SARS-CoV-2 Immune Responses After COVID-19 Therapy and Subsequent Vaccine
Phase: PHASE4
Conditions: Covid19, SARS-CoV2 Infection
Sponsor: National Institute of Allergy and Infectious Diseases (NIAID)

A5404, sIRB Version 2.0 Clarification Memo #1 (11Jan2023) 
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ACTG NETWORK COORDINATING CENTER 
Social & Scientific Systems, Inc., a DLH Holdings Company 
8757 Georgia Avenue, 12th Floor 
Silver Spring, MD 20910-3714 
Phone: 301-628-3000 
 
 
CLARIFICATION MEMO 
 
DATE:  
January 11, 2023 
 
TO: 
 
ACTG CTU Principal Investigators, CRS Leaders, and CTU/CRS Coordinators 
 
FROM:  
A5404 Protocol Team  
 
SUBJECT: 
Clarification Memo #1 for Protocol A5404 
 
 
The Division of AIDS does not require you to forward it to your institutional review board (IRB); 
however, you must follow your IRB's policies and procedures. If IRB review of clarification memos 
is required at your site, please submit this document for review. 
 
Each site should file a copy of this CM with the protocol for reference. 
 
The protocol clarification(s) contained in this memo should be implemented immediately.  
 
The main reasons for this CM are to inform A5404 study sites that the study will end follow-up earlier than 
expected, that several Secondary Objectives were moved to Other Objectives, and to inform participants 
and sites about an increased risk of myocarditis and pericarditis in individuals vaccinated with some 
COVID-19 vaccines containing S- antigen. Participant follow-up will end at the Day 365 visit, and not at 
Day 730 as initially planned. Please note that the change in some Secondary Objectives to Other will not 
impact the data that have already been collected nor does it require sites to take any action. Information 
on an increased risk of myocarditis and pericarditis should be communicated with study participants via a 
Dear Participant Letter that the A5404 team will provide to study sites.  
 
 

A5404, sIRB Version 2.0 Clarification Memo #1 (11Jan2023) 
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TABLE OF CONTENTS 
 
1.2 
Secondary Objectives ....................................................................................................................... 3 
1.3 
Other Objectives ............................................................................................................................... 3 
10.2.2 
Secondary Outcome Measures..................................................................................................... 4 
10.2.3 
Other Outcome Measures ............................................................................................................. 4 
10.2 
Outcome Measures ........................................................................................................................... 5 
10.4 
Sample Size ...................................................................................................................................... 5 
10.6 
Analyses ............................................................................................................................................ 5 
Risk of Myocarditis and Pericarditis .............................................................................................................. 5 
 
 

A5404, sIRB Version 2.0 Clarification Memo #1 (11Jan2023) 
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The following are clarifications (noted in bold and strikethrough) to Protocol A5404, Version 2.0, 
07May2021, titled, “SARS-CoV-2 Immune Responses after COVID-19 Therapy and Subsequent 
Vaccine.” These clarifications will be included in the next version of the A5404 protocol if it is amended at 
a future date. 
 
1. 
Shortening participant follow-up to end at the Day 365 study visit instead of at the Day 730 visit: 
(Protocol sections impacted: SCHEMA (sections “DESIGN” and “DURATION”); section 3.0 (Study 
Design), section 6.1 (Schedule of Evaluations), and section 6.2.3 (Post-Entry Evaluations).  
 
2. 
Secondary Objectives (section 1.2): The team re-prioritized the analysis of secondary objectives and 
moved several to Other Objectives (section 1.3). As a result, section 1.2 was updated to move 
Secondary Objectives 1.2.2–1.2.5 to section 1.3—now reflected as Other Objectives 1.3.1–1.3.4. 
Remaining Other Objectives in this section were renumbered accordingly. Associated changes were 
made to section 10.2.2 (Secondary Outcome Measures) and a new section 10.2.3 was added for 
Other Outcome Measures.  
 
Refer to item #3 for changes that were made to section 10.6 (Analyses), which relate to the re-
prioritization of objectives. 
 
The following updates resulted from this change:  
 
1.2 
Secondary Objectives 
 
1.2.1 
To explore the safety of mRNA-based COVID-19 vaccines among participants with prior 
COVID-19 who received investigational therapy or its comparator for COVID-19 and 
persons who are SARS-CoV-2 naïve. 
 
1.2.2 
To explore the difference in humoral and cellular immune responses to mRNA-based 
COVID-19 vaccines among participants with prior COVID-19 who received 
investigational therapy compared to participants without prior investigational therapy 
(placebo or corresponding active comparator) exposure and persons who are SARS-
CoV-2 naïve. 
 
1.2.3 
To explore the difference in humoral and cellular immune responses, including NAb 
levels, B and T cell responses, and serologic responses to COVID-19 vaccination by 
duration of time of vaccination from prior investigational therapy versus active 
comparator/placebo exposure and compared to persons who are SARS-CoV-2 naïve. 
 
1.2.4 
To explore whether investigational therapy drug levels at time of first COVID-19 
vaccination is associated with humoral and cellular responses in participants with prior 
COVID-19 who received investigational therapy or its comparator for COVID-19. 
 
1.2.5 
To explore B and T cell exhaustion before and after COVID-19 vaccination in persons 
with prior COVID-19 who received investigational therapy or corresponding comparator 
for COVID-19 and persons who are SARS-CoV-2 naïve. 
 
1.3 
Other Objectives 
 
1.3.1 
To explore the difference in humoral and cellular immune responses to mRNA-
based COVID-19 vaccines among participants with prior COVID-19 who received 
investigational therapy compared to participants without prior investigational 
therapy (placebo or corresponding active comparator) exposure and persons who 
are SARS-CoV-2 naïve. 
 
1.3.2 
To explore the difference in humoral and cellular immune responses, including 

A5404, sIRB Version 2.0 Clarification Memo #1 (11Jan2023) 
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NAb levels, B and T cell responses, and serologic responses to COVID-19 
vaccination by duration of time of vaccination from prior investigational therapy 
versus active comparator/placebo exposure and compared to persons who are 
SARS-CoV-2 naïve. 
 
1.3.3 
To explore whether investigational therapy drug levels at time of first COVID-19 
vaccination is associated with humoral and cellular responses in participants with 
prior COVID-19 who received investigational therapy or its comparator for COVID-19. 
 
1.3.4 
To explore B and T cell exhaustion before and after COVID-19 vaccination in 
persons with prior COVID-19 who received investigational therapy or 
corresponding comparator for COVID-19 and persons who are SARS-CoV-2 naïve. 
 
10.2.2 Secondary Outcome Measures  
 
10.2.2.1 Relative pre-vaccine to post-vaccine change in NAb response defined as the ratio of 
post-vaccine level/pre-vaccine level. The pre-vaccine NAb measurement will be 
obtained before the first dose of the vaccine, and the post-vaccine measurement will be 
obtained at least 56 days after the first dose of the vaccine. 
 
10.2.2.2 New Grade 3 or higher AE, or SAE, or AE leading to change or discontinuation in 
vaccine receipt from first dose of the mRNA-based COVID-19 vaccine and through 140 
days after the first dose of vaccine. 
 
10.2.2.3 Grade 1 or higher allergic reaction from first dose of the mRNA-based COVID-19 
vaccine through the visit 56 days after the first dose of the vaccine. 
 
10.2.2.4 Grade 2 or higher injection site reaction from first dose of the mRNA-based COVID-19 
vaccine through the visit 56 days after the first dose of the vaccine. 
 
10.2.2.5 CD4+ and CD8+ T cell responses to SARS-CoV-2 spike protein and IgG and IgM 
serologic responses to SARS-CoV-2 spike protein at receptor binding domain (RBD) 
and N terminal domain (NTD) and Matrix (M) protein at study entry/Day 0 and 56 days 
after the first vaccine dose.  
 
10.2.2.6 Flow cytometry of PBMC for markers of exhaustion on B and T cells at study entry/Day 
0 and 56, and 140 days after the first vaccine dose.  
 
10.2.2.7 10.2.2.5 Relative pre-vaccine to post-vaccine change in NAb response defined as  
the ratio of post-vaccine level/pre-vaccine level by received vaccine, i.e., Moderna versus Pfizer. 
The pre-vaccine NAb measurement will be obtained before the first dose of the vaccine, 
and the post-vaccine measurement will be obtained at least 56 days after the first dose 
of the vaccine. 
 
10.2.3 Other Outcome Measures  
 
10.2.3.1 CD4+ and CD8+ T cell responses to SARS-CoV-2 spike protein and IgG serologic 
responses to SARS-CoV-2 spike protein at receptor binding domain (RBD) and N 
terminal domain (NTD) at study entry/Day 0 and 56 days after the first vaccine 
dose.  
 
10.2.3.2 Flow cytometry of PBMC for markers of exhaustion on B and T cells at study 
entry/Day 0, 56, and 140 days after the first vaccine dose.  
 
3. 
Section 10.2 (Outcome Measures) was expanded to include revisions to the analysis plan 

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addressing mitigation strategies that will be implemented should study accrual be low and insufficient 
to provide meaningful estimates. In the case that accrual is too low to produce meaningful estimates, 
analyses will instead be reported as descriptive estimates within participant groups rather than as 
comparisons between groups. Further revisions related to this change are reflected in section 10.4 
(Sample Size) first paragraph and section 10.6 (Analyses) second paragraph, as detailed below. 
 
10.2 
Outcome Measures 
 
Primary and secondary outcome measures listed below will be addressed in the study’s primary 
Statistical Analysis Plan, which will define the content of the Primary Analysis Report. This report 
will form the basis for the primary study manuscript and results reporting to 
https://ClinicalTrials.gov. Outcome measures will be analyzed as originally pre-specified if 
accrual is sufficiently high to provide meaningful estimates. Otherwise, analyses will 
instead be reported as descriptive estimates within participant groups rather than as 
comparisons between groups. Additional details are pre-specified in the primary 
Statistical Analysis Plan.  
 
10.4 
Sample Size 
 
The following considers sample size for a comparison of responses among participants who 
previously received an investigational agent versus among participants who previously received 
placebo. Similar considerations apply if instead the comparison is of responses among 
participants who previously received an investigational agent versus among participants who 
previously received an active control. It was originally intended to consider the following 
sample sizes: 50, 70, and 90 for each investigational therapy group separately. Due to 
lower than anticipated enrollment numbers, revisions to the protocol and Statistical 
Analysis Plan (SAP) now consider combining the active arms from some investigational 
therapy groups together for comparisons against the pooled placebo group or active 
comparator (sample sizes: 10, 20, 30, 50, and 70). 
 
10.6 
Analyses 
 
Statistical analysis plans will be developed describing analyses to address the primary and 
secondary objectives of the study.  
 
The primary outcome analysis is descriptive and was originally intended to be carried out 
separately for each investigational therapy and associated combined placebo group or 
investigational agent and associated active comparator group. Due to lower than anticipated 
enrollment into the study, the primary outcome analysis may be amended to be carried out 
in a combined group of participants exposed to particular ACTIV-2/A5401 investigational 
agents. Additional details are described in the Statistical Analysis Plan. The analysis will 
combine participants regardless of which mRNA-based COVID-19 vaccine they received. An 
exploratory analysis may be carried out separately for each mRNA-based COVID-19 vaccine if 
sample size permits. 
 
Risk of Myocarditis and Pericarditis 
 
4. 
In response to FDA comments on recent available data regarding an increased risk of myocarditis 
and pericarditis reported in individuals vaccinated with some COVID-19 vaccines containing S- 
antigen, the following language was included in a Dear Participant Letter that will be provided to the 
43 participants that have been enrolled into the study: 
 
There is an increased risk of myocarditis and pericarditis after getting the study-provided 
Moderna mRNA-1273 COVID-19 vaccine. Myocarditis is inflammation of the heart muscle, and 
pericarditis is inflammation of the lining around the heart. In both cases, the body’s immune 

A5404, sIRB Version 2.0 Clarification Memo #1 (11Jan2023) 
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system is causing inflammation in response to the vaccine. Symptoms can include chest pain, 
shortness of breath, or palpitations. Symptoms usually start within a few days after receipt of 
the Moderna mRNA-1273 COVID-19 vaccine. Most individuals who have sought medical care 
have responded well to medications and rest, and symptoms have resolved for most persons 
who experienced this side effect. It is not known if either myocarditis or pericarditis from the 
vaccine causes long-term health effects.  
 
Myocarditis and pericarditis have been reported in greatest numbers in males under the age of 
40 years following a second dose of mRNA vaccines (including the COVID-19 vaccine), but 
cases have been reported in older males and in females as well, and also following other 
doses. Risk for myocarditis and pericarditis has been observed to be highest in males between 
12 to 17 years of age. While some cases required intensive care support, data suggests that 
symptoms got better in most people with some management. Information is not yet available 
about the potential long-term affects of myocarditis and pericarditis in these people. While 
there is limited data on the risk of myocarditis and pericarditis in children younger than 12 
years old (especially compared to the risk data that is available in adolescents and adults), it is 
an area of science that is currently being studied.  
 
Please let a member of the study staff know if you experience any of the following symptoms of 
myocarditis or pericarditis, following vaccination provided through the study:  
• 
Chest pain 
• 
Shortness of breath 
• 
A fast heartbeat, fluttering, or pounding heart 
 
Study staff will provide you with appropriate contact information so that you can reach out 
should you experience any of these symptoms.