior to study entry 
or expected receipt within 4 weeks after study entry*. 
c. Subjects received of any inactivated vaccine within 2 weeks or expected receipt 
within 2 weeks after study entry*. 
3. Presence of co morbidities or immunosuppressive states such as: 
o Chronic medical problems including (but not limited to) insulin dependent 
diabetes, severe heart disease, severe lung disease, severe liver disease, 
cerebrospinal fluid leaks, severe kidney disease, autoimmune diseases, severe 
gastrointestinal diseases and grade 4 hypertension per CTCAE criteria**.  
o Alcohol, drug abuse or psychiatric conditions that in the opinion of the 
investigator would preclude compliance with the trial or interpretation of safety 
or endpoint data. 
o Impaired immune function or known chronic infections including, but not 
limited, to known HIV,  hepatitis B or C; organ transplant; immunosuppression 
due to cancer; current and/or expected receipt of chemotherapy, radiation 
therapy, steroids*** (i.e., more than 20 mg of prednisone given daily or on 
alternative days for 2 weeks or more in the past 90 days , or high dose inhaled 
corticosteroids**** or any other immunosuppressive therapies (including anti-

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TNF 
therapy), 
 
functional 
or 
anatomic 
asplenia 
and 
congenital 
immunodeficiency. 
4.  Conditions that could affect the safety of the volunteers such as: 
o Severe reactions to prior vaccinations. 
o An allergy to any component of the study vaccines (phenol, aluminum, CRM197 
protein, succinic acid, Polysorbate 80). 
o History of Guillain-Barré syndrome. 
o History of bleeding disorders. 
5. Volunteers with any acute illness* including, but not limited to,   fever (> 100.4 F [> 38 
C], regardless of the route)  within 3 days prior to study entry. 
6. Volunteers with social conditions or occupational conditions or any condition that in the 
opinion of the investigator might interfere with compliance with the study and vaccine 
evaluation. 
7. Pregnant or breast feeding or women expected to conceive within 30 days after vaccination 
***** 
 
*An individual who initially is excluded from study participation based on one or more of 
the time-limited exclusion criteria (e.g., acute illness, receipt or expected  receipt of live or 
inactivated vaccines ) may be reconsidered for enrollment once the condition has resolved 
as long as the subject continues to meet all other entry criteria. 
** Grade 4 hypertension per CTCAE criteria is defined as Life-threatening consequences 
(e.g., malignant hypertension, transient or permanent neurologic deficit, hypertensive crisis) 
urgent intervention indicated. 
***Subjects receiving > 20 mg/day of prednisone or its equivalent daily or on alternate days 
for more than 2 weeks may enter the study after therapy has been discontinued for more 
than 3 months. 
****High dose ICS is defined as: > 960 mcg/day of beclomethasone dipropionate or 
equivalent. 
***** Women of child-bearing potential (not surgically sterile via tubal ligation, bilateral 
oophorectomy or hysterectomy or who are not postmenopausal for ≥1 year) must agree to 
practice adequate contraception that may include, but is not limited to, abstinence, 
monogamous relationship with vasectomized partner, barrier methods such as condoms, 

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diaphragms, spermicides, intrauterine devices, and licensed hormonal methods for 30 days 
before and 30 days after receiving PPV23 or PCV13. 
4.3 
 Early Study Termination 
Participants may be terminated early from the study for the following reasons: 
a. The participant elects to withdraw consent from all future study activities, including follow-
up. 
b. The participant is considered by the PI to be “lost to follow-up” (i.e., no further follow-up is 
possible because attempts to reestablish contact with the participant have failed). 
c. The participant dies. 
d. The participant develops a medical condition or is started on new medication(s) not 
previously mentioned in the list of prohibited medications that, in the opinion of the 
investigator, may pose additional risks from participation in the study, may interfere with the 
participant’s ability to comply with study requirements or that may impact the quality of the 
data obtained from the study. 
 e. Blood not able to be drawn (for technical or other reasons) or participant not tolerating 
multiple blood draw attempts.  
f. As deemed necessary by the PI or her designee for noncompliance or other reasons. 
g. As deemed necessary by the PI after development related AE/SAE. 
h. The participant meets the individual stopping rule -delineated in section 8. 
Participants with early termination from this study may be replaced as needed to preserve the 
statistical power needed to prove the primary endpoint (Refer to section 9.1). 
Note:  
Up to the discretion of the PI, participants receiving prohibited medications before blood draw 
at day 30 (+/-7 days) or missing any of the blood draws required for the primary endpoint 
[meaning draws at days  1, 3, 7(+1), and 30 (+7)]  may still continue with the scheduled study 
blood draws required for secondary and exploratory study endpoints. 
Subjects receiving prohibited medications before blood draw at day 30 (+/-7 days) or missing 
any of the blood draws required for the primary endpoint [meaning draws at days 1, 3, 7(+1), 
and 30 (+7)], along with participants with early termination from this study for any reason may 

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be replaced as needed to preserve the statistical power needed to prove the primary endpoint. 
(Refer to section 9.1)  
 

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5. 
INVESTIGATIONAL PRODUCT(S)/INTERVENTION 
MATERIAL(S), OTHER STUDY PRODUCTS 
(CONTROLS/PLACEBOS) 
5.1 
Investigational Product(s)/Intervention(s) 
The Emory Investigational Drug Service will purchase PNEUMOVAX® 23 from its 
manufacturer (Merck, Whitehouse Station, NJ) and PREVNAR®13 from its manufacturer 
(Pfizer, New York, NY) or their distributors. The Emory Investigational Drug Service will store 
the vaccines and will monitor temperatures of refrigerator containing the vaccines. 
Refer to section 1.6, and applicable product labeling for known and potential risks to human 
participants associated with the investigational product(s) intervention(s). 
5.2 
Formulation, Packaging, and Labeling 
PNEUMOVAX® 23 (Pneumococcal Vaccine Polyvalent) is a sterile, liquid vaccine for 
intramuscular or subcutaneous injection. It consists of a mixture of highly purified capsular 
polysaccharides from the 23 most prevalent or invasive pneumococcal types of Streptococcus 
pneumoniae, including the serotypes that most frequently cause invasive drug-resistant 
pneumococcal infections among children and adults in the United States.  
 
 
PNEUMOVAX 23 is manufactured according to methods developed by the Merck Research 
Laboratories. Each 0.5 mL dose of vaccine contains 25 micrograms of each polysaccharide type 
in isotonic saline solution containing 0.25% phenol as a preservative. 
PNEUMOVAX 23 will be supplied as a single-dose vial of liquid vaccine. 
PREVNAR 13®, Pneumococcal 13-valent Conjugate Vaccine (Diphtheria CRM197 Protein) is a 
sterile suspension of saccharides of the capsular antigens of Streptococcus pneumonia serotypes 1, 
3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F, individually linked to nontoxic diphtheria 
CRM197 protein. Each serotype is grown in soy peptone broth. The individual polysaccharides 

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are purified through centrifugation, precipitation, ultrafiltration, and column chromatography. 
The polysaccharides are chemically activated to make saccharides, which are directly 
conjugated by reductive amination to the protein carrier CRM197, to form the glycoconjugate.  
The individual glycoconjugates are compounded to formulate Prevnar®13. Potency of the 
formulated vaccine is determined by quantification of each of the saccharide antigens and by 
the saccharide to protein ratios in the individual glycoconjugates. Each 0.5 mL dose of the 
vaccine is formulated to contain approximately 2.2 μg of each of Streptococcus pneumoniae 
serotypes 1, 3, 4, 5, 6A, 7F, 9V, 14, 18C, 19A, 19F, 23F saccharides, 4.4 μg of 6B saccharides, 34 μg 
CRM197 carrier protein, 100 μg polysorbate 80, 295 μg succinate buffer and 125 μg aluminum as 
aluminum phosphate adjuvant. 
 
Note: No additional labeling of the vaccines will be required 
5.3 
Preparation, Administration, and Dosage 
PNEUMOVAX®23: 
Vaccine vials will be stored at +2ºC to +8ºC (36ºF to 46ºF) and administered per label as below: 
The vaccine will first be inspected visually for particulate matter and discoloration prior to 
administration and will not be used if particulate matter or discoloration is found. The vaccine 
is used directly as supplied. No dilution or reconstitution is necessary.  
A single 0.5 mL dose of PNEUMOVAX®23 will be administered via the intramuscular route in 
the deltoid muscle. 
PREVNAR®13: 
Vaccine vials will be stored at +2ºC to +8ºC (36ºF to 46ºF) and administered per label as below: 
The vaccine will first be inspected visually for particulate matter and discoloration prior to 
administration and will not be used if particulate matter or discoloration is found. The prefilled 
syringe will be shaken vigorously immediately prior to use to obtain a homogenous, white 
suspension in the vaccine container.  
A single 0.5 mL dose of PREVNAR®13 will be administered via the intramuscular route in the 
deltoid muscle.  

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5.4 
Accountability of Investigational 
Product(s)/Intervention(s) 
Under Title 21 of the Code of Federal Regulations (21CFR §312.62) the investigator will 
maintain adequate records of the disposition of the investigational product(s)/intervention 
material(s), including the, date and quantity of the drug received, to whom the drug was 
dispensed (participant-by-participant accounting), and a detailed accounting of any 
investigational product(s)/intervention material(s) accidentally or deliberately destroyed. 
Records for receipt, storage, use, and disposition will be maintained by the study site. A 
dispensing log will be kept current for each participant. This log will contain the identification 
of each participant, the name of the vaccine administered to the subject, the lot of vaccine 
received by the subject and the date and quantity of vaccine dispensed. 
All records regarding the disposition of the investigational product(s)/intervention material(s) 
will be available for inspection by the site monitor, the health authorities, and DAIT/NIAID 
personnel. 
5.5 
Assessment of Compliance with Investigational 
Product(s)/Intervention Material(s) 
Number of used vaccine vials will be tracked and reconciled by the nursing staff prior to 
sending the vaccine back to the Emory Investigational Drug Service. 
5.6 
Modification or Discontinuation of Investigational 
Product(s)/Intervention Material(s) 
5.6.1 
Modification of Investigational Product(s)/Intervention(s) 
Unless the lots of PNEUMOVAX®23 or PREVNAR®13 used in the study are recalled by the 
manufacturers, there will be no discontinuation of administration of study vaccines. 
5.6.2 
Premature Discontinuation of Investigational 
Product(s)/Intervention(s) 
Refer to sections 4.3 for possible causes of early study termination. 

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If a subject withdraws from the study for any reason, the subject will be then be censored from 
the study.  
Refer to section 8.1.3 for safety follow-up after early study termination. 

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6. 
OTHER MEDICATIONS 
6.1 
Concomitant Medications 
In accordance with exclusion criteria, subjects expected to receive prohibited medications (see 
section 6.4) will be considered non-eligible for the study. All medications, therapies or vaccines 
administered to study subjects after study entry will be documented at each visit. 
6.2 
Prophylactic Medications 
Prophylactic medications will not be administered before vaccination or any study procedure. 
6.3 
Rescue Medications 
We do not anticipate the use of any rescue medication; however should anaphylactic or 
hypersensitivity reactions occur, an epinephrine (1:1000) and diphenhydramine injections are 
readily available at the Hope Clinic during vaccine use. 
When facing a medical emergency, the clinic staff will follow the institutional Hope Clinic SOP 
by calling 911 first. If needed, participant will be transferred to Emory University Emergency 
department for further care. 
Subjects are allowed to use acetaminophen or NSAIDs if they experience a moderate to severe 
local or systemic side effects after vaccine administration. 

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6.4 
Concomitant Study Medications 
All medications and vaccines received by study participants after administration of 
study vaccine should be reported to the study staff and recorded including (but not 
limited to) the following: 
- blood products, chemotherapy, immunosuppressive therapy (including anti-INF 
therapy) and radiation therapy (administered at any time after study vaccination)  
- inactivated vaccines (administered before the day 14 blood draw) 
- live-attenuated vaccine (administered before the day 30 blood draw)  
Any of the above medications can affect the innate and adaptive assay results and 
should not be used unless medically indicated.  
Up to the discretion of the PI, participants receiving concomitant medications may still 
continue with scheduled study blood draws. 
Subjects receiving concomitant 
medications, along with participants with early termination from this study for any 
reason, may be replaced as needed to preserve the statistical power needed to prove 
the primary endpoint. (Refer to section 9.1.). 

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7. 
STUDY VISITS AND PROCEDURES 
7.1 
Enrollment and Randomization 
This research study will be explained in lay terms to each potential research participant. The 
potential participant will sign an informed consent form before undergoing any study 
procedures. Participants who are deemed eligible for the study (see sections 4.1 and 4.2) will be 
enrolled and assigned a unique participant number. Approximately eighteen months are 
needed for enrollment. The duration of participation for each subject is approximately 6 
months. An additional optional blood draw will be offered 2-3.5 years after enrollment. 
Eighty eight subjects ( 22 subjects (ages 25-40) and 66 subjects ( ages 60-89)) will be randomized 
to receive PPV23 or PCV13 in a 1:1 ratio. 
7.2 
Screening Visit(s) 
Refer to 7.3 
7.3 
Baseline Visit(s) 
Interested subjects will call recruiters for a telephone screening where the eligibility criteria of 
the subject will be reviewed. To confirm that participant has never received pneumococcal 
vaccine in the past, vaccination records may be requested from participant’s physician after 
obtaining a release of information from the participant. If the subject is found to be eligible and 
continues to be interested in participating after reading the informed consent (emailed or 
mailed to him/her), an appointment will be scheduled.  
Study staff will review with the subject the study informed consent form and will answer all 
questions related to the study. Once the subject signs the informed consent, a study 
participation number will be assigned and subject will be randomized to receive PPV23 or 
PCV13. The participant will be asked to provide demographic information and information 
related to his/her medical history including current medications and vaccination history to 
verify eligibility. The volunteer’s vital signs will be recorded and a targeted physical exam will 
only be performed if needed based on findings during review of health status. For female 
volunteers of age bearing potential, a urine pregnancy test is obtained. Only females with a 

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negative urine pregnancy test will be enrolled in the study. Females of child bearing potential 
will be asked to use effective contraceptive method thirty days before and 30 days after 
vaccination. Blood for immunological assays will be drawn at this visit. For female participants 
aged 25-40 blood for immunological assays will be drawn after results of the urine pregnancy 
test are available and shown to be negative. 
The participant will get the pneumococcal Vaccine Information Sheet and then receive 1 dose 
per label of either PNEUMOVAX®23 or PREVNAR®13 according results of randomization.  
Any Adverse Event (including – but not only- vaccine reactions and local or systemic 
Reactogenicity Events) of grade 3 or higher severity or any SAE occurring after vaccination 
while the subjects is still at the clinical site will be recorded and reported. 
The participant will be provided with a written description of what represents a local and 
systemic vaccine reaction of mild, moderate and severe intensity (Refer to Appendix 3 and 
Appendix 4). Subjects will be instructed to notify the study center by telephone if they develop 
any severe reactions within 1 week following vaccination.  
At the end of the visit, the participant will also be instructed to promptly call the site if he/she 
develops any of the following: 
 becomes sick or has been treated at the doctor’s office or emergency department or has 
been hospitalized for any illness throughout D180 of the study; 
 develops any adverse event that limits self-care activities of daily living (e.g.  bathing, 
dressing and undressing, feeding self, using the toilet, taking medications, and not bed 
ridden) even if he/she decides not to get medical care; or 
 starts or stops any medications/therapies during enrollment in the study. 
 Becomes pregnant. 
Refer to section 8.2.5 for safety data that must be recorded and reported. 
Note:  Subjects calling the site for any of the above will receive further instructions on the 
proper course of action, including a return to the clinic for immediate evaluation if appropriate. 
The Baseline visit will last approximately 90 minutes. 

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7.4 
Main Study Visit(s) 
All participants will return for the study-related blood draws on Days 1, 3, 7(+1), 14(+2), 30 (+7)  
180 (+14) and year 2-3.5 (optional visit) after immunization. These visits will last approximately 
20 minutes. 
On days 1, 3, 7, 14, 30 and 180 study personnel will review current health status including: 
 
Evaluation of local REs and systemic REs of grade 3 or higher severity developing after 
the last visit (only until Day 7 Visit). 
 
Any adverse event (AE) that limited self-care activities of daily living or serious  adverse 
event (SAE) which may not have been reported by the participant by calling the site as 
directed at a prior visit. 
 
Any medications administered after vaccination. 
At the end of the visits on days 1, 3 and 7, 14 and 30 the participant will be instructed to 
promptly call the site if he/she becomes sick or has been treated at the doctor’s office or 
emergency department or has been hospitalized for any illness throughout D180 of the study. 
The participant will also be instructed to call the site if he/she develops any adverse event that 
limits self-care activities of daily living even if he/she decides not to get medical care, or 
starts/stops any medications/therapies. 
Refer to section 8.2.5 for safety data that must be recorded and reported. 
 
A focused physical exam will be conducted -if indicated- based on results of the review of 
health status as above. 
At year 2-3.5 visit, participant will be asked about any major change in health status and if they 
have received any pneumococcal vaccine since last study visit. 
7.5 
Follow-up Visit(s) 
Please refer to 7.4 
7.6 
Visit Windows 
Study visits should take place within the time limits below: 

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D0, D1, D3, D7 (+1), D14 (+2), D30 (+7), D180 (+14) and year 2-3.5 
7.7 
Study Procedures 
Refer to sections 7.3 and 7.4 
7.8 
Study Arm Assignment Procedures 
7.8.1 
Blinding and Randomization 
 
In this study 88 healthy subjects 22 subjects (ages 25-40) and 66 subjects (ages 60-89)) will be 
randomized to receive PPV23 or PCV13 in a 1:1 ratio. 
The randomization of the pre-filled vaccine syringes will be performed by the Emory 
Investigational Drug Service.  
7.8.2 
Securing Randomization Information 
The information on and randomization is kept at the Emory Investigational Drug Service.  
7.8.3 
Requirements for Unblinding 
HIPC: VAX-003 is an open study. Subjects will be made aware of which vaccine they are 
receiving 
at 
the 
time 
of 
vaccine 
administration 
and 
will 
be 
informed 
about: 
1.  the need for a second dose of vaccine depending on age at entry and randomization status. 
2.  the commitment of the investigators to inform subjects if any changes in recommendations 
for revaccination develop during subject's participation in the study. 
7.8.4 
Documenting an Unblinding 
N/A 
 

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8. 
SAFETY PROCEDURES 
8.1 
Stopping Rules 
8.1.1 
Study Stopping Rules 
Study enrollment will be suspended pending expedited review of all pertinent data by the 
institutional review board, the ISM, and the NIAID, if any of the following occurs:  
 
One unexpected SAE related to the vaccination 
 
Two unexpected AEs of grade 3 or higher severity of similar nature related to the 
vaccination 
 
Study vaccine is recalled by the manufacturer 
 
Occurrence of a case of Guillain-Barré Syndrome, radiculoneuropathy, anaphylactoid 
reaction,  anaphylaxis  or serum sickness considered related to vaccination 
8.1.2 
Individual Stopping Rules 
 Individual stopping rules include: 
 
Failure to receive a full dose of vaccine. 
8.1.3 
Follow-up after early study termination 
Participants who are prematurely terminated from the study due to a related AE/SAE will be 
followed until resolution of the AE or until 30 days after a participant terminates from the 
study, whichever comes later.  
 Note: 
Resolution of an AE is defined as the return to baseline status or as stabilization of the condition 
with the expectation that it will remain chronic. 
8.1.4 
Participant Replacement 
Up to the discretion of the PI, participants receiving concomitant medications may still continue 
with scheduled study blood draws. Subjects receiving concomitant medications, along with 
participants with early termination from this study for any reason, may be replaced as needed 
to preserve the statistical power needed to prove the primary endpoint (Refer to section 9.1). 

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8.2 
Adverse Events 
This section defines the types of adverse events and outlines the procedures for appropriately 
collecting, grading, recording, and reporting them. Information in this section complies with 
ICH Guideline E2A: Clinical Safety Data Management: Definitions and Standards for Expedited 
Reporting and  ICH E6: Guideline for Good Clinical Practice, and applies the standards set forth 
in the National Cancer Institute (NCI), Common Terminology Criteria for Adverse Events 
Version 4.0 [Published: May 28, 2009; revised version 4.03; June 14. 2010)]. These criteria have 
been reviewed by the study investigators and have been determined appropriate for this study 
population. 
8.2.1 Definitions 
8.2.1.1  
Adverse Events 
An adverse event (AE) is any occurrence or worsening of an undesirable or unintended sign, 
symptom, laboratory finding, or disease that is experienced during participation in the trial. An 
AE can therefore be any unfavorable and unintended sign, symptom, or disease temporarily 
associated with the use of a medicinal (investigational) Study Agent(s)/Intervention(s), whether 
or not related to the medicinal (investigational) Study Agent(s)/Intervention(s). 
8.2.1.2  
Adverse Events Associated with Study Vaccines and Study 
Procedures 
The most common adverse reactions after vaccine administration are fully described in Section 
1.6.1 . 
Adverse events after blood draws may include: 
 
Fainting /Vasovagal events 
 
Bruising at puncture site larger than 2 cm diameter 
 
Bleeding from puncture site lasting more than 30 minutes 
 
Swelling at puncture site larger than 2 cm 
 
8.2.2. Serious Adverse Event (SAE) 
An adverse event or suspected adverse reaction is considered ‘‘serious’’ if, in the view of either 
the investigator or sponsor, it results in any of the following outcomes:  

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-Death 
- A life-threatening adverse event 
- Inpatient hospitalization or prolongation of existing hospitalization 
- A persistent or significant incapacity or substantial disruption of the ability to conduct normal 
life functions 
 -A congenital anomaly/birth defect 
Important medical events that may not result in death, be life-threatening, or require 
hospitalization may be considered serious when, based upon appropriate medical judgment, 
they may jeopardize the patient or subject and may require medical or surgical intervention to 
prevent one of the outcomes listed in this definition.  
Examples of such medical events include allergic bronchospasm requiring intensive treatment 
in an emergency room or at home, blood dyscrasias or convulsions that do not result in 
inpatient hospitalization, or the development of drug dependency or drug abuse. 
Note: 
An adverse event or suspected adverse reaction is considered ‘‘life-threatening’’ if, in the view 
of either the investigator or sponsor, its occurrence places the patient or subject at immediate 
risk of death.  
It does not include an adverse event or suspected adverse reaction that, had it occurred in a 
more severe form, might have caused death. 
8.2.3. Unexpected Adverse Event or Adverse Reaction 
An adverse event or suspected adverse reaction is considered ‘‘unexpected’’ if it is not listed in 
the product label information of PNEUMOVAX®23 nor PRENAR®13 or is not listed at the 
specificity or severity that has been observed.  
For example, under this definition, hepatic necrosis would be unexpected (by virtue of greater 
severity) if the investigator brochure referred only to elevated hepatic enzymes or hepatitis. 
Similarly, cerebral thromboembolism and cerebral vasculitis would be unexpected (by virtue of 
greater specificity) if the investigator brochure listed only cerebral vascular accidents. 
‘‘Unexpected,’’ as used in this definition, also refers to adverse events or suspected adverse 
reactions that are mentioned in the product label information as occurring with a class of 
vaccine or as anticipated from the pharmacological properties of the product but are not 
specifically mentioned as occurring with the particular drug under investigation. 

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8.2.4. Independent Safety Monitor 
The ISM is a physician with relevant expertise whose primary responsibility will be to provide 
independent safety monitoring in a timely fashion and to provide recommendations regarding 
the safe continuation of the study.  
The ISM is a physician independent from the study team and will evaluate adverse events, 
including SAE, against the known safety profile of the study product to assess for possible 
changes to the overall risk of the study. Contact information for the ISM and the NIAID Medical 
Officer is listed in page 3 of this protocol.  
The ISM and the NIAID Medical Officer will communicate as needed to discuss any safety 
events of special interest developing during the study and when conducting the review of 
periodic reports of cumulative safety data. The study has provisions for a back-up to ensure that 
independent safety monitoring happens at all times during the study. Additional roles and 
responsibilities of the ISM are described in sections 8.2.7 and 8.3 below. 
8.2.5  Collecting, Recording and Managing Adverse Events 
8.2.5.1  
Collecting and reporting Adverse Events 
Adverse events occurring after the subject has signed the consent will be collected and reported 
as follows: 
 
Any Adverse Event (including – but not only- vaccine reactions and local or systemic 
Reactogenicity Events) of grade 3 or higher severity or SAE occurring after vaccination 
while the subjects is still at the clinical site. 
 
Local REs and systemic REs of grade 3 or higher severity occurring from Day 0 to Day 7 
reported over the telephone by the participant and/or assessed at the clinic. 
 
AEs of grade 3 or higher severity throughout D180 of the study (including -but not only 
– AEs linked to blood draws). 
 
All SAEs throughout D180.  
Adverse events may be identified during this study through any of these methods: 
1.  Examination of the participant during study visits. 
2.  Questioning the participant during study visits. 

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3.  Receiving a safety report from the participant by phone or during a site visit at any time 
during the study 
 Note: Not all safety events identified may require recording and reporting 
A complete recording of safety events in the CRF will include event term, date of onset and 
resolution/stabilization, 
assessment 
of 
severity, 
relationship 
to 
study 
vaccine 
or 
procedures/intervention(s) such as phlebotomy, expectedness, determination of whether the 
AE qualifies as serious, treatment required, action taken with study participation and outcome. 
AEs qualifying as SAEs also require a narrative of the event. Updates in safety events will be 
recorded as additional information becomes available. 
 
8.2.5.2 
Managing Adverse Events 
 
The site investigator must apply his or her clinical judgment as to whether an AE is of sufficient 
severity to require that the participant immediately be removed from further treatment under 
the protocol. The investigator must institute any necessary medical therapy to protect a 
participant from any immediate dangers.  
Severe related AEs and all SAEs will be followed until they are resolved.  
Participants who are prematurely terminated from the study due to a safety event will be 
followed until resolution of the AE or until 30 days after a participant terminates from the 
study, whichever comes later.  
Note:  
Resolution of an AE is defined as the return to baseline status or as stabilization of the condition 
with the expectation that it will remain chronic. 
 

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8.2.6. Grading and Attribution  
8.2.6.1.  
Grading criteria 
Adverse events requiring reporting in this study will be graded according to the criteria set 
forth in the National Cancer Institute’s Common Terminology Criteria for Adverse Events  
(Version 4.03; June 14, 2010). 
Adverse events requiring reporting in this study if not listed in the NCI-CTCAE (Version 4.03; 
June 14, 2010) will be graded on a scale from 1 to 5 according to the following general 
guideline in the NCI-CTCAE manual): 
Grade 1 Mild; asymptomatic or mild symptoms; clinical or diagnostic observations only; 
intervention not indicated.  
Grade 2 Moderate; minimal, local or noninvasive intervention indicated; limiting age-
appropriate instrumental ADL*. 
Grade 3 Severe or medically significant but not immediately life-threatening; 
hospitalization or prolongation of hospitalization indicated; disabling; 
limiting self-care ADL**. 
Grade 4 Life-threatening consequences; urgent intervention indicated. 
Grade 5 Death related to AE. 
*Instrumental Activities of Daily Living (ADL) refer to preparing meals, shopping for groceries 
or clothes, using the telephone, managing money, etc. 
**Self-care  Activities of Daily Living (ADL)   refer to bathing, dressing and undressing, feeding 
self, using the toilet, taking medications, and not bedridden. 
 Anaphylaxis is a disorder characterized by an acute inflammatory reaction resulting from the 
release of histamine and histamine-like substances from mast cells, causing a hypersensitivity 
immune response. Clinically, it presents with breathing difficulty, dizziness, hypotension, 
cyanosis and loss of consciousness and may lead to death. 
Severity grading of anaphylaxis as per the NCI-CTCAE (Version 4.03; June 14, 2010) manual is 
as follows: 
Grade 1=  
Grade 2=  
Grade 3= Symptomatic bronchospasm, with or without urticaria; parenteral intervention 

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indicated; allergy-related edema/angioedema; hypotension 
Grade 4= Life-threatening consequences; urgent intervention indicated 
Grade 5= Death  
8.2.6.2. 
Definition of Attribution 
The attribution of an adverse event to the study will be determined by the Principal Investigator 
or designated physician co/sub-investigator. The Principal Investigator or designee will record 
the determination of attribution on the appropriate adverse event or serious adverse event 
form.   
For the purpose of this study, the attribution of an AE to PNEUMOVAX®23 or PREVNAR 13® 
will be determined using the descriptors in the following table:  
 
Attribution of adverse events 
Code 
Descriptor 
Definition (guidelines) 
UNRELATED CATEGORY  
1 
Unrelated 
The adverse event is clearly not related to study. The event is 
completely related to an etiology other than the study 
product or study intervention (the alternative etiology must 
be documented in the study subject’s medical record) 
RELATED CATEGORIES  
2 
Unlikely 
The adverse event is doubtfully related to study and likely to 
be related to factors other than study product or study 
intervention. 
3 
Possible 
The adverse event may be related to study. There is an 
association between the event and the administration of 
study product and there is a plausible mechanism for the 
event to be related to the study product; there may be also 
an alternative etiology, such as characteristics of the subject’s 
clinical status and/or underlying disease 
 
4 
Probable 
The adverse event is likely related to study. There is (1)  an 
association between the event and the administration of 
study product or study intervention, (2) a plausible 
mechanism for the event to be related to the study product,  
and (3) the event could not be reasonably explained by 
known characteristics of the subject’s clinical status and  or 
an alternative etiology is not apparent 
5 
Definite 
The adverse event is clearly related to study. There is (1) an 

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association between the event and the administration of the 
study product or study intervention, (2) a plausible 
mechanism for the event to be related to the related to the 
study product, and (3) causes other than the study product 
have been ruled out and/or the event re-appeared on re-
exposure to the study product 
 
8.2.7. 
SAE Reporting Criteria and Procedures 
The Principal Investigator will be notified by the study staff as soon as a staff member becomes 
aware of the SAE. In the absence of the Principal Investigator, a physician sub-investigator will 
be notified. 
8.2.7.1. Notifying the Independent Safety Monitor and the NIAID Medical 
Officer of SAEs and pregnancy 
The Principal Investigator will notify the ISM and the NIAID Medical Officer by email 
simultaneously of any related SAE within 24 hours of becoming aware of the event.  
The investigator will be informed immediately of any pregnancy and will report all pregnancies 
within 24 hours to the ISM and the NIAID Medical Officer utilizing the SAE report form. This 
report is for tracking purposes only. All pregnancies that are identified during the study will be 
followed to conclusion and the outcome of each will be reported. The investigator will discuss 
with the participant and/or the treating physician the known possible risks of the 
investigational product(s) on the fetus. Monitoring of the participant will continue until the 
conclusion of the pregnancy, and a follow-up SAE report form detailing the outcome of the 
pregnancy will be submitted to the NIAID Medical Officer and Project Manager. Subject will 
not be terminated from the study if pregnancy occurred after day 30. 
The investigator will also report within 24 hours to the ISM and the NIAID Medical Officer any 
of the following events: 
- Guillain-Barré Syndrome 
- Radiculoneuropathy 
- Anaphylactoid reactions 
-Anaphylaxis 

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- Serum Sickness 
For non-related SAEs, the Principal Investigator will notify the ISM and the NIAID Medical 
Officer by email simultaneously of any related SAE within 7 days of becoming aware of the 
event.  
The initial SAE CRF should be signed by the PI or co-PI and include as much information as 
possible. The SAE case report form will re-submitted and signed by the PI or co-PI to the ISM 
the NIAID Medical Officer with updated relevant medical information as needed until the 
event is considered closed by the ISM and the NIAID Medical Officer.    
The study biostatistician, PI or study data manager will provide the ISM and the NIAID 
Medical Officer with cumulative periodic safety reports (tables and data listings of all AEs, 
including SAEs) during the conduct of the study. Resulting memorandums following 
evaluations of safety data will be sent to the IRB as needed in accordance with IRB rules and 
regulations. 
8.2.7.2. Notifying the FDA 
N/A 
8.2.7.3. 
Notifying the Institutional Review Board 
The Principal Investigator (or co-PI) will ensure the timely dissemination of SAE information, 
including SAEs requiring expedited ISM review and resulting memorandums following 
evaluations of safety data, to the IRB in accordance with IRB regulations and guidelines. 
 
8.3. 
Protocol Deviations 
Deviations occur when the Investigator, site study staff, or participants fail to adhere to protocol 
requirements or when there is non-adherence to (GCP) as delineated in ICH E6 (R1) guidelines.  
NIAID will not allow any waivers or planned deviations from the protocol.   
Upon determination that a protocol deviation has occurred, the study staff will a) notify the 
Principal Investigator, b) notify the NIAID Project Manager(refer to investigator’s signature 

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page for contact information) and c) will complete the Protocol Deviation form. NIAID may 
request discussion with the Principal Investigator and the ISM to determine the effect of the 
protocol deviation on the study participant and his/her further study participation, the effect of 
the protocol deviation on the overall study and corrective actions.   
The Principal Investigator will complete and sign the Protocol Deviation form and submit it to 
the NIAID Medical Officer and Project Manager, to the ISM Monitor and to the site IRB, per IRB 
regulations.   
Identification of protocol deviations will be done through the quality manager at the study site, 
or the NIAID project manager and/or Medical Officer. Reviewing and reporting of minor 
protocol deviations will be discussed at the Hope Clinic monthly meetings and among the Hope 
Clinic investigators. Major protocol deviations will be discussed with the PI, the ISM and 
NIAID study teams and will be promptly communicated to the regulatory agencies as needed.  
All study deviations will be captured in monthly reports along with safety data and forwarded 
to the study sponsor and the ISM. 

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9. SAMPLE SIZE CALCULATIONS AND STATISTICAL PLAN 
9.1. 
Sample Size and Power Calculations 
The study is explorative. Not enough preliminary data exists to support accurate calculation of 
the sample size. However we conducted a sample size analysis based on hypothetical scenarios 
and knowledge of similar studies. Based on previous studies performed at the Hope Clinic and 
the Vaccine Research Trials Center, the rate of subjects that become ineligible during the study 
(i.e. do not meet exclusion/inclusion criteria anymore, lost to follow-ups, unable to have blood 
draws) is between 5 to 10%. Assuming 10% attrition rate, 88 subjects will be recruited and 1:1 
randomized into the two treatment groups, resulting in an expected 80 subjects for data 
analysis. The sample size is on-par with similar studies. In the case that the sample size of 
subjects missing any of the 4 draws required for the primary endpoint [meaning draws at days 
1, 3, 7(+1), and 30 (+7)]   is   higher than 10% of the 88 subjects to be recruited for the study, we 
will recruit extra patients to maintain the target sample size of 80 subjects.  
The randomization process will be detailed in the MOP. At the center of this study is the 
identification of generic innate signatures and finding their correlations with the adaptive 
immune response. The generic innate signatures will be identified from both traditional 
immune parameters measured by FACS/Luminex assays and array-based gene expression will 
be measured by microarray experiments. The generic innate signatures will be identified for 
different treatment groups separately.  The traditional immune parameters and array-based 
gene expression that change after immunization are considered generic innate signatures. The 
traditional immune parameters and array-based gene expression  that are correlated with the 
adaptive immune responses (day 30 OPA titers, day 30 IgG levels, day 180 serotype specific 
avidity indexes, plasmablasts also) are considered correlation signatures of the innate immune 
responses.  
Both for sample size consideration and data analysis, we will use different stringency levels for 
the traditional immune parameters and microarray data, because the traditional immune 
parameters are measured with less noise, and a traditional immune parameter is more likely 
than an average gene to be associated with the immune response.  
 

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Primary Endpoint 1. 
The innate signatures will be detected in each treatment group separately. A two-sided paired 
paired t-test will be used to test each immune parameter, in order to find immune parameters 
that change significantly over the baseline. As multiple immune parameters are studied, we use 
the alpha level of 0.01 to offset multiple testing. With 30 samples in each treatment group in the 
elderly, we can reject the null hypothesis of equal means with 80% power if the true effect size 
(mean difference/sigma) is 0.66, using a two-sided paired t-test and the alpha level of 0.01.  
For the gene expression, again the innate signatures will be detected in each treatment group 
separately. The actual data analysis will be performed using the method Significance Analysis 
of Microarrays (SAM) with paired design. For sample size consideration, we will consider the 
simpler case of a paired t-test. As the number of genes tested is in the order of tens of 
thousands, we use the alpha level of 0.0005 to offset the effect of multiple testing. This means an 
average of one false positive for every 2000 null genes tested, which is an acceptable level as we 
expect >100 truly differentially expressed genes. In actual data analysis false discovery rate 
(FDR) will be used. With 30 samples in each elderly treatment group, we can reject the null 
hypothesis of equal means with 80% power if the true effect size (mean difference/sigma) is 
0.88, using a two-sided paired t-test and the alpha level of 0.0005. 
 
Primary Endpoint 3, Secondary Endpoints 2&4. 
The correlation signatures will be identified for each treatment group separately. The innate 
signature markers/genes identified in the analysis of Primary Endpoint 1 will be used in this 
step for the identification of correlation signature. For the traditional immune parameters, with 
30 samples in each elderly treatment group, at the alpha level of 0.01, we can reject the null 
hypothesis of zero correlation with 80% power if the true correlation is 0.57 using a two-sided 
test for Pearson’s correlation coefficient.  
For the gene expression data, the actual data analysis will be performed using SAM with 
quantitative outcome. For sample size consideration, we will consider the simpler case of 
testing the significance of Pearson’s correlation coefficient. We use the alpha level of 0.005 to 
offset the effect of multiple testing. This means an average of one false positive for every 200 
null genes tested, which is an acceptable level as we expect the number of innate signature 
genes under study will be in the hundreds. The alpha level used here is different from that in 

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Primary Aim 1, because the numbers of multiple tests being conducted are different (several 
hundreds v.s. tens of thousands in Aim 1). With 30 samples in each elderly treatment group, at 
the alpha level of 0.005, we can reject the null hypothesis of zero correlation with adaptive 
immune responses with 80% power if the true correlation is 0.60 using a two-sided test for 
Pearson’s correlation coefficient.  
9.2. 
Data Analysis 
9.2.1. General considerations 
The young treatment groups are of limited size. The main purpose of the young treatment 
groups is to provide some indication whether the elderly respond to the vaccines differently 
than the young. By themselves, the young groups do not have sufficient statistical power to 
generate reliable innate and correlation signatures. However when used in comparison against 
elderly groups, and by only considering biological pathways (collections of genes contributing 
to the same biological process) that are affected by the vaccine, they can provide some 
indication as to how different the response is in the elderly compared to the young.  Thus for 
data analysis, the young treatment groups will be used only in exploratory endpoints. The 
primary and secondary endpoints will focus on the elderly groups.  
 
The analyses will be based on population with critical time points met, defined as those who 
received vaccine per label and got the 4 draws required for the primary endpoint, i.e. draws at 
days 1, 3, 7 (+1), and 30 (+7)  within the required windows. Data from the study will be 
analyzed using the statistical software R31 .High-throughput data will be analyzed using 
appropriate methods, either by stand-alone software or modules in leading statistical softwares, 
e.g. the Bioconductor in the R framework32 .For cytokine data, missing values will be dealt with 
using multiple imputations. For microarray data, nearest neighbor method and local least 
squares may be used to fill missing values. Unsupervised learning techniques such as PCA, 
PLSDA, clustering, and factor analysis 33 will be used for the visualization and identification of 
global patterns. For descriptive endpoint (primary endpoint 2), we will generate summary 
statistics, and visualize the data using histograms and boxplots when applicable. For the 
identification of innate signatures, the two treatment groups will be analyzed separately.  
 

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Analyses of primary endpoints: 
1. Identification of generic innate immune signatures 
[Traditional immune parameters measurements 
+ array-based gene expression] at days 1, 3 and 7 post vaccination with either PPV23 or PCV13 in the 
elderly. 
The innate signatures will be detected in each elderly treatment group separately. We will take 
the measurements on the day of vaccination as baseline. For traditional immune parameters, we 
will test if an immune parameter shows significant change over baseline at day 1, 3, and 7 after 
each vaccination, using a two-sided paired t-test. In addition, for each immune parameter, the 
fold-change over baseline will be calculated for every subject. The average (arithmetic mean) 
fold change over the 30 subjects will be combined with the test p-value in a selection criterion as 
appropriate. Based on previous studies similar in nature, the tentative selection criterion is p-
value ≤ 0.01 and average fold change ≥ 3.  
For the gene expression data, again the innate signatures will be detected in each elderly 
treatment group separately. We will use the method Significance Analysis of Microarrays 
(SAM) 34 with paired design to find differentially expressed genes over the baseline. False 
discovery rate (FDR) will be used as selection criterion. The tentative selection criterion is FDR ≤ 
0.1.  
2. Measurement of adaptive immune responses [Opsonophagocytosis assay (OPA) titers] at day 30 post 
vaccination with either PPV23 or PCV13 in the elderly. 
The OPA titers will be presented as descriptions of the actual values separately in both study 
elderly populations (PPV23 and PCV13 recipients). Summary statistics, boxplots and 
histograms will be used to summarize the data.    
3. Correlation of signatures of generic innate immune responses at days 1, 3 and 7 that correlate to 
adaptive immune responses [Opsonophagocytosis assay OPA titers] at day 30 post vaccination with 
either PPV23 or PCV13 in the elderly. 
The correlation signatures will be detected in each elderly treatment group separately. The 
innate signature markers/genes identified in Primary Endpoint 1 will be used in this step for 
the identification of correlation signature.  
For traditional immune parameters, we will calculate the correlation coefficient between the 
immune parameter and the adaptive immune response (day 30 OPA titers). The p-values 
associated with the correlation coefficients will be used to select traditional immune parameters 

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that are associated with the respective adaptive immune responses (day 30 OPA titers). The 
tentative selection criterion is p-value ≤ 0.01.  
For gene expression data, we will use the method Significance Analysis of Microarrays (SAM) 
with quantitative outcome to identify genes that are significantly associated with the respective 
adaptive immune responses (day 30 OPA titers). False discovery rate (FDR) will be used as 
selection criterion. The tentative selection criterion is FDR ≤ 0.1.  
 
Analyses of secondary endpoints: 
1. Comparison of the serotype specific IgG levels at day 30 post vaccination with either PPV23 or PCV13 
in the elderly. 
Descriptive analysis, boxpots and histograms, will be conducted to present the data. Testing 
between the two elderly treatment groups will be conducted using unpaired t-test after proper 
data transformation. In the case that near-normality cannot be achieved with data 
transformation, we will resort to the Wilcoxon test.  
2.  Correlation of signatures of generic innate immune responses at days 1, 3 and 7 with serotype specific 
IgG levels at day 30 post vaccination with either PPV23 or PCV13 in the elderly.  
The analysis will be conducted in each elderly treatment group separately. For traditional 
immune parameters, we will calculate the correlation coefficient between the immune 
parameter and the adaptive immune response (IgG levels at day 30 post vaccination). The p-
values associated with the correlation coefficients will be used to select traditional immune 
parameters that are associated with the respective adaptive immune responses (IgG levels at 
day 30 post vaccination). The tentative selection criterion is p-value ≤ 0.01.  
For gene expression data, we will use the method Significance Analysis of Microarrays (SAM) 
with quantitative outcome to identify genes that are significantly associated with the respective 
adaptive immune responses (IgG levels at day 30 post vaccination). False discovery rate (FDR) 
will be used as selection criterion. The tentative selection criterion is FDR ≤ 0.1. 
3. Comparison of the serotype-specific avidity indexes in a subset of up to 6 vaccinees per vaccine group 
at day 180 post vaccination with either PPV23 or PCV13 in the elderly. 
Descriptive analysis, boxpots and histograms, will be conducted to present the data. Testing 
between the two elderly treatment groups will be conducted using unpaired t-test after proper 
data transformation. In the case that near-normality cannot be achieved with data 
transformation, we will resort to the Wilcoxon test.  

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4. Correlation of signatures of generic innate immune responses at days 1, 3 and 7 with serotype specific 
avidity indexes in a subset of up to 6 vaccinees per vaccine group at day 180 post vaccination with either 
PPV23 or PCV13 in the elderly. 
The analysis will be conducted in each elderly treatment group separately. For traditional 
immune parameters, we will calculate the correlation coefficient between the immune 
parameter and the adaptive immune response (serotype specific avidity indexes at day 180 p) 
the p-values associated with the correlation coefficients will be used to select traditional 
immune parameters that are associated with the respective adaptive immune responses 
(serotype specific avidity indexes at day 180). The tentative selection criterion is p-value ≤ 0.01.  
For gene expression data, we will use the method Significance Analysis of Microarrays (SAM) 
with quantitative outcome to identify genes that are significantly associated with the respective 
adaptive immune responses (serotype specific avidity indexes at day 180). False discovery rate 
(FDR) will be used as selection criterion. The tentative selection criterion is FDR ≤ 0.1. 
5.  Comparison of the adaptive immune responses [Opsonophagocytosis assay (OPA) titers] at day 30 
post vaccination with either PPV23 or PCV13 in the elderly. 
Descriptive analysis, boxpots and histograms, will be conducted to present and visually 
contrast the data. Testing between the two elderly treatment groups will be conducted using 
unpaired t-test after proper data transformation. In the case that near-normality cannot be 
achieved with data transformation, we will resort to the Wilcoxon test.  
 
Analyses of exploratory endpoints 
1. Correlation of signatures of generic innate immune responses at days 1, 3 and 7 with adaptive immune 
responses [Opsonophagocytosis assay OPA titers specifically] at day 30 post vaccination among subjects 
in different age strata  
First, we will identify innate signatures in each young treatment group, as well as potentially in 
each age stratum of each elderly treatment group. There are a total of potentially 8 groups: 
participants between the ages of 25-40 receiving PPV23, participants between the ages of 25-40 
receiving PCV13, participants between the ages of 60-69 receiving PPV23, participants between 
the ages of 60-69 receiving PCV13, participants between the ages of 70-79 receiving PPV23, 
participants between the ages of 70-79 receiving PCV13, participants between the ages of 80-89 

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receiving PPV23, participants between the ages of 80-89 receiving PCV13. The analysis will be 
done using the same method described in the analysis plan of Primary Aim 1.  
For correlation analysis, the analysis is similar to primary endpoint 3. Instead of using all the 
data, we will analyze each age stratum within each treatment group separately.  
2. Comparison of the kinetics and magnitude of select serotype specific plasmablasts (days 7, 14, 30 (with 
day 30 on a subset of vaccinees only)) and memory B cells (days 30, 180) post vaccination with either 
PPV23 or PCV13 in the elderly. 
Summary statistics, boxplots and histograms will be used to summarize and visually contrast 
the data. We will use t-test or Wilcoxon test to compare each immune parameter (magnitude, 
kinetics) from D0 to D180 post vaccination between the two treatment groups at the pre-
specified time points for serotype specific plasmablasts (days 7, 14, 30 with day 30 on a subset of 
vaccinees only)) and for memory B cells (days 30, 180).  
3. Comparison of the plasmablats repertoire and monoclonal antibodies from plasmablasts in a subset of 
vaccinees per vaccine group at day 7 post vaccination with either PPV23 or PCV13 in the elderly. 
The repertoire and monoclonal antibody levels will be presented as descriptions of the actual 
values. Summary statistics, boxplots and histograms will be used to summarize the data. 
Testing between the two treatment groups will be conducted using t-test or Wilcoxon test.  
4. Comparison of identified innate signature variables and correlation signature variables 
between PPV23 and PCV13 recipients 
After identifying the innate immune signatures and correlation immune signatures within each 
elderly treatment group and each young treatment group, there is an interest in comparing the 
signatures between PPV23 and PCV13 recipients. Here we consider four groups: elderly PPV23, 
elderly PCV13, young PPV23 and young PCV13. Each group has two signatures – innate 
signature and correlation signature. For each group, the correlations signature is a subset of the 
innate signature. For both the innate and the correlation signature, we will make comparisons  
between:  
# A-- the two vaccine groups in the same age category: elderly (60-89) receiving PPV23 v.s. 
elderly (60-89) receiving PCV13 and young (25-40) receiving PPV23 v.s. young (25-40) 
receiving PCV13),  

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# B-- all the other possible combinations: elderly (60-89) receiving PPV23 v.s. young (25-40) 
receiving PPV23; elderly (60-89) receiving PPV23 v.s. young (25-40) receiving PCV13; elderly 
(60-89) receiving PCV13  v.s. young (25-40) receiving PPV23; elderly (60-89) receiving PCV13 
v.s. young (25-40) receiving PCV13. 
This part of the analysis will depend on the results of the aforementioned analysis and hard to 
specify at this stage.  
As a preliminary consideration, the identified innate signature variables and correlation 
signature variables can be contrasted between groups using descriptive statistics, such 
tabulation and Venn diagrams.  
5. 
Comparison of generic innate immune responses at days 1, 3 and 7 with adaptive immune 
responses [Opsonophagocytosis assay OPA titers and ELISA] at years 2-3.5 post vaccination with either 
PPV23 or PCV13. 
For correlation analysis, the analysis is similar to primary endpoint 3. Instead of using all the 
data, we will analyze data in the elderly.  
 
Enriched biological pathways can be identified using each type of signature in each of the four 
groups considered above (i.e. elderly (60-89) receiving PPV23, elderly (60-89) receiving 
PCV13, young (25-40) receiving PPV23 and young (25-40) receiving PCV13),  using gene 
ontology (computer program that generates biological networks from gene lists). Then the 
enriched pathways can be manually compared between the different treatment groups as per 
#A and #B above. Biological interpretations of the differences will be made.  
9.2.2. 
Patient populations 
For all endpoints, our data analysis will be based on all subjects who are randomized, receive 
vaccination per label, and for whom there is a blood sample taken at the 2 required time points 
(Day 0 and Day 30 +/- 7 days) and or Day 0 and Day 180.  
  

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9.2.3 Study Participant Baseline Characteristics and Demographics 
Summary of descriptive statistics for baseline and demographic characteristics will be provided 
for all enrolled participants. Demographic data will include age, race, sex, medical history 
including medication, vaccination history and previous documented Pneumococcal disease will 
be recorded.  
9.2.4 Status of Study Subjects  
Status of study subjects (continue in the study vs. left the study and reasons for discontinuation) 
will be incorporated to the periodic safety reports. 
9.3. 
Interim Analyses  
N/A 
 
9.4. 
Deviations from Statistical Plan 
The principal features of the study design and of the plan for statistical analysis of the data are 
outlined in this protocol. Any changes in these principal features will require a protocol 
amendment and will be described in the final report. These changes will be subject to review by 
the IRB, ISM and NIAID.  
Although our statistical methods and time-points for measurements will adhere to what is 
proposed herein, our experience with analyses of similar studies in the past has underscored the 
need for flexibility and adaptability in trying different statistical approaches to arrive at the 
most informative results.  
As such, we may use alternative approaches such as the gene set enrichment analyses, or other 
approaches, and run additional statistical analyses of data generated by use of assays at time 
points other than those stated in the primary, secondary and exploratory endpoints, on an ad 
hoc basis.  
 

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10. 
 IDENTIFICATION AND ACCESS TO SOURCE DATA  
10.1 
Identifying Source Data 
The investigator will keep accurate records to ensure that the conduct of the study is fully 
documented. Data forms are either considered source or protocol-specific CRFs as detailed in 
the MOPs.  
10.2 Updating Source Documentation 
Documents describing the safety profile of investigational products, such as the investigator’s 
brochure and the package insert, will be amended as needed by the investigational products 
manufacturer to ensure that the description of safety information adequately reflects any new 
clinical findings.  
The Principal Investigator (or co-PI) will provide the ISM, the NIAID Medical Officer, and the 
IRB with the most up-to-date versions of the above documents as soon as the Principal 
Investigator (or co-PI) becomes aware of any changes. For purchased investigational products, 
the Principal Investigator (or co-PI) will confirm that there are no changes to the package insert 
every 3 months. In case of package insert changes, the Principal Investigator (or co-PI) will 
notify the ISM, the NIAID Medical Officer, and the IRB.     
  
10.3 
Permitting Access to Source Data 
The investigator will keep accurate records to ensure that the conduct of the study is fully 
documented.  Data forms are either considered source or protocol-specific CRFs as detailed in 
the MOPs. 
The NIAID will provide the ISM and the Principal Investigator with the most up-to-date 
version of the package insert of PNEUMOVAX®23 AND PREVNAR®13 as soon as it becomes 
aware of any changes and the Principal Investigator will, in turn inform the IRB.   
 

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The investigational site participating in this study will maintain the highest degree of 
confidentiality for the clinical and research information obtained from the participants in this 
study.  Medical and research records will be maintained at each site in the strictest confidence.  
However, as a part of the quality assurance and legal responsibilities of an investigation, the 
investigational site will permit authorized representatives of regulatory authorities and NIAID 
to examine (and when required by applicable law, to copy) clinical records for the purpose of 
quality assurance reviews, audits, and evaluations of the study safety and progress.  Unless 
required by the laws that permit copying of records, only the coded identity associated with 
documents or with other participant data may be copied (and all personally identifying 
information will be removed).  Authorized representatives as noted above are bound to 
maintain the strict confidentiality of medical and research information that is linked to identify 
individuals.   
 
 

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11. 
QUALITY CONTROL AND QUALITY ASSURANCE 
The Principal Investigator (or co-PI) will keep accurate records to ensure that the conduct of the 
study is fully documented.  The investigator will ensure that all CRFs and participant study 
files are legible and complete for every participant. 
When the CRFs are complete, they will be reviewed and signed by the Principal Investigator or 
co-PI.  All discrepancies identified by the site monitor or NIAID will be reviewed, and any 
resulting queries will be resolved with the Principal Investigator (or co-PI) and the CRFs will be 
amended as needed.  
The Principal Investigator (or co-PI), through the use of an internal Quality management Plan 
and appropriate site quality control and quality assurance monitoring staff will be responsible 
for the regular review of the conduct of the trial, for verifying adherence to the protocol, and for 
confirming the completeness, consistency, and accuracy of all documented data and accuracy of 
source documentation verification.  The reports of the internal site monitor will be submitted to 
the Principal Investigator (or co-PI) and the NIAID Project Manager.  NIAID will review these 
reports. 
As per the clinical monitoring plan, site monitoring will be conducted by the independent site 
monitor in accordance with established Good Clinical Practices (ICH GCP 5.1.1, 5.2, 5.18.1) and 
the Code of Federal Regulations, as applicable.  The overall objectives of site monitoring visits 
are to ensure: 
1. Site compliance with the current version of the approved protocol, consent, documents 
and local Institutional Review Board requirements. 
2. Accuracy and completeness of data entry. 
3. Required regulatory documents are current and maintained in the protocol-specific 
regulatory binder. 
4. A designated percent of signed consent forms, inclusion/exclusion criteria, primary, 
secondary, and tertiary endpoints, safety monitoring parameters, deviations, and serious 
adverse events are documented. 

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5. Procedures are in place to administer and monitor study drug / product accountability 
and documentation of destruction policies. 
6. The research staff is adequately trained with respect to GCP and GLP. 
7. All observed anomalies or protocol deviations are reported and identify an action plan 
to minimize study dropouts and non-compliance with defined study procedures. 
 
The results of the site monitoring report will be discussed with the PI, the staff and the NIAID 
to ensure compliance with the monitor’s findings.  
 

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12. 
ETHICAL CONSIDERATIONS AND COMPLIANCE WITH   
GOOD CLINICAL PRACTICE 
12.1  
Statement of Compliance 
This study was designed to ensure the protection of subjects according to the ethical principles 
of the Declaration of Helsinki and amendments concerning medical research in human subjects. 
This clinical study will be conducted using current good clinical practice (cGCP), as delineated 
in Guidance for Industry: E6 Good Clinical Practice Consolidated Guidance 1, and according to 
the criteria specified in this study protocol. Before study initiation, the protocol the informed 
consent documents and the CRFs will be reviewed and approved by NIAID, IRB, as well as any 
other appropriate health authorities. Any amendments to the protocol or to the consent 
materials will also be approved by the appropriate bodies listed above prior to implementation. 
 
12.2  
Informed Consent and Assent  
The informed consent form will provide information about the study to a prospective 
participant or subject’s legal representative to allow for an informed decision about 
participation in the study. Prospective participant or subject’s legal representative must be 
given ample opportunity to review the informed consent and inquire about the results of the 
study. All participants (or their legally acceptable representative) must read, sign, and date a 
consent form prior to study participation. Consent materials for participants who do not speak 
or read English will be translated into the participants’ appropriate language. 
The informed consent form will be revised and receive IRB approval whenever important new 
safety information is available, whenever the protocol is amended, and/or whenever any new 
information becomes available that may affect participation in the trial. 
A copy of the informed consent form will be given to a prospective participant for review. The 
Principal Investigator or an approved designee will discuss the consent with the prospective 
participant and answer questions. The prospective participant will be told that being in the trial 
is voluntary and that he or she may withdraw from the study at any time, for any reason. 

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12.3 
Privacy and Confidentiality 
A participant’s privacy and confidentiality will be respected throughout the study. Each 
participant will be assigned a sequential identification number and these numbers rather than 
names will be used during collection, storage, and reporting of participant information. 
 

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13. 
PUBLICATIONS 
Publication of any data from this study must be carried out in accordance with the HIPC 
publication policy. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
14. 
REFERENCES 
1- ICH Expert Working Group. Guidance for Industry: E6 Good Clinical Practice Consolidated 
Guidance International Conference on Harmonization of Technical Requirements for 
Registration of Pharmaceuticals for Human Use. (1996). 
 
2- Knoll, M.D., et al. Standardizing surveillance of pneumococcal disease. Clin Infect Dis 48 
Suppl 2, S37-48. (2009). 
 
3- Marrie, T.J., Durant, H. & Yates, L. Community-acquired pneumonia requiring 
hospitalization:5-year prospective study. Rev Infect Dis 11, 586-599. (1989). 
 
4- Jackson, L.A. & Janoff, E.N. Pneumococcal vaccination of elderly adults: new paradigms for 
protection. Clin Infect Dis 47, 1328-1338. (2008). 
 
5- Lexau, C.A., et al. Changing epidemiology of invasive pneumococcal disease among older 
adults in the era of pediatric pneumococcal conjugate vaccine. JAMA 294, 2043-2051. (2005). 
 
6- Romero-Steiner, S., et al. Reduction in functional antibody activity against Streptococcus 
pneumoniae in vaccinated elderly individuals highly correlates with decreased IgG antibody 
avidity. Clin Infect Dis 29, 281-288. (1999). 
 
7- Pilishvili T, Lexau C, Farley MM, Hadler J, Harrison LH, Bennett NM, Reingold A, Thomas 
A, Schaffner W, Craig AS, Smith PJ, Beall BW, Whitney CG, Moore MR; Active Bacterial Core 
Surveillance/Emerging Infections Program Network. Sustained reductions in invasive 
pneumococcal disease in the era of conjugate vaccine. J Infect Dis 201(1):32-41. (2010).   
 
8- Khoie T, Tiernan R, deVore N. Prevnar 13™ (PCV13): Pneumococcal 13-valent Conjugate 
Vaccine (Diphtheria CRM197 Protein). Applicant: Wyeth Pharmaceuticals Inc. (2011). 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
9- Hak E, Grobbee DE, Sanders EA, Verheij TJ, Bolkenbaas M, Huijts SM, Gruber WC, Tansey S, 
McDonough A, Thoma B, Patterson S, van Alphen AJ, Bonten MJ. Rationale and design of 
CAPITA: a RCT of 13-valent conjugated pneumococcal vaccine efficacy among older adults. 
Neth J Med.;66(9):378-83. (2008).  
10- Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, 
Marzolf B, Kennedy K, Wu H, Bennouna S, Oluoch H, Miller J, Vencio RZ, Mulligan M, Aderem 
A, Ahmed R, Pulendran B. Systems biology approach predicts immunogenicity of the yellow 
fever vaccine in humans. Nat Immunol.; 10(1):116-25. (2009). 
 
11- Nakaya HI, Wrammert J, Lee EK, Racioppi L, Marie-Kunze S, Haining WN, Means AR, 
Kasturi SP, Khan N, Li GM, McCausland M, Kanchan V, Kokko KE, Li S, Elbein R, Mehta AK, 
Aderem A, Subbarao K, Ahmed R, Pulendran B. Systems biology of vaccination for seasonal 
influenza in humans. Nat Immunol. ; 12(8):786-95 (2011).  
 
12- Alonso de Velasco, E., A. F. Verheul, J. Verhoef, and H. Snippe. Streptococcus pneumoniae: 
virulence factors, pathogenesis, and vaccines. Microbiol. Rev. 59:591-603. (1995). 
 
13- Antilla, M., M. Voutilainen, V. Jäntti, J. Eskola, and H. Käyhty. 1999. Contribution of 
serotype-specific IgG concentration, IgG subclasses and relative antibody avidity to 
opsonophagocytic activity against Streptococcus pneumoniae. Clin. Exp. Immunol. 118:402-407. 
(1999). 
 
14- Anttila, M., J. Eskola, H. Ahman, and H. Käyhty. Differences in the avidity of antibodies 
evoked by four different pneumococcal conjugate vaccines in early childhood. Vaccine. 17:1970-
1977. (1999). 
 
15- Rose, M. A., R. Schubert, N. Strnad, and S. Zielen. Priming of immunological memory by 
pneumococcal conjugate vaccine in children un responsive to 23-valent polysaccharide 
pneumococcal vaccine. Clin. Diagn. Lab Immunol. 12:1216-1222. (2005). 
 

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16- Shapiro, E.D., et al. The protective efficacy of polyvalent pneumococcal polysaccharide 
vaccine. N Engl J Med 325, 1453-1460. (1991). 
 
17- Schenkein, J.G., Park, S. & Nahm, M.H. Pneumococcal vaccination in older adults induces 
antibodies with low opsonic capacity and reduced antibody potency. Vaccine 26, 5521-5526. 
(2008). 
 
18- de Roux A, Schmole-Thoma B, Siber GR, et al. Comparison of pneumococcal conjugate 
polysaccharide and free polysaccharide vaccines in elderly adults: conjugate vaccine elicits 
improved antibacterial immune responses and immunological memory. Clin Infect 
Dis.;46(7):1015-1023. (2008). 
 
19- Sen, G., Khan, A.Q., Chen, Q. & Snapper, C.M. In vivo humoral immune responses to 
isolated pneumococcal polysaccharides are dependent on the presence of associated TLR 
ligands. JImmunol 175, 3084-3091. (2005). 
 
20-Centers for Disease Control and Prevention (CDC); Advisory Committee on Immunization 
Practices. Updated recommendations for prevention of invasive pneumococcal disease among 
adults using the 23-valent pneumococcal polysaccharide vaccine (PPSV23). MMWR Morb Mortal 
Wkly Rep.; 59(34):1102-6. (2010). 
 
21-Licensure of 13-Valent Pneumococcal Conjugate Vaccine for Adults Aged 50 years and 
Older. MMWR Morb Mortal Wkly Rep: 61 (21): 395-5. (2012). 
21a- Smit et al. Protective efficacy of pneumococcal polysaccharide vaccines. JAMA ; 238 (24): 
2613-16. (1977). 
 
22- PNEUMOVAX®23 package insert. March, 2013. 
 
23- PREVNAR®13 package insert. January, 2013. 

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Systems Biology of PPV23 and PCV13                               Version 7.0.March 30, 2017 
23a- Cordonnier et al. Randomized study of early versus late immunization with pneumococcal 
conjugate vaccine after allogeneic stem cell transplantation.  Clin Infect Dis. ;48(10):1392-401. 
(2009) 
23b Crum-Cianflone et al. A randomized clinical trial comparing revaccination with 
pneumococcal conjugate vaccine to polysaccharide vaccine among HIV-infected adults. J Infect 
Dis.; 202(7):1114-25 (2010) 
24-Torling J, Hedlund J, Konradsen HB, Ortqvist A. Revaccination with the 23-valent 
pneumococcal polysaccharide vaccine in middle-aged and elderly persons previously treated 
for pneumonia. Vaccine; 22:96–103. (2003). 
 
25- Ortqvist A, Hedlund J, Burman LA, Elbel E, Höfer M, Leinonen M, Lindblad I, 
Sundelöf B, Kalin M. Randomised trial of 23-valent pneumococcal capsular polysaccharide 
vaccine in prevention of pneumonia in middle-aged and elderly people. Swedish Pneumococcal 
Vaccination Study Group. Lancet. ;351(9100):399-403.(1998). 
 
26-Ortqvist, A., I. Henckaerts, J. Hedlund, and J. Poolman. Non-response to specific serotypes 
likely cause for failure to 23-valent pneumococcal polysaccharide vaccine in the elderly. Vaccine 
25:2445-2450. (2007). 
 
27- Manoff, S., C. Liss, M.J. Caufield, R. Marchese, J. Sibbler, J. Boslego, S. Romero-Steiner, G. 
Rajam, N. Glass, C. G. Whitney, G. M. Carlone and the Pneumococcal Revaccination Study 
Group. Revaccination with a 23-valent pneumococcal polysaccharide vaccine induces elevated 
and persistent functional antibody responses in adults >65 years of age. J Infect Diseas. 201:525-
533. (2009). 
 
28- de Roux, A., B. Schmöle-Thoma, G.R. Siber,  J.G. Hackell, A. Kuhnke, N. Ahlers, S.A. Baker, 
A. Razmpour, E.A .Emini, P.D. Fernsten, W.C. Gruber, S. Lockhart, O. Burkhardt, T. Welte, and 
H.M. Lode. Comparison of pneumococcal conjugate polysaccharide and free polysaccharide 
vaccines in elderly adults: conjugate vaccine elicits improved antibacterial immune responses 
and immunological memory. Clin. Infect. Dis. 46:1015-23. (2008). 
 

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29- Jackson, L.A., K.M. Neuzil, C.G. Whitney, P. Starkovich, M. Dunstan, O.Yu, J.C. Nelson, 
D.R. Feikin, D.K. Shay, J. Baggs, B. Carste, M.H. Nahm, and G. Carlone. Safety of varying 
dosages of 7-valent pneumococcal protein conjugate vaccine in seniors previously vaccinated 
with 23-valent pneumococcal polysaccharide vaccine. Vaccine. 23:3697-703. (2005). 
 
30- Lazarus R, Clutterbuck E, Yu LM, et al. A randomized study comparing combined 
pneumococcal conjugate and polysaccharide vaccination schedules in adults. Clin Infect 
Dis.52(6):736-742. (2011). 
 
31- Development Core Team: R: A Language and Environment for Statistical Computing. 
(2007). 
 
32-Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, 
Gentry J et al: Bioconductor: open software development for computational biology and 
bioinformatics. Genome Biol, 5 :R80. (2004). 
 
33- Hastie T, Tibshirani R, Friedman J: The Elements of Statistical Learning: Data Mining, 
Inference, and Prediction. New York: Springer. (2009). 
 
34-Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing 
radiation response. Proc Natl Acad Sci U S A , 98 :5116-5121. (2001). 
 
 
 

Appendixes 
CONFIDENTIAL 
HIPC: VAX-003 
Systems Biology of PPV23 and PCV13  
Version 7.0 
March 30, 2017 
Appendix 1. Schedule of Events 
Day or Year 
0 
1 
3 
7 
+/-1 
14 
+/-2 
30 
+/-7 
180 
+/-
14 
2-3.5 
Visit 
1 
2 
3 
4 
5 
6 
7 
8 
Informed consent & HIPAA  
X 
 
 
 
 
 
 
 
Demographic and Medical History 
(including medication and vaccine 
history). 
X 
 
 
 
 
 
 
 
Verify eligibility 
X 
 
 
 
 
 
 
 
PID assignment 
X 
 
 
 
 
 
 
 
Vital signs 
X 
 
 
 
 
 
 
 
Focused physical exam (only if indicated 
based on review of health status) 
X 
X 
X 
X 
X 
X 
X 
 
X 
Randomization 
X 
 
 
 
 
 
 
 
Vaccination* 
X 
 
 
 
 
 
 
 
Urine Pregnancy Test ***** 
X 
 
 
 
 
 
 
 
Record additional pneumococcal 
vaccines given outside study 
 
 
 
 
 
 
 
X 
** Instruction given to study participants 
on immediate notification of safety 
events and concomitant medications. 
X 
X 
X 
X 
X 
X 
 
 
Assessment of health status *** and 
concomitant medications after 
administration of study vaccine 
 
X 
X 
X 
X 
X 
X 
 
X***** 
Blood draw for Innate Assays 
(microarray, FACS, Luminex) and 
Adaptive Assays (Plasmablasts, 
monoclonal Ab, memory B cells, 
serotype specific ELISA IgG levels, 
avidity assay, OPA) **** 
X 
X 
X 
X 
X 
X 
X 
 
 
X 
 
Footnotes: 

Appendixes 
CONFIDENTIAL 
HIPC: VAX-003 
Systems Biology of PPV23 and PCV13  
Version 7.0 
March 30, 2017 
* Any Adverse Event (including – but not only- vaccine reactions and local or systemic 
Reactogenicity Events) of grade 3 or higher severity or serious adverse event (SAE) occurring 
after vaccination while the subjects is still at the clinical site will be recorded and reported. 
** Instruction includes the following: 
1. Participants will be provided (on Day 0 only ) with a written description of what represents a 
local and systemic vaccine reaction of mild, moderate and severe intensity and instructed to call 
the site to report reactogencity events of grade 3 (severe) or higher severity within 1 week 
following vaccination. 
2. Participants will also be instructed to promptly call the site if he/she develops any of the 
following: 
 Becomes sick or has been treated at the doctor’s office or emergency department or has 
been hospitalized for any illness throughout D180 of the study; 
 Develops any adverse event that limits self-care activities of daily living (e.g.  bathing, 
dressing and undressing, feeding self, using the toilet, taking medications, and not bed 
ridden) even if he/she decides not to get medical care; or 
 he/she starts/stops medications during enrollment in the study. 
 Becomes pregnant. 
*** Assessment of health status includes: 
 
Evaluation of local REs and systemic REs of grade 3 or higher severity developing after 
the last visit (only until Day 7 Visit) 
 
Any adverse event (AE) that limited self-care activities of daily living or any serious  
adverse event (SAE) which may not have been reported by the participant by calling the 
site as directed at a prior visit 
 
Any medications administered after vaccination. 
**** Innate assays will not be conducted at days 30 and 180. Adaptive assays will not be 
conducted at day 1. 
***** Eligible female subjects aged 25-40 years will use effective contraception 1 month prior and 
one month following vaccination. 
***** Only for major health problems 

Appendixes 
CONFIDENTIAL 
HIPC: VAX-003 
Systems Biology of PPV23 and PCV13  
Version 7.0 
March 30, 2017 
 
Appendix 2. Definitions 
 
“Generic innate immune signatures”=traditional immune parameters measurements + array-
based gene expression, which change in response to vaccination. 
 «  Traditional immune parameters » =FACS + Luminex. 
« FACS »= Fluorescence Activated Cell Sorting, a method for sorting a heterogeneous mixture 
of biological cells. 
« Luminex »= multiplex analysis technique for measuring of cytokines and chemokines 
“Array-based gene expression” =microarray. 
“Adaptive immune responses” = OPA + avidity indexes+ ELISA IgG+ studies on plasmablasts. 
 “Correlation innate immune signatures” =traditional immune parameters measurements + 
array-based gene expression, which correlate with adaptive immune responses. 
“Gene ontology”: a set of standard terminology that group gene products based on their 
biological functions.  

Appendixes 
CONFIDENTIAL 
HIPC: VAX-003 
Systems Biology of PPV23 and PCV13  
Version 7.0 
March 30, 2017 
 
Appendix 3. Severity Scale for Local Vaccine Reactions (local 
reactogenicity events) 
 
INJECTION SITE REACTIONS 
 
Grade 
 
1 
2 
3 
Swelling/ 
Induration/ 
Mild induration, 
able to move skin 
parallel to plane 
(sliding) and 
perpendicular to 
skin (pinching up) 
Moderate 
induration, able to 
slide skin, unable 
to pinch skin; 
limiting 
instrumental 
activities of daily 
living 
Severe induration, unable to slide or 
pinch skin; limiting arm movement 
limiting self-care activities of daily 
living 
Redness/ 
erythema 
Asymptomatic or 
mild symptoms; 
intervention not 
indicated 
Moderate; minimal, 
local; limiting age-
appropriate 
instrumental 
activities of daily 
living 
Severe but not immediately life-
threatening; hospitalization or 
prolongation of existing 
hospitalization indicated; disabling;  
limiting self-care activities of daily 
living 
Pain/tenderness 
Mild 
Moderate pain; 
limiting 
instrumental 
activities of daily 
living 
Severe pain; limiting self-care 
activities of daily living 
Limitation of 
arm movement 
Some limitation of 
arm movement, 
Unable to move 
arm above head 
but able to move 
arm above 
shoulder 
Unable to move arm above shoulder. 
 
 
 
 
 
Note: 
Instrumental Activities of Daily Living refer to preparing meals, shopping for groceries or clothes,  
using the telephone, managing money, etc. 
Self-care Activities of Daily Living refer to bathing, dressing and undressing, feeding self,  
using the toilet, taking medications, and not bedridden. 

Appendixes 
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Systems Biology of PPV23 and PCV13  
Version 7.0 
March 30, 2017 
 
Appendix 4. Severity Scale for Generalized Vaccine Reactions 
(systemic reactogenicity events) 
 
GENERAL ADVERSE REACTIONS  
 
Grade 
 
1 
2 
3 
Fatigue/asthenia 
Fatigue relieved by 
rest 
Fatigue not relieved by rest; 
limiting instrumental 
activities of daily living 
Fatigue not relieved by rest, 
limiting self-care activities of 
daily living 
Body 
ache/myalgia 
Mild pain 
Moderate pain; limiting 
instrumental activities of 
daily living 
Severe pain; limiting self-care 
ADL 
Headache 
Mild pain 
Moderate pain; limiting 
instrumental activities of 
daily living 
Severe pain; limiting self-care 
activities of daily living 
Joint pain 
Mild pain 
Moderate pain; limiting 
instrumental activities of 
daily living 
Severe pain; limiting self-care 
activities of daily living 
 
 
 
 
Loss of appetite 
Loss of appetite 
without 
alteration in eating 
habits 
Oral intake altered without 
significant weight loss or 
malnutrition; oral 
nutritional 
supplements indicated 
Associated with significant 
weight loss or malnutrition 
(e.g., inadequate oral caloric 
and/or fluid intake); tube 
feeding or intravenous 
nutrition indicated 
 
 
 
 
 
 
 
 
 
 
 
 
 
Note: 
Instrumental Activities of Daily Living refer to preparing meals, shopping for groceries or clothes,  
using the telephone, managing money, etc. 
Self-care Activities of Daily Living refer to bathing, dressing and undressing, feeding self, using the toilet, taking 
medications, and not bedridden.