Real-World Effectiveness of Perinatal RSV Immunoprophylaxis
Conditions: RSV Infection
Sponsor: Yale University

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
CLINICAL STUDY PROTOCOL
Real-World Effectiveness of Perinatal RSV Immunoprophylaxis
IRB:
Protocol Version
1/29/2025
Version 6
Confidentiality Statement:
This document is confidential and is to be distributed for review only to investigators, 
potential investigators, consultants, study staff, and applicable independent ethics 
committees or institutional review boards. The contents of this document shall not be 
disclosed to others without written authorization unless it is necessary to obtain informed 
consent from potential study participants.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
2
Synopsis
Purpose
Vaccination plays a critical role in reducing respiratory viral illnesses and in preventing 
ongoing disease transmission. Assessing the real-world post-licensure impact of 
vaccines to measure their effectiveness as used in clinical practice is an essential public 
health activity to monitor how patient, vaccination, and virus characteristics influence 
effectiveness. The purpose of this proposal is to assess the effectiveness of Respiratory 
Syncytial Virus (RSV) vaccines for the prevention of medically attended respiratory 
diseases in ambulatory settings.
Primary Objective
To determine the real-world effectiveness of perinatal RSV immunoprophylaxis against 
medically attended infections in infants ≤60 months of age.
Secondary Objective
-To quantify the extent to which viral genomic diversity impacts the effectiveness of 
immunoprophylaxis.
-To define the impact of immunoprophylaxis on the immune trajectories of infants during 
medically attended acute RSV infection.
-To uncover immune phenotypes of patients ≤60 months of age with RSV.
-To examine the clinical epidemiology of RSV and testing practices in children ≤60 months 
of age during 2018-2028.
-To develop and validate a Natural Language Processing (NLP) tool to extract relevant 
data from the narrative portion of electronic medical records (EHRs) to determine clinical
characteristics for optimal RSV syndromic surveillance.
 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
3
Study Design
This study will use a bidirectional test-negative case-control design to estimate the 
effectiveness of licensed RSV vaccines against medically attended acute respiratory 
illness (ARI). A patient with ARI will be defined as one who has defined
as having an acute onset (<10 days) of at least one of the following symptoms: cough, 
coryza, labored breathing (including wheezing), apnea (or cyanosis), sore throat, or 
sepsis (defined as fever or hypothermia, shock or seriously ill without apparent 
cause).Patients will be identified with two strategies: a) case finding in clinical sites 
during the medical encounter, and b) next-day case-finding in electronic health records 
(EHR). All participants will be ≤12 months of age who sought care for acute respiratory 
illness (ARI) at the Yale New Haven Health System (YNHHS) hospital or primary, 
urgent, and emergency care centers. There will be no discrimination based on gender 
or race/ethnicity. Cases will be defined as individuals who had a clinical encounter for 
ARI symptoms and test positive for RSV. Controls will be individuals who test negative 
for the respective virus. Interviews, reviews of medical records, and immunization 
registry searches will be done similarly for cases and controls to provide information on 
patient characteristics, immunization history, potential confounders, and effect 
modifiers. Respiratory specimens will be collected from all participants for testing using 
standardized RT-PCR assays and genomic sequencing. In a subset of patients, acute 
and convalescent sera will be collected for investigations of immune responses to 
infection.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
4
For our secondary aims, we will conduct two sub-studies. First, we will conduct viral 
genomic epidemiology studies. To this end, we will request remnant nasal swab 
samples from RSV confirmed YNHHS patients ≤12 months of age to perform 
genomic sequencing of the virus and investigate the impact of RSV variants on 
immune escape and vaccine breakthrough infections. Second, we will conduct 
clinical epidemiology studies. To this end, we will perform chart reviews of all 
pediatric patients ≤60 months of age who were tested inpatient or outpatient for RSV 
at Yale- New Haven Health System from 7/1/2018 and will continue forward until 
7/1/2028. The patients’ medical records will be abstracted and pertinent 
demographic, epidemiologic, clinical, laboratory, and radiographic data will be 
recorded. We will develop and validate a Natural Language Processing (NLP) tool 
that will allow us to extract data from the narrative portion of EHR's and conduct a 
rigorous, model-based investigation to identify sets of clinical characteristics (i.e., 
clinical syndromes) that are highly predictive of RSV infection and determine and 
quantify the impact of vaccine introduction.
Study Date Range and Duration
This will be a 5-year study. Enrollment of the case-control study will begin 10/1/2024 and 
will end 11/30/2028. Review of medical records will include data from 7/1/2018 to 
7/1/2028.
Number of Study Sites
Patients will be screened for eligibility in inpatient and outpatient sites affiliated with the 
Yale New Haven Health System.
Primary Outcome Variables
The primary outcome measured is laboratory confirmed ARI infection (case/control status) 
by exposure (immunization history).
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
5
Secondary and Exploratory Outcome Variables (if applicable)
Secondary measures included estimated VE by clinical symptoms, number of vaccine 
doses received, and elapsed time from immunization.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
6
Study Population
Participants will include those who are ≤60 months of age and had a medically- 
attended ARI at one of the clinical recruitment sites. We will enroll males and females 
of all racial and ethnic groups meeting our inclusion criteria.
For the genomic epidemiology studies, we will include only infants ≤12 months of age 
who tested positive for RSV and have residual clinical specimens.
Number of Participants
For the case-control study, we aim to enroll 1250 RSV-positive and 2500 RSV-negative 
infants ≤12 months of age, and 500 RSV-positive and 1000 RSV-negative patients from 
12-60 months of age for a total sample size of 5250. For the clinical and genomic 
epidemiology studies, it is difficult to anticipate the number of subjects that will be 
eligible, given that RSV epidemiology changes from year to year. In a typical respiratory 
season, YNHHS tests approximately 3,000 infants for RSV, with around 30%—
approximately 1,000—testing positive.
Study Schedule
For the case-control study, each patient will have 2-3 total contacts with investigators. 
Contact #1: For patients who participate in person, consent will be collected by the field 
team daily at participating sites. Patients who are seen remotely for symptoms or who 
are identified by EHR recruitment strategies will be contacted by telehealth for consent 
procedures. Contact #2: Follow-up surveys will be conducted on all enrolled participants 
4-12 weeks after diagnosis. We will make every effort to coordinate encounters with 
already planned visits. If no routine follow-up visits are planned during our time frame, 
we will schedule a follow-up visit at the Church Street Research Unit (CSRU). Contact 
#3 may occur for hospitalized patients during their inpatient stay.
No direct patient contact will take place for the clinical and genomic epidemiology 
analysis.  
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
7
Protocol Revision History
Version Date
Summary of Substantial Changes
10/27/23
Congruency changes for NIH funding
7/30/2024
Congruency changes for NIH funding, expanded objectives, age of subjects,
schedule and sample types.
12/10/2024
Added email recruitment of eligible participants.
1/29/2025
Requesting remnant RSV confirmed nasal swab samples of patients ≤12 months of age for viral 
genomic studies as part of our secondary objectives.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
8
Statement of Compliance
This document is a protocol for a human research study. The purpose of this protocol is to 
ensure that this study is to be conducted according to the Common Rule at 45CFR46 
(human subjects) and other applicable government regulations and Institutional research 
policies and procedures.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
9
Abbreviations
Abbreviation
Explanation
ARI
Acute Respiratory Infection
VE
Vaccine Effectiveness
RSV
Respiratory Syncytial Virus
CSRU
Church Street Research Unit
EHR
Electronic Health Records
YNHHS
Yale New Haven Health System
US
United States
NHPC
C NLP
New Haven Primary Care Consortium 
Natural Language Processing
YNHH
Yale New Haven Hospital
ED
Emergency Department
YHC
Yale Health Center
YCH
Yale Children’s Hospital
Yale-PED
Yale pediatric Emergency Department
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
10
Table                   of                    Contents Preface................................................................2
Synopsis...................................................................................................................................3
Purpose ................................................................................................................................3
Primary Objective .................................................................................................................3
Secondary Objective ............................................................................................................3
Study Design ........................................................................................................................3
Study Date Range and Duration...........................................................................................4
Number of Study Sites..........................................................................................................4
Primary Outcome Variables..................................................................................................4
Secondary and Exploratory Outcome Variables (if applicable) ............................................4
Number of Participants .........................................................................................................5
Study Schedule ....................................................................................................................5
Protocol Revision History .....................................................................................................6
Statement of Compliance.........................................................................................................7
Abbreviations ...........................................................................................................................8
Glossary of Terms....................................................................................................................9
1
Background/Literature Review........................................................................................13
1.1
Background..............................................................................................................13
1.2
Prior Experience (if applicable)................................................................................13
2
Rationale/Significance ....................................................................................................14
2.1
Rationale and Study Significance............................................................................14
2.2
Purpose of Study/Potential Impact ..........................................................................14
2.3
Potential Risks and Benefits....................................................................................14
2.3.1
Potential Risks..................................................................................................14
2.3.2
Potential Benefits..............................................................................................15
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
11
3
Study Purpose and Objectives .......................................................................................15
3.1
Hypothesis...............................................................................................................15
3.2
Primary Objective ....................................................................................................15
3.3
Secondary Objective (if applicable).........................................................................15
4
Study Design ..................................................................................................................16
4.1.1
General Design Description .............................................................................16
4.1.2
Study Date Range and Duration ......................................................................16
4.1.3
Number of Study Sites .....................................................................................16
4.2
Outcome Variables..................................................................................................16
4.2.1
Primary Outcome Variables .............................................................................16
4.2.2
Secondary and Exploratory Outcome Variables (if applicable)........................16
4.3
Study Population .....................................................................................................16
4.3.1
Number of Participants.....................................................................................17
4.3.2
Eligibility Criteria/Vulnerable Populations.........................................................17
5
Study Methods/Procedures .........................................................................................18
5.1
Study Procedures....................................................................................................18
5.1.1
Data Collection.................................................................................................18
5.1.2
Adverse Events Definition and Reporting.........................................................18
5.2
Study Schedule .......................................................................................................18
5.3
Informed Consent....................................................................................................19
5.3.1
Screening (if applicable)...................................................................................19
5.3.2
Recruitment, Enrollment and Retention (if applicable).....................................19
5.3.3
Study Visits (is applicable) ...............................................................................19
5.4
Statistical Method ....................................................................................................20
5.4.1
Statistical Design..............................................................................................20
5.4.2
Sample Size Considerations ............................................................................20
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
12
5.4.3
Planned Analyses.............................................................................................20
5.4.4
Analysis of Subject Characteristics (if applicable)............................................20
5.4.5
Interim Analysis (if applicable)..........................................................................20
5.4.6
Handling of Missing Data .................................................................................20
6
Trial Administration.........................................................................................................20
6.1
Ethical Considerations: Informed Consent/Assent and HIPAA Authorization .........21
6.2
Institutional Review Board (IRB) Review................................................................22
6.3
Subject Confidentiality.............................................................................................22
6.4
Deviations/Unanticipated Problems.........................................................................23
6.5
Data Quality Assurance...........................................................................................25
6.6
Study Records.........................................................................................................25
6.7
Access to Source.....................................................................................................25
6.8
Data or Specimen Storage/Security ........................................................................25
6.9
Retention of Records...............................................................................................25
6.10
Study Monitoring......................................................................................................26
6.11
Study Modification ...................................................................................................26
6.12
Study Completion ....................................................................................................26
6.13
Funding Source .......................................................................................................26
6.14
Conflict of Interest Policy.........................................................................................26
6.15
Publication Plan.......................................................................................................27
Appendices ............................................................................................................................28
List of Tables..........................................................................................................................29
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
13
1
Background/Literature Review
Acute respiratory infections (ARI) are one of the leading causes of death in the US and 
Respiratory syncytial virus (RSV) is one of the leading causes of morbidity and mortality in 
children. RSV is an RNA virus that infects the human respiratory system, causing illnesses 
ranging from mild upper respiratory tract symptoms to severe pneumonia. The inflammatory 
reactions inside the bronchiole lining cause the most severe manifestations of RSV, 
especially in infants. Globally, RSV is second only to malaria as the leading cause of infant 
death worldwide.1 In the United States (US), RSV is associated with 1.5 million annual 
medical encounters in children less than five years and is the leading cause of 
hospitalization among infants under one year of age.2 Not surprisingly, the most vulnerable 
subgroups of the population, such as those of lower socioeconomic status, consistently 
bear the burden of severe RSV.3,4
Vaccination is one of the greatest successes in modern medicine and is crucial for the 
control of respiratory viruses. Passive immunization with long-acting monoclonal antibodies 
(mAb) or maternal vaccines hold promise for reducing the burden of RSV in infants.
Palivizumab was the first mAb approved by the Food and Drug Administration (FDA) for the 
prevention of lower respiratory tract disease caused by RSV. However, it has a short half-life 
(28 days) and needs to be given repeatedly throughout the RSV season to be effective.
Thus, only infants at high risk are eligible for palivizumab, such as preterm infants, those 
with chronic lung illness, or those with impaired immune systems (<2% of infants). After 
years of slow progress, the RSV field is at a turning point, with multiple promising vaccines 
in the home stretch of clinical testing and a novel mAb that has already been authorized for 
use.5 Nirsevimab (AstraZeneca and Sanofi) is an extended half-life mAb that is designed to 
be routinely administered as a single dose to all newborns, much like a vaccine. Given the 
safety and efficacy of nirsevimab in the phase 3 clinical trials (efficacy >75%),6,7 it has 
already been authorized for use in the European Union and is expected to be authorized by 
the US FDA ahead of the 2023/2024 respiratory season.8
Vaccination of mothers during pregnancy can also provide passive immunity to infants. 
Currently, there are two notable RSV vaccines for pregnant women that aim to protect 
infants through transplacental transfer of antibodies (GlaxoSmithKline; NCT04605159 and 
Pfizer; NCT04424316). In December 2022, the FDA accepted a Biologics License 
Application for Pfizer’s maternal RSV vaccine (RSVpreF). Given the vaccine’s safety and
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
14
efficacy profile in phase 3 clinical trials (efficacy >82%),9 it is also likely that this vaccine will 
be authorized for use during the 2023/24 respiratory season.10
However, the degree of protection a vaccine provides in real-world settings (i.e., its 
effectiveness) does not always equate to its efficacy in the highly controlled setting of a 
clinical trial. This gap between a vaccine’s efficacy and its effectiveness is in large part due 
to the increased heterogeneity of the post-licensure target population, and the inconsistency 
of immunization practices in real-world settings. Immunization programs post-licensure 
target a far more heterogeneous group of people than can feasibly be studied in a clinical 
trial, many of whom may have underlying health conditions or other differences that can 
significantly influence the protective effect of the vaccine. Further, it is rarely feasible to 
replicate the strict protocols of a vaccine trial in day-to-day clinical practice. Thus, various 
other factors, including the storage of vaccines (e.g., ultra-cold storage) and adherence to 
the dosing schedules may contribute to the lower post-licensure benefits of vaccines.11 
Finally, temporal changes in the circulating viral strains may further impact effectiveness if 
strains with different properties emerge in the post-licensure period. It is, therefore, critical 
to continually monitor the effectiveness of vaccines as they are being used in real-world 
clinical practice to demonstrate their actual effectiveness in preventing disease. These data 
can provide evidence of gaps in our immunization programs that need to be addressed for 
optimal disease prevention and population health.
1.1
Prior Experience (if applicable)
Studies of vaccine effectiveness: Members of the research team have extensive expertise 
in studies to assess vaccine effectiveness. Dr. Niccolai, Dr. Oliveira, and Dr. Weinberger 
have conducted case-control studies to determine the effectiveness of vaccines for over 20 
years, including studies on human papillomavirus (HPV),12,13 varicella,14 Lyme,15 rotavirus,16 
and adult and pediatric COVID-19 vaccines,17-21 human papillomavirus (HPV),12,13 
varicella,14 and Lyme.15 In the studies of varicella and COVID-19 vaccines, effectiveness 
was shown to decrease substantially over time; these findings contributed to the revised 
recommendations from the Advisory Committee on Immunization Practices to include a 
booster dose.22,23 Our analyses of COVID-19 vaccines were among the first reports globally 
of the effectiveness of booster doses and of the effects of the vaccine on transmission, and 
they directly influenced decision-making in the US.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
15
Yale Genomic Surveillance Initiative: Dr. Grubaugh and members of his laboratory have 
extensive experience with the laboratory techniques that will be used in this study.24-28 He 
founded the Yale SARS-CoV-2 Genomic Surveillance Initiative, which has been tracking the 
evolution and epidemiology of SARS-CoV-2 since the start of the pandemic 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
16
2
Rationale/Significance
2.1
Rationale and Study Significance
The upcoming arrival of these novel immunoprophylactic strategies (Nirsevimab for 
newborns and the vaccines for pregnant mothers) provides unprecedented possibilities to 
confront the challenge of RSV. However, the degree of protection an immunization 
provides in real-world settings (i.e., its effectiveness) does not always equate to its efficacy 
in the highly controlled setting of a clinical trial. This gap between efficacy and 
effectiveness is in large part due to the increased heterogeneity of the post-licensure target 
population and the inconsistency of immunization practices in real-world settings. 
Immunization programs post- licensure target a far more heterogeneous group of people 
than can feasibly be studied in a clinical trial, many of whom may have underlying health 
conditions or other differences that can significantly influence the protective effect of the 
vaccine or mAb.11 Developmentally programmed immune system responses with different 
normal responses as a function of age are another factor impacting RSV disease severity 
and responses to vaccines. Thus, post-licensure monitoring is crucial to ensure the 
benefits are being realized in the target populations.
Empirical estimates that quantify the real-world benefit of immunization are also important 
because they help build confidence and boost acceptance by patients. Vaccine hesitancy is 
often multifactorial; however, studies suggest that it is largely driven by a lack of trust and 
confidence.30 The perception that vaccines are not effective has consistently been shown to 
be an important driver of hesitancy.31 Mistrust in the vaccine development process is also 
an important driver of hesitance, especially for racial and ethnic minority groups who are 
often underrepresented in clinical trials.32 Thus, scientifically rigorous, independent, and 
transparent studies that assess the real-world effectiveness of immunizations in the target 
population are critical.
There is also a need to improve capacity for identifying children with RSV. While laboratory- 
based surveillance provides excellent specificity, it is costly, not always available, and results 
can take a long time to return. Surveillance using an RSV syndromic case definition offers the 
potential to improve case-detection. A clinical syndrome is defined as a set of signs and 
symptoms that occur together more often than what would be expected by chance alone.
Although a large body of work has been done to study the clinical manifestations of RSV, there 
are still no syndromic definitions that are suitable for the prediction of RSV infection.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
17
2.2
Purpose of Study/Potential Impact
Empirical estimates that quantify the benefit of immunization on a yearly basis and within 
different relevant subgroups of the population can be a potent incentive to increase the 
strength and consistency of health care provider recommendations and the acceptance by 
patients. Additionally, we seek to understand developmental immune phenotypes 
associated with RSV responses to help inform future vaccinations and treatments. Lastly, 
at the completion of the EHR sub-aims, we will have an NLP tool that could be adapted in 
the future to efficiently identify patients with RSV based on their symptoms using routinely 
collected clinical data. These data may not only provide evidence for sustaining the uptake 
of these vaccines but may also fuel the development of strategies that increase their use 
so that they more fully realize their potential.
2.3
Potential Risks and Benefits
2.3.1
Potential Risks
This study presents minimal risks to the subjects as it only includes the collection of clinical 
data from EHRs and surveys, the collection of residual clinical specimens, and the 
collection of respiratory specimens by noninvasive means, and blood draws of small 
volumes.
Risk of phlebotomy and respiratory swabs/aspirates/induced sputum: The primary risks of 
phlebotomy include local discomfort, occasional bruising of the skin at the site of needle 
puncture, and rarely hematoma, infection, or fainting. The primary risk of a nasopharyngeal 
or oropharyngeal swab, respiratory aspirate and induced sputum is local discomfort. Rarely, 
there can be local bleeding from the nasal mucosa, which is controlled with local measures 
such as pressure or packing with gauze. Additionally, the swab can cause coughing, 
gagging, or infrequently vomiting.
Risks to privacy: Subjects will be asked to provide personal health information (PHI). 
There is a slight risk regarding the loss of confidentiality.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
18
Protection Against Risks:
Risk of phlebotomy and respiratory swabs/aspirates/induced sputum: Investigators will 
prioritize the use of residual clinical specimens, when available, rather than collect fresh 
samples. When fresh samples need to be collected, the blood will be sampled through 
indwelling venous or arterial lines when in place. We will try to obtain the blood when other 
clinical labs are obtained. All blood draws will be performed by skilled practitioners. For 
children, parents will be present at the time of sampling. If study subjects express a desire 
to discontinue the protocol for any reason, the study procedures will be immediately 
terminated, and consent to participate may be rescinded at the subject’s discretion.
Phlebotomy will only be attempted in infants older than 1 month of age, and will be 1 
tablespoon for infants 6-12 months of age and ½ a tablespoon for those 1-6 months of age. 
This is in line with United States NIH policy and is well below the recommended maximum 
of 3 ml/kg of blood per 24 hours (3.8% of TBV). For patients 12-60 months of age blood 
volumes will be drawn in compliance with National Institutes of Health (NIH) and Yale 
Guidelines (for pediatric patients: not exceeding 5 mL/kg in a single day or the lesser of 3 
mL/kg or 50 mL over eight weeks. Respiratory aspirates will be collected as part of clinical 
care for select patients (such as those with endotracheal tubes).
Surveys: Based on the safety profile of the surveys, there is minimal risk of adverse events. 
Should any subjects experience adverse effects related to the intervention, these will be reported 
using a standard form to the Yale Human Research Protection Program.
Minimizing risk to study team: We will follow the YNHHS Infection Prevention guidelines and 
use appropriate Personal Protective Equipment when encountering subjects who are 
suspected of having RSV infection and following EHS guidelines while handling their 
specimens in BSL2 laboratories.
Minimizing risks of risks to privacy: All attempts will be made to keep this PHI confidential 
within the limits of the law. Only people who are involved in the conduct, oversight, 
monitoring, or auditing of this trial will be allowed access to the PHI that is collected. Only 
HIPAA-trained individuals will be conducting the study. Information will be kept in files on a 
secure system that requires a Yale net ID and password for access. Subject identifiers will 
be de-identified at the earliest reasonable time after we receive them. If information from 
this study is presented publicly or published in a medical journal, no research subject will 
be identified by name, picture, or any other personally identifying manner. For clinical and 
viral genomic epidemiology aims, no direct contact with participants is required, reducing 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
19
the risk of privacy breaches. 
2.3.2
Potential Benefits
We do not anticipate that there will be a direct benefit to the individual participants in the study. 
The proposed studies, however, do offer the potential benefit of generalizable knowledge. The 
creation of a platform to monitor the effectiveness of RSV vaccines will improve confidence in 
the vaccines and will yield evidence to guide the development of new approaches to the 
prevention and control of RSV.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
20
3
Study Purpose and Objectives
3.1
Hypothesis
The key questions this study is expected to answer are:
1) How effective are RSV vaccines in real-world settings?
2) To what extent is the effectiveness of vaccines affected by age, vaccination patterns, 
and virus type?
3) What are the immunologic and clinical drivers of vaccine failure?
4) What is the immune phenotype of children with RSV?
3.2
Primary Objective
The primary objectives of this study are to determine the real-world effectiveness of perinatal 
RSV immunoprophylaxis against medically attended infections in infants less than 12 
months of age.
3.3
Secondary Objective (if applicable)
To quantify the extent to which viral genomic diversity impacts the effectiveness of 
immunoprophylaxis.
To define the impact of immunoprophylaxis on the immune trajectories of infants during 
medically attended acute RSV infection.
To uncover immune phenotypes of patients ≤60 months of age with RSV.
To examine the clinical epidemiology of RSV and testing practices in children ≤60 months of age 
during 2018-2028.
To develop and validate a Natural Language Processing (NLP) tool to extract relevant data from 
the narrative portion of electronic medical records (EHRs) to determine clinical 
characteristics for optimal RSV syndromic surveillance.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
21
4
Study Design
4.1.1
General Design Description
We will conduct an epidemiologic test-negative case-control study, a design that is well- 
established as valid for studies of vaccine effectiveness. Cases will be defined as 
individuals who had a clinical encounter for ARI symptoms and test positive for RSV. 
Controls will be individuals who test negative for the respective virus. Interviews, reviews of 
medical records, and immunization registry searches will be done similarly for cases and 
controls to provide information on patient characteristics, immunization history, potential 
confounders, and effect modifiers. Respiratory specimens will be collected from all 
participants for testing using standardized RT-PCR assays and genomic sequencing. In a 
subset of patients, acute and convalescent sera will be collected for investigations of 
immune responses to infection.
Multivariate logistic regression will be used to estimate the vaccine’s effectiveness, adjusting for 
potential confounders, and stratified by patient characteristics, vaccination patterns, and virus 
types/variants to determine salient influencing factors. 
For our secondary aims, we will conduct two sub-studies. First, we will conduct viral genomic 
epidemiology studies. The main question we are trying to answer is whether specific mutations or 
groups of mutations, predict reduced vaccine or mAb effectiveness. To address this, we will 
request remnant nasal swab samples from RSV-confirmed YNHHS patients ≤12 months of age to 
perform genetic characterization of all RSV viruses and conduct formal sieve analyses to 
compare breakthrough infections with time-matched unimmunized infections, Second, we will 
conduct clinical epidemiology studies. To this end, we will perform a chart review of all pediatric 
patients ≤60 months of age who were tested inpatient or outpatient for RSV at Yale-New Haven 
Health System from 7/1/2018 and will continue forward until 7/1/2028. The patients’ medical 
records will be abstracted and pertinent demographic, epidemiologic, clinical, laboratory, and 
radiographic data will be recorded. We will develop and validate a Natural Language Processing 
(NLP) tool that will allow us to extract data from the narrative portion of EHR's and conduct a 
rigorous, model-based investigation to identify sets of clinical characteristics (i.e., clinical 
syndromes) that are highly predictive of RSV infection and determine and quantify the impact of 
vaccine introduction. 
4.1.2
Study Date Range and Duration
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
22
This will be a 5-year study. Enrollment of the case-control study will begin 10/1/2024 and will end 
11/30/2028. Review of medical records will include data from 7/1/2018 to 7/1/2028.
4.1.3
Number of Study Sites
Patients will be screened for eligibility in inpatient and outpatient sites affiliated with the Yale 
New Haven Health System
4.2
Outcome Variables
4.2.1
Primary Outcome Variables
The primary outcome measured is laboratory confirmed ARI infection (case/control 
status).Respiratory samples will be obtained by study investigators on-site, or if 
samples have already been collected for clinical purposes, we will request residual 
specimens from the participating clinical virology laboratory. For the identification of 
RSV, all samples will be tested using FDA-authorized assays using standard clinical 
procedures, and positive samples will be stored for subsequent genomic 
sequencing.
4.2.2
Secondary and Exploratory Outcome Variables (if applicable)
The primary exposure of interest will be immunization status. Only written 
documentation of receipt of vaccines will be accepted as evidence of prior 
immunization as determined in either medical records or the state immunization 
information system. The vaccine effect will be captured using a series of categorical 
variables that represent the time since the most recent dose. Additional potential 
confounders will also be considered, such as the use of other preventative or 
therapeutic interventions, like masks, social distancing, and monoclonal antibodies.
4.3
Study Population
Eligible participants will include those who have a medically-attended ARI at one of the 
inpatient or ambulatory recruitment sites. To decrease potential selection biases that can 
arise from variability in physician testing practices, we enroll patients who meet the ARI 
case definition regardless of whether they were tested for RSV. Participants will include 
those who are ≤60 months of age. We will enroll males and females of all racial and ethnic 
groups meeting our inclusion criteria. However, we will restrict participation to residents of 
Connecticut so that immunizations can be verified in the state immunization registry.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
23
4.3.1
Number of Participants
During the 5-year study period, we aim to enroll 1250 RSV-positive and 2500 RSV-negative 
infants ≤12 months of age, and 500 RSV-positive and 1000 RSV-negative from 12-60 
months of age for a total sample size of 5250. For priority groups, such as hospitalized 
infants, all eligible patients will be contacted, whereas for clusters with large numbers, a 
simple random sample will be used until our yearly goals are met (250 cases and 500 
controls).
4.3.2
Eligibility Criteria/Vulnerable Populations
In order to be eligible for inclusion in the case-control study, an individual must meet all of 
the following criteria:
●
Male or female ≤60 months of age at the time of presentation for evaluation for an
ARI
●
Infants should weigh at least five pounds upon enrollment.
●
Documentation of an ARI, which is defined as an acute onset (<10 days) illness that 
includes:
At least two of the following symptoms: fever (measured or subjective), chills, 
rigors, myalgia, headache, sore throat, nausea or vomiting, diarrhea, fatigue, 
congestion OR any one of the following: cough, shortness of breath, difficulty 
breathing, olfactory disorder, taste disorder, confusion, persistent chest pain, pale, 
gray, hypoxia, clinical or radiographic evidence of pneumonia or respiratory 
distress syndrome.
●
Residents of Connecticut
Any individual who meets any of the following criteria will be excluded from participation in 
the case-control study:
●
Illness duration of >10 days at the time of respiratory specimen collection, 
measured from the date of the first symptom of the current acute illness.
●
Parent/guardian is not able to provide informed consent
We will also enroll a subgroup of healthy controls. To be eligible for inclusion in the study 
as a healthy control, an individual must meet any of the following criteria:
●
Immunized against RSV ≤60 months of age
●
Residents of Connecticut
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
24
●
Match an enrolled case that was a vaccine failure by date of birth (±1 month), sex, 
and immunoprophylactic agent received (i.e., maternal vaccine vs mAb). Vaccine 
failures are cases who were immunized yet tested positive for RSV.
For our viral genomic sub-study, we will request remnant nasal swabs from YNHHS virology labs 
during the 5-year study period. This will include all RSV-confirmed patients aged 12 months or 
younger who did not opt out of research participation. 
For our EHR aims, patients will be included if they received care at one of the Yale-New Haven 
Health System inpatient units or outpatient clinics between 7/1/2018 to 7/1/2028, were tested for 
RSV with a PCR or antigen test, were ≤60 months of age.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
25
5
Study Methods/Procedures
5.1
Study Procedures
Recruitment plan: Point of care recruitment will be performed by the field team daily at 
participating sites. The field team will be comprised of trained staff who will review the roster 
of patients who receive care at the sites to identify subjects who fulfill the inclusion criteria. 
We will request a HIPAA waiver for screening/recruitment purposes and will contact eligible 
patients at the time of identification to verify eligibility criteria and invite them to participate in 
the study. Written informed consent will be obtained for all patients meeting enrollment 
criteria who are willing to participate in the study.
Patients who are seen remotely for symptoms or who are identified by EHR recruitment 
strategies will be contacted by telehealth for consent procedures. They will be sent an 
electronic message either through our EHR’s patient portal (MyChart) or through the study 
email (peds.prove@yale.edu), inviting them to participate in the study. The JDAT team will 
send out MyChart invitations to eligible participants; however, since these invitations are 
scheduled to be sent only once every two weeks, this method might not be the most 
efficient for our study. To meet eligibility criteria, participants must be acutely ill (within 10 
days of symptom onset), and to collect residual nasal swabs, the research team must enroll 
participants within 5 days of the swab being performed. As an alternative, for potential 
participants identified through EHR recruitment strategies who received medical care at the 
Yale New Haven Health System but could not be enrolled in person, we propose sending 
email invitations to participate in the study. To facilitate this, we will collaborate with JDAT 
to generate an EPIC report that includes all patients who had a medical encounter within 
the Yale New Haven Health System in the past 7 days and meet our study’s eligibility 
criteria.
The research team will then review this report, identify potential participants, and send email 
invitations through peds.prove@yale.edu. Potential participants who respond to the initial 
electronic invitation with interest will be contacted within 48 hours of their encounter by 
telephone and given the option to participate in the study. When participants are enrolled 
remotely, we will request electronic signatures through electronic informed consent (E- 
consent through RedCap) that can be accessed through mobile devices. Subjects who have 
difficulty navigating or using electronic systems will be mailed a paper version of the 
consent form.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
26
Recruitment will start in the 2024/25 RSV season and plan to continue enrollment for 5 
consecutive seasons. We will leverage our partnership with the CT-EIP (RSV-NET and CT-Wiz) 
to determine the onset of the RSV season and the overall uptake of vaccine/mAb in our region. 
To optimize our resources, will initiate active surveillance after vaccine uptake among newborns 
is >20% and the mean percentage of specimens testing positive by PCR for RSV is ≥3% for 2 
consecutive weeks. For priority groups, such as hospitalized infants, all eligible patients will be 
contacted, whereas for clusters with large numbers, a simple random sample will be used until 
our yearly goals are met (250 cases and 500 controls).
We will work with JDAT to build a study dashboard using a combination of billing codes 
and routinely collected clinical data such as demographics, vital signs, laboratory results, 
and free-text chief complaint or reason-for-visit data fields. This dashboard will allow us to 
both identify study-eligible patients in real-time and estimate weekly aggregate counts of 
ARI visits, all-cause patient visits (denominator), total patients tested, and percent positive 
lab results, by age group and key demographic variables. This informatics infrastructure 
will allow us to perform several other important study tasks, such as tracking our 
enrollment progress across demographic categories, and identifying problems related to 
study recruitment.
Interviews: Standardized questionnaire will be used to ascertain core measures (see Table 
1). For in-person interviews, research coordinators will read questions to participants, and 
record the answers directly into a secure web-based data collection platform (RedCap).
Participants will also be given an option to complete the survey using a computer-assisted 
survey interviewing (CASI) program on their own device at the time of their choosing. If 
there is no response by the participant to the request to complete the required surveys, the 
study team will (as needed) continue reaching out to participants via email, phone call, or 
text beyond this point.
Table 1. Proposed core measures to be ascertained
Category
Variable
Method
Sociodemographic
Age, gender, race, language, insurance, and 
address.
Survey, 
EHR
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
27
Medical History
Date of illness onset, symptoms and their severity, 
previous respiratory infections, medical history (ICD- 
10, CPT codes), healthcare utilization, medication 
history (antibodies, antivirals, immunosuppressants).
Survey, 
EHR
Immunization 
History
Dates, types, and names of all vaccines received. 
Name and address of vaccine providers.
Survey, 
EHR,
Registries
Exposure History
Use of masks, adherence to social distancing, and 
exposure history (e.g., household, occupation, 
schools, long-term facilities, social gatherings).
Survey
Community-level 
Social Determinants
Of Health
Area-based measures of race/ethnicity, poverty, 
income, vulnerability, and disadvantage.
US
Census 
Data
*NIH PhenX toolkits, WHO’s Global COVID-19 Clinical Platform, Social Vulnerability Index.
Medical record review: After identifying prior sources of care, members of the research 
team will review the medical records of each participant. Records from all offices at which 
the infant received care within the YNHHS, including those of subspecialists, will be 
ascertained to ascertain data about previous or subsequent visits (up to 2 months post-ARI) 
for symptoms that could be related to their index respiratory illness. The dates for the visits, 
diagnostic tests performed, and treatments received (ICD-10 and CPT codes) will be 
recorded. The presence of any other acute or chronic diseases also will be recorded.
Trained staff will complete a standardized abstraction form by directly entering information 
into a computerized form. The core variables that we propose to capture during reviews of 
medical records are also shown in Table 1.
Respiratory specimen collection. Respiratory samples (nasal swabs) will be collected from all 
participants. If samples have already been collected for clinical purposes, we will request 
residual specimens from the participating clinical virology laboratory. Self-collected specimens 
(saliva or nasal swabs) will be used for participants who do not have residual clinical specimens 
and are enrolled via telehealth. For these patients, we will provide the parents/guardians with a 
sample-collection kit, and the study team will supervise self-collection using video conferencing. 
Specimens will be collected in media that neutralizes the virus yet stabilizes the RNA, which 
alleviates biosafety concerns related to sample collection and transportation. Respiratory 
specimens will be transported to Dr. Grubaugh’s BSL-2+ laboratory at the YSPH for viral 
classification and sequencing. A subset of patients will have respiratory aspirates and/or 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
28
induced sputum collected, processed and stored in the Lucas lab for immunophenotyping.
Acute and convalescent blood: Blood samples will be collected for participants who provide 
consent. We will collect acute samples within 1 week of diagnosis and convalescent specimens 
4-12 weeks after diagnosis. We will make every effort to coordinate blood samples with already 
planned visits and/or will collect residual/excess clinical specimens from their outpatient visits 
when available. If no routine follow-up visits are planned during our time frame, we will schedule a 
follow-up visit for a blood draw at the Church Street Research Unit (CSRU). The amount of blood 
drawn for research purposes will not exceed the lesser of 50 ml or 3 ml/kg in an 8-week period 
and collection will not occur more frequently that 2 times per week. Study team members will be 
trained in consenting and collecting samples as well as proper Personal Protective Equipment. In 
addition to in-person blood collection, we will provide parents with the option of using a home 
blood biospecimen collection kit (Tasso device). The Tasso device is an FDA-approved Class I 
product.
Follow-up assessments: We will also conduct follow-up surveys 4-12 weeks after the initial 
ARI using a similar approach. The follow-up surveys will aim to assess the infant’s 
treatment and clinical outcomes, as well as parental outcomes, such as physical, 
emotional, and social health, as well as health-related quality of life measures. We will use 
instruments that have been extensively validated for proxy-report (PedsQL).33If participants 
do not have access to a computer or Internet, they will be given the option to fill out the 
questionnaire in person at the Yale medical campus.
Immunological markers: We hypothesize that maternal immunization and antibody-
mediated passive immunity modulates immune priming and memory responses in infants 
who are infected with RSV. To test this hypothesis, we will collect acute and convalescent 
blood from a subset of infants (N=75), and recruit an additional 50 healthy community 
controls, and we will employ a single-cell and multi-omics approach to study the dynamics 
of the innate and adaptive immune responses during RSV infection and derive systems-
level mechanistic models of effective and aberrant vaccine response. These findings might 
help guide management decisions involving precision vaccinology.
We will make every effort to coordinate blood samples with already planned visits and/or 
will collect residual/excess clinical specimens from their outpatient visits when available. 
Serum from immunized and unimmunized infants who were RSV positive will be collected 
during acute illness and longitudinally after recovery to be analyzed together with serum 
from healthy community controls who were also immunized. Community controls will be 
individually matched to enrolled vaccine failures (immunized and RSV+) by date of birth (±1 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
29
month), sex, and/or immunoprophylactic agent received (i.e., maternal vaccine vs mAb). We 
will obtain a list of potential controls from the YNHHS EHR and will use a random number 
generator to establish the order in which controls will be contacted until one control per case 
has been successfully enrolled. All blood samples will be processed at the Lucas 
Laboratory, labeled with bar codes and labels containing study ID, and kept frozen at -80 
degrees Celsius or liquid nitrogen tank until ready for testing via immunologic assays. 
Handling, transport, and storage of the samples will be according to Infectious Disease 
requirements.
Clinical Epidemiology: For our EHR aims, we will collaborate with Yale’s Joint Data 
Analytics Team (JDAT), to create a secure data warehouse that will receive abstract 
relevant clinical information and full-length clinical notes for all children who meet eligibility 
criteria and were tested for RSV within the YNHHS during our study period. We will begin 
by building a dataset as early as 7/1/2018 and will set up a system that continually 
prospectively extracts data going forward. We will use natural language processing (NLP) 
to extract relevant data from clinical notes. Once all desired entities are identified, coded, 
and labeled based on their context, we will build a program that generates a structured 
output that can then be analyzed. Variables that will be extracted from EHR include date of 
birth, insurance information, self-reported demographics (gender, race/ethnicity, preferred 
language, marital status, religion, city, state of residence, zip code), visit specific variables 
(date of visits/admission, visit diagnosis), ICD9 diagnoses, laboratory tests and imaging 
studies performed to aid in diagnosis (RSV PCR with cycle threshold, typing results, white 
blood cell count with differential, hemoglobin, platelet count, electrolyte, ALT, AST, total 
bilirubin, creatinine, c-reactive protein, sedimentation rate, ferritin, coagulation panel, 
procalcitonin, d-dimer, cytokine panel, troponin, brain natriuretic peptide, TEG mapping, 
EKG results, echocardiogram, chest X-ray findings, and computed tomography scan), 
management of diagnosis (what treatment was offered, what doses were used, how long 
where they treated, were there drug side effects, duration of fever, respiratory distress, 
oxygen requirement, ventilator days, duration of hospitalization, and outcome). Full length 
encounter notes. Immunization history, including dates of prior RSV immunizations.
Viral Genomic Epidemiology: For our viral genomic sub-study, no contact with human subjects by 
the PI or any research team member is involved. Instead, we will collaborate with YNHHS 
virology labs to collect clinical specimens that are leftover from routine diagnostic tests. 
Specifically, we will request remnant RSV-positive nasal swabs from all patients aged 12 months 
or younger who have not opted out of research participation. Viral RNA from all RSV-positive 
samples with PCR cycle threshold values below 35 will be sequenced using amplicon-based 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
30
protocols. The viral sequencing data will not be shared with the patient or used for clinical 
purposes. In addition to the residual specimens, we will collect a limited dataset from the EHR on 
these patients for the planned analysis. This limited dataset will include patient demographics 
(age, sex, race/ethnicity, state of residence), sample collection date, PCR assay or platform used, 
and the cycle threshold (CT) value from the PCR diagnostic test, which indicates the amount of 
virus present in the specimen. If applicable, we will collect dates of vaccination, maternal 
vaccination, previous positive RSV tests, and the outcome of the index infection (mild, moderate, 
or severe disease). After data collection is complete, individuals for these genomic analyses are 
assigned a unique ID, and any information not listed above (including all personal identifying 
information) will be removed from this analysis on any other device. Identifiers will be destroyed 
at the earliest possible stage, in compliance with institutional policies, so that the specimens 
cannot be linked or re-linked to identifiable human subjects. At no point will this information be 
linked back to personal identifiers.
Data Collection
For in-person interviews, research coordinators will record the answers directly into a 
secure web-based data collection platform. Participants will also be given an option to 
complete the survey using their own device and an online computer-assisted survey 
interviewing (CASI) program. For medical record reviews, trained staff will complete a 
standardized abstraction form by directly entering information into a computerized form. 
The biological samples will be stored in locked freezers. Information about the subject-
donors will be maintained in a password-protected computer and password-protected data 
files. We will follow EHS requirements while processing of specimens from suspected RSV 
infections under BSL2 procedures. All clinical data, and results of tests on biological 
samples will be entered into an electronic RedCap database. The database is a HIPAA- 
compliant electronic data management system. The RedCap registry is fully integrated with 
the labs allowing linkage of biospecimens to the database. Subject identifiers will be de-
identified at the earliest reasonable time after we receive it, meaning we will replace the 
identifying information with a code that does not directly identify each subject. The principal 
investigator will keep a link that identifies PHI to the coded information, and this link will be 
kept secure and available only to selected members of the research team. Only people who 
are involved in the conduct, oversight, monitoring, or auditing of this trial will be allowed 
access to the PHI that is collected.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
31
5.1.1
Adverse Events Definition and Reporting
This study will include the collection of data from medical records, surveys, residual clinical 
specimens, and the collection of nasal swabs by noninvasive means, and blood draws of 
small volumes for research purposes. Thus, we would consider this protocol to be of 
Minimal Risk to patients.
The principal investigator is responsible for monitoring the data, assuring protocol 
compliance, and conducting the safety reviews every 6 months. During the review process, 
the principal investigator will evaluate whether the study should continue unchanged, 
require modification/amendment, or close to enrollment. The principal investigator and the 
Institutional Review Board (IRB) have the authority to stop or suspend the study or require 
modifications.
This protocol presents minimal risks to the subjects and Unanticipated Problems Involving 
Risks to Subjects or Others (UPIRSOs), including adverse events, are not anticipated. In 
the unlikely event that such events occur, Reportable Events (which are events that are 
serious or life-threatening and unanticipated (or anticipated but occurring with a greater 
frequency than expected) and possibly, probably, or definitely related) or Unanticipated 
Problems Involving Risks to Subjects or Others that may require a temporary or permanent 
interruption of study activities will be reported immediately (if possible), followed by a written 
report within 5 calendar days of the Principal Investigator becoming aware of the event to 
the IRB (using the appropriate forms from the website) and any appropriate funding and 
regulatory agencies. The investigator will apprise fellow investigators and study personnel 
of all UPIRSOs and adverse events that occur during the conduct of this research project 
through regular study meetings and via email as they are reviewed by the principal 
investigator.
5.2
Study Schedule
Each patient will have 2-3 total study visits. The first visit will be for the collection of 
informed consent, core survey, and biospecimens (nasal swabs and if participating in sub-
study, acute blood). The first visit will take between 30-60 minutes. The second visit will 
entail the collection of follow-up surveys and for those participating in the immunologic sub-
study, the collection of convalescent blood. A follow-up visit will be 4-12 weeks after 
enrollment and take between 15-30 minutes. We will make every effort to coordinate 
encounters with already planned visits. If no routine follow-up visits are planned during our 
time frame, we will schedule a follow-up visit at the Church Street Research Unit (CSRU). 
Contact #3 may occur for hospitalized patients during their inpatient stay.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
32
5.3
Informed Consent
Written consent from parents will be required for participation in the case-control study as these 
patients will be identified prospectively. For the clinical epidemiologic and viral genomic studies, 
which involve chart reviews and secondary analysis of residual specimens, we will request a 
Waiver of HIPAA Authorization for the use of identifiable private information. 
5.3.1. Screening (if applicable)
Eligibility for the case-control study will be determined based on the daily screening of 
candidate patients through the review of patient registries by research staff stationed on 
each participating ambulatory site. The research coordinator will screen these patients for 
eligibility based on the inclusion and exclusion criteria. To identify eligible patients using the 
EHR, we will utilize Joint Data Analytics Team (JDAT) to build dashboards to assist in 
identifying all patients seeking care in our sites who have not opted out of research and 
meet our case definition. We will contact eligible patients at the time of identification for 
recruitment and to obtain written informed consent. We are requesting a HIPAA Waiver of 
Authorization for screening purposes to allow us to review medical records to recruit 
subjects for the study. No direct contact with these subjects will be made other than as 
specified in the recruitment strategies. 
5.3.2. Recruitment, Enrollment and Retention (if applicable)
If appropriate subjects are identified while still in the ambulatory site, investigators will 
approach the provider to refer subjects to study personnel when appropriate. For patients 
identified through EHR, an email or myChart message will be sent to the patient inviting 
them to participate in the study. After determining that a subject is eligible, the PI or 
designee will approach the patient or parent/guardian to offer participation in the study. The 
patient or parent/guardian will be informed about the objectives of the study and the 
potential risks and benefits of participation. They will receive a concise and focused 
presentation of key information about the study verbally and with a written consent form. 
The key information about the study will be organized and presented in lay terminology and 
language that facilitates understanding why one might or might not want to participate. After 
this, patients or parents/guardians will be asked to read and review the consent form. Once 
signed, a copy of the consent and assent form will be given to the subject for their records. 
If the patient or parent/guardian refuses to consent OR refuses permission for their child to 
participate, then all clinical management for the patient will be provided by the clinical staff 
in accordance with institutional practice and judgment.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
33
When able, we will use electronic consents/assents that are identical to the paper version. 
All communications through our E-consent platform are encrypted and support HIPAA 
certification. Subjects who have difficulty navigating or using electronic systems (i.e., a lack 
of familiarity with electronic systems, poor eyesight, or impaired motor skills) will not be 
enrolled with E-consent. Instead, they will be given a paper version of the consent form 
and will be asked to send the signed consent form back to the research staff.
Study participation will be voluntary and confidential, and participants will be informed that 
none of their information will be shared with anyone outside the study team unless required 
by law, nor will their participation or decision not to participate affect their medical care in 
any way. Infants and children will be eligible for this study. Safeguards against coercion or 
undue influence will be in place, and the children’s rights and welfare will be protected at all 
times.
For healthy controls, it will be the same procedure as those enrolled remotely. Namely, 
healthy controls that meet inclusion/exclusion criteria will be sent an electronic message 
through our EHR’s patient portal (MyChart), inviting them to participate in the study. Healthy 
controls will match the vaccine failure by date of birth (±1 month), sex, and/or 
immunoprophylactic agent received (i.e., maternal vaccine vs mAb). A vaccine failure is a 
case that was previously immunized yet tested positive for RSV. Eligible healthy control 
subjects will be contacted until one control per vaccine failure has been successfully 
enrolled.
Gift Cards: Participants who complete the study protocol will be given gift cards for 
participation in different phases of the study: $50 for initial recruitment, and additional $25 
for each blood collection.
Retention: All participants will be encouraged to participate by appropriate staff training in 
recruitment techniques. Various additional retention strategies will be employed, including 
the use of messaging strategies that are culturally tailored and that underscore the study's 
gain and impact on society, as well as maintaining meticulous recruitment and retention 
data. To enable follow-up, detailed contact information will be collected, and participants 
will be asked if they wish to be contacted by phone, text, regular mail, or electronic mail.
5.3.1
Study Visits (if applicable)
Visit 1 (30-60 minutes): At diagnosis of ARI (or routine visit for healthy controls)
●
Consent
●
Intake survey
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
34
●
Collection of respiratory specimens (not for healthy controls)
●
Collection of acute blood (if participating in sub-study, or healthy control)
Visit 2 (15-30 minutes): 4-12 weeks after diagnosis of ARI
●
Follow-up surveys
●
Collection of convalescent blood (if participating in sub-study)
●
Collection of convalescent nasal swab/induced sputum (if participating in sub-
study)
Visit 3 (15 minutes; for inpatients): 2-3 days after Visit 1.
●
Collection of acute blood (if participating in sub-study, or healthy control)
●
Collection of respiratory specimens (if participating in sub-study)
5.4
Statistical Method
5.4.1
Statistical Design
For case-control studies, the standard measure of association is the odds ratio, and the vaccine’s 
protective effect can be estimated as 1-OR X100%. For our primary analysis, we will estimate the 
overall effectiveness of each immunoprophylactic strategy (mAb and maternal immunization) 
separately. Logistic regression models will be used for analysis, with the outcome being 
case/control status and immunization status as the main predictor, controlling for known 
confounders such as the time period (penalized spline for time), age, disease severity, 
breastfeeding, and race/ethnicity. To ensure rigor, we will perform extensive model validation and 
testing through the comparison of alternative modeling structures, uncertainty analyses, and 
internal consistency checks. For our primary analyses of the vaccine’s effectiveness, we will use 
backward selection to identify covariates to include in the final model.
For our EHR aims, we will estimate the impact of introduction of the vaccine on the age- 
standardized rate (ASR) of monthly and annual disease by analyzing trends with an 
interrupted time-series model. This model fits the monthly outcomes of interest to an 
ordinary least-squares regression model including a linear trend, an indicator variable for 
the post-vaccine period, and Fourier terms (sine and cosine functions) to control for 
seasonality. For these models, we will use Newey-West standard errors and a first-order 
autoregressive function. For comparison, counterfactual outcomes will be calculated to 
predict the outcome of interest (RSV-related disease) during the post-vaccine period had 
the vaccine not been introduced. Counterfactuals will be predicted by carrying forward the 
pre-intervention trend estimates to the last month of observation while also controlling for 
the trends of other health care utilization. This will allow us to more effectively estimate the 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
35
changes in incidence of RSV that may have occurred as a consequence of the vaccine 
while accounting for pre-existing trends. Absolute reduction in the rates of each outcome 
will be 
calculated by taking the incidence rate of each outcome from the first year of the study and 
subtracting the same rate from the last year of the study. The attributable reduction in RSV 
will be similarly calculated but rather than using incidence of the first year of observation, 
we will use the predicted incidence of the last counterfactual year. This will allow us to 
estimate the reduction of RSV at the end of the study accounting for the pre-existing trends. 
Lastly, to assess if the incidence of RSV infection and disease varies significantly by RSV 
vaccine coverage in this population, we will fit logistic regression change-point models that 
account for various degrees of vaccine coverage post-vaccine introduction.
5.4.2
Sample Size Considerations
The number of cases needed to detect a range of estimates of effectiveness with α<.05 and 
80% power. We calculated the sample sizes presented for different proportions of controls 
that might be immunized and for a 2:1 ratio of controls to cases using established formulas.34 
It is not known what proportion of patients will be immunized. However, we can model our 
sample size calculations based on our experience with the implementation of neonatal 
hepatitis B vaccine and uptake of influenza vaccine in pregnant women. In Connecticut, 
within a year of the CDC issuing the recommendation that all newborns receive their first 
dose of hepatitis B vaccine before hospital discharge, coverage of the vaccine was 55% by 3 
days of life.35 For the 2022/23 season, the coverage of influenza vaccine was 47.1% for all 
pregnant women, lowest (28.4%) for Black, and highest (65.2%) for Asians.
During the 5-year study period, we aim to enroll 1250 RSV-positive and 2500 RSV-negative 
infants ≤12 months of age, and 500 RSV-positive and 1000 RSV-negative 12-60 month old 
children for a total sample size of 5250. For priority groups, such as hospitalized infants, all 
eligible patients will be contacted, whereas for clusters with large numbers, a simple 
random sample will be used until our yearly goals are met (250 cases and 500 controls). 
Healthy community controls will only be enrolled if an enrolled case is identified as a 
vaccine failure. A maximum of 50 healthy controls will be enrolled during the study period.
5.4.3
Planned Analyses
VE will be estimated using multivariate logistic regression with RSV status as the outcome and 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
36
vaccination status as the main predictor with an estimated VE = (1 – adjusted odds ratio) x 100. 
The effect of immunization over time will be captured using a series of categorical variables that 
represent the time since the most recent dose. As an indicator of the level of exposure at different 
time points, we will also consider the number of positive tests performed at focal time throughout 
the study population. Additional analyses will also consider disease severity. If effect modification 
is observed by disease severity, or other participant characteristics (e.g., race, ethnicity, social 
determinants of health), the effectiveness for each will be determined separately if a sufficient 
sample size allows.
Additional analyses will be performed to address the secondary aims of the study. If effect 
modification is observed by participant characteristics (race, ethnicity, social determinants of 
health), vaccine regimens (number of doses, or products), or viral variants in circulation, the 
effectiveness for each will be determined separately if a sufficient sample size allows. 
Hierarchical modeling approaches will be used to allow robust estimates of variability in the 
vaccine’s effectiveness by subgroup. Since it is possible (indeed, it is likely) that in some 
instances, the vaccine may modify the severity of disease rather than prevent it, cases will 
be stratified according to the clinical severity of their illnesses (mild, moderate, or severe) 
and the protective effect of the vaccine within each of these strata will be assessed using 
the methods described previously.
We will conduct several additional analyses to assess whether bias might have been 
introduced in the selection of the controls. First, since we do not expect the vaccine to 
induce an immune response during the first 7 days following its receipt, we will use this as a 
negative control period and create an indicator variable for vaccines given within this period. 
Any significant effect for this variable could indicate the presence of residual confounding.19 
We will also assess and compare the completeness of other immunizations. Receipt of 
other vaccines could be used as a variable in the multivariable analyses to assess whether 
adjusting for this potential marker for selection bias has an effect on the estimate of the 
vaccine's effectiveness. Conversely, if there is no significant difference between the cases 
and the controls in the proportion who had received other vaccines, it would suggest that 
selection bias from vaccine ascertainment is not likely to have been an important factor. 
From serum, we will look for differences in the proportion of innate immune cell populations 
(neutrophils, dendritic cells, monocytes, and natural killer cells) and adaptive immune cells 
(B cells and T cells) in infants with breakthrough infections compared to healthy matched 
controls and test-negative controls. Second, we will assess if maternal antibodies can 
impede the infant’s immune response following exposure to the virus. To define the kinetics 
of the innate and adaptive immune response at the cellular level, we will quantify the 
frequency and phenotypic differences of peripheral blood immune cells during acute and 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
37
convalescent blood of RSV+ infants who were both immunized and unimmunized. We will 
use unpaired T- tests for between-groups comparisons and paired T-test to compare acute 
vs convalescent data. Third, we will examine for prenatal priming. To do this, we will select 
samples collected during the acute phase of illness of RSV-positive infants whose mothers 
were immunized or who received mAb, and samples of infants who were not immunized 
and compare the proportions of naïve T cells and memory cells, as well as RSV-specific 
immune responses on acute presentation.
EHR subaims: We will conduct a rigorous, model-based investigation to identify sets of clinical 
characteristics that are highly predictive of RSV infection. To determine which set of clinical 
predictors to use in the optimal case definition, we will use latent class analysis and compare the 
probabilities of various sets of clinical features. Last, we will explore the utility of using an 
integrative and adaptative case definition. That is, one that integrates multiple levels of data (i.e., 
individual, provider, and community) and that adapts to various age groups. We will use 
optimization algorithms to identify the ideal cutoffs for the dynamic variables and select the 
approach that maximizes accuracy. Next, using an ecological study design, trends in RSV testing 
patterns and disease will be assessed using EHR data within the Yale New-Haven Health System 
(YNHH). A database will be created with data extracted from the EHR electronically with support 
of Yale’s Joint Data Analytics (JDAT) team. This database includes encounter specific data from 
inpatient and outpatient visits at YNHH clinics. Data will be collected for all patients age ≤60 
months who are Connecticut residents, were tested for RSV, and received care at the YNHHS 
between 7/1/2018 to 7/1/2028, which includes 2 seasons of pre-COVID-19 data.
For our viral genomic analysis, the first question we aim to answer here is whether the 
effectiveness of the vaccine and mAb differs significantly between the major groups or 
clades. To do this, we will perform a case-only analysis in which we compare the immune 
status among cases infected with RSV group A versus B and assess the relative 
effectiveness of immunization. For this analysis, logistic regression will be used to control 
for the time of testing and other relevant confounders. The second question we intend to 
answer is whether the viral mutations that were previously linked with F-protein antibody 
neutralization resistance (N67I/N208Y in RSVA; N208S, N208D, K68N/N208S, and 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
38
K68N/N201S in RSV B), are overrepresented in the vaccine breakthrough group, relative 
to non-immunized RSV cases in the same respiratory season. The third question we will 
consider is whether the vaccines/mAb are more likely to prevent infections from RSV 
strains that are genetically closest to the strains used to derive the vaccine/mAb (i.e., 
“vaccine reference”). We will conduct pairwise genetic distance comparisons between 
breakthrough cases and “vaccine reference” and test for statistical significance using two-
way ANOVA with Tukey’s for multiple comparisons. We will then compare the Hamming 
distance between immunized and unimmunized cases using logistic regression models 
adjusting for the calendar time.
Analysis of Subject Characteristics (if applicable)
We will compare baseline characteristics of cases versus controls using chi-square test, 
conditional logistic regression, or the Wilcoxon signed-rank test (depending on the nature of 
the variable). To assess the possibility of selection bias, we will compare demographic 
variables of cases we enroll with those who decline to participate.
5.4.4
Interim Analysis (if applicable)
We will conduct analyses every year to assess the annual VE. Analyses of the clinical 
characteristics of patients with medically attended acute respiratory illness will be 
repeated at regular intervals to identify changes in the clinical presentation of RSV, as well 
as changes in proportions of patients with ARI due to the different viruses. An interim 
analysis will be conducted to estimate the number of patients infected with RSV other 
respiratory viruses, in the source population (over a given period of time) based on the 
number of positive enrollees in the study and an estimate of the number or proportion of 
study-eligible patients that were missed (i.e., not enrolled).
5.4.5
Handling of Missing Data
We will address missing data via modern imputation methods as appropriate for each 
analysis. For any situation in which missing data are substantial, we will conduct sensitivity 
analyses.
6
Trial Administration
6.1
Ethical Considerations: Informed Consent/Assent and HIPAA Authorization
Screening every individual that is seen during a clinical encounter can obstruct the clinical 
workflow and be overburdening for ineligible patients. Thus, we are requesting a HIPAA 
Waiver of Authorization for this study to allow the study coordinator and investigators to 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
39
review medical records at YNHHS as pre-screening for recruitment. No direct contact with 
these subjects will be made other than as specified in the recruitment strategies above. The 
PHI viewed and used during the pre-screening process for ineligible patients will never be 
reused or disclosed to any person or entity other than those listed in this study application. 
We are also requesting a waiver for the clinical epidemiologic studies, which involve retrospective 
chart reviews and secondary analysis patients who were tested for RSV. Obtaining individual 
authorization for the clinical epidemiologic studies is impracticable due to the retrospective nature 
of the study and the necessity of analyzing a large, diverse cohort.
Additionally, we seek a waiver of consent for infants who test positive for RSV so that we may 
collect their residual respiratory swabs for viral genomic studies. This waiver is critical for several 
reasons. First, the research cannot be conducted without identifiable information, as linking viral 
genetic sequences to clinical outcomes and vaccination status is essential for accurately classifying 
breakthrough infections and performing time-matched comparisons. Second, requiring 
authorization would reduce statistical power and introduce selection bias by restricting the dataset 
to individuals who consent, thereby compromising the scientific validity of epidemiologic estimates 
and time-matched analyses. An underpowered and biased dataset undermines the very purpose 
of this research—to generate reliable, generalizable findings that can guide clinical and policy 
decisions. Third, it will be impracticable to conduct the genomic studies if the waiver is not granted. 
Many infants are tested at Yale but do not receive ongoing care within the system, making direct 
contact challenging. Further, virology labs store residual respiratory swabs for only 2–7 days before 
discarding them. In that short window, it is simply not feasible to reach every parent and obtain 
authorization before the samples are lost. Finally, granting this waiver would facilitate participation 
in the main case-control study by reducing subject burden. Many parents are willing to contribute 
to research but are hesitant to subject their child to additional swabbing. By accessing and storing 
residual RSV-positive samples from all Yale labs, we can reduce the burden on families who are 
willing to participate in the full study. This approach would allow us to reach out to potential 
participants after their initial swab, giving them time to consider enrollment without losing valuable 
specimens. If a patient opts out of research or declines participation all corresponding samples and 
data will be discarded.
For all other aspects of this protocol, including participation in the case-control study, an 
informed consent form approved by the Yale School of Medicine Human Investigation 
Committee will be used to explain the purpose of the study and the risks and benefits of 
study participation before the subject is entered into the study. A member of the 
investigative research team will approach subjects or authorized representatives/surrogates 
and discuss the information provided on the consent form in detail. Subjects and authorized 
representatives/surrogates will be given time to read the form and ask questions during the 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
40
process of consent. After they sign the consent form, they will be given a copy of the signed 
form and informed to contact the PI or study coordinator if they have further questions or 
concerns. Informed consent will be obtained from each subject or authorized 
representative/surrogate with appropriate signatures and dates on the informed consent 
documents prior to the performance of any protocol procedures (see Recruitment 
Procedure above). When an authorized representative/surrogate provides the initial 
consent, the subject will be asked to continue their participation when and if they regain the 
capacity to make decisions. Subjects refusing to continue participation in the study will be 
withdrawn from the study and their study samples and information will be 
discarded/destroyed if requested.
To reduce exposure to potentially infected paper, when able, we will request electronic 
signatures through electronic informed consent that can be accessed through mobile 
devices. Subjects who have difficulty navigating or using electronic systems because of, for 
example, a lack of familiarity with electronic systems, poor eyesight, or impaired motor 
skills, will not be enrolled with electronic consent. Instead they will be given a paper version 
of the consent form, and after signing the consent form, will be asked to send the complete 
signed consent form to the research staff.
The ability and capacity to consent/assent will be determined by the Principal Investigator or 
research team members by questioning during the informed consent process and by 
discussion with the inpatient medical staff. Potential subjects will be asked, “Could you 
explain to me what we are going to ask you to do in this study? This will help me be to be 
sure that you understand the research,” as well as, “What more would you like to know 
about this study?” If the subject is unable to understand, we will not continue to pursue 
consent.
Consent documents will be translated into Spanish versions for Spanish-speaking subjects. 
Spanish version consent documents will be submitted to the HIC for review and approval before 
administration. For eligible participants who speak Spanish, a translated consent form will be 
provided, and consenting procedures will proceed in Spanish by study personnel fluent in 
Spanish.
Study participation will be voluntary and confidential, and participants will be informed that 
none of their information will be shared with anyone outside the study team unless required 
by law, nor will their participation or decision not to participate affect their medical care in 
any way. Infants and children will be eligible for this study. Safeguards against coercion or 
undue influence will be in place, and the children’s rights and welfare will be protected at all 
times.
The results from assays that are FDA-authorized will be returned directly to participants if 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
41
they indicated on the consent form that s/he would like the results returned. For positive test 
results, participants will be advised to begin early isolation while they consult with their 
primary care provider for confirmatory testing and treatment. Tests that are exploratory in 
nature, such as the sequencing, will not be conducted in an actionable timeframe post 
sample collection. Therefore, these results will not be reported back to the individuals or their 
families but may be aggregated for deidentified publication of study results.
6.2
Institutional Review Board (IRB) Review
The protocol will be submitted to the IRB for review and approval. Approval of the protocol 
must be obtained before initiating any research activity. Any change to the protocol or study 
team will require an approved IRB amendment before implementation. A study closure 
report will be submitted to the IRB after all research activities have been completed.
6.3
Subject Confidentiality
Participant confidentiality and privacy is strictly held in trust by the participating investigators, their 
staff, and the sponsor(s) and their interventions. Therefore, the study protocol, documentation, 
data, and all other information generated will be held in strict confidence. No information 
concerning the study or the data will be released to any unauthorized third party without prior 
written approval. All research activities will be conducted in as private a setting as possible.
The study monitor, representatives of the Institutional Review Board (IRB), or regulatory 
agencies may inspect all documents and records required to be maintained by the 
investigator. The study participant's contact information will be securely stored at each 
clinical site for internal use during the study. At the end of the study, all records will continue 
to be kept in a secure location for as long a period as dictated by the reviewing IRB, 
Institutional policies, or, if applicable, sponsor requirements.
Study participant research data, which is for purposes of statistical analysis and scientific 
reporting, will be transmitted to and stored in a RedCap folder. This will not include the 
participant's contact or identifying information. Rather, individual participants and their 
research data will be identified by a unique study identification number. The study data 
entry and study management systems used will be secured and password protected. At the 
end of the study, all study databases will be de-identified and archived in the Yale Secure 
Box folder.
6.4
Deviations/Unanticipated Problems
A protocol deviation is any noncompliance with the study protocol. The noncompliance may 
be either on the part of the participant, the investigator, or the study site staff. As a result of 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
42
deviations, corrective actions are to be developed by the site and implemented promptly.
The principal investigator will report the following types of events to the IRB: a) adverse 
events that are serious or life-threatening AND unanticipated (or anticipated but occurring 
with a greater frequency than expected) AND possibly, probably or definitely related to the 
drug/device/intervention; and b) other unanticipated problems involving risks to subjects or 
others. These adverse events or unanticipated problems involving risks to subjects or 
others will be reported to the IRB in accordance with IRB Policy 710, using the appropriate 
forms found on the website.
6.5
Data Quality Assurance
The use of computer-assisted data entry will be used to help minimize data entry errors. All 
variables will be examined for missing and out-of-range values by examining the frequency 
distributions of each variable. Consistency and logic checks will be conducted, and any 
errors will be corrected.
6.6
Study Records
Study records include regulatory documents, protocols, consent forms, subject medical 
records, surveys, and specimens.
6.7
Access to Source
Source data will be maintained per Medical Records policy in a password-protected, secure, 
Health Insurance Portability and Accountability Act (HIPAA) compliant, web-based electronic 
database with a built-in audit trail. Only Institutional Review Board (IRB) approved research 
team members who have current HIPAA and Collaborative Institutional Training Initiative 
(CITI) and human subjects protection training will be authorized to access records.
6.8
Data or Specimen Storage/Security
The samples contained in the repository will be coded and stored in a freezer in a locked 
laboratory. The link to the code will be stored in a separate password-protected file. 
Information about the subjects will be maintained in a password-protected computer and 
password-protected data files. The information resides on a server considered by ITS-Med to 
adhere to the HIPAA Security Rule.
6.9
Retention of Records
At the completion of the study, the link to personal information will be kept for 5 years, after 
which time the link will be destroyed and the data will become anonymous. Data 
destruction will occur according to Yale policy. The data will be kept in this anonymous 
form indefinitely. If a research subject withdraws permission for identifiable biologic 
material or data to be used for future research purposes, the data and specimens from 
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
43
those subjects will be destroyed and not used to generate any further data.
6.10 Study Monitoring
The principal investigator will be responsible for monitoring the data, assuring protocol 
compliance, and conducting the safety reviews at the specified frequency, which must be 
conducted at a minimum of every 6 months.
6.11 Study Modification
During the review process, the principal investigator (monitor) will evaluate whether the 
study should continue unchanged, require modification/amendment. Either the principal 
investigator or the Yale Human Investigations Committee have the authority to stop or 
suspend the study or require modifications.
6.12  Study Completion
The study is expected to be completed on 11/30/2028. The PI will submit a study closure 
report to the IRB after all research activities have been completed.
6.13 Funding Source
NIH R01AI179874
The Hartwell Foundation 
NIH 1K08AI177743
6.14 Conflict of Interest Policy
The independence of this study from any actual or perceived influence, such as by the 
pharmaceutical industry, is critical. Therefore, any actual conflict of interest of persons who 
have a role in the design, conduct, analysis, publication, or any aspect of this trial will be 
disclosed and managed. Furthermore, persons who have a perceived conflict of interest will 
be required to have such conflicts managed in a way that is appropriate to their participation 
in the trial. The study leadership in conjunction with the appropriate conflict of interest 
review committee has established policies and procedures for all study group members to 
disclose all conflicts of interest and will establish a mechanism for the management of all 
reported dualities of interest. All investigators will follow the applicable Yale conflict of 
interest policies.
6.15 Publication Plan
The PI will be primarily responsible for publishing the results of this work. If information from 
this study is presented publicly or published in a medical journal, no research subject will be 
identified by name, picture, or any other personally identifying manner.
Appendices
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
44
Appendix #
Title
Section
Topic
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
45
REFERENCES
1.
Mazur NI, Lowensteyn YN, Willemsen JE, et al. Global Respiratory Syncytial 
Virus- Related Infant Community Deaths. Clin Infect Dis 2021;73(Suppl_3):S229-
S237. DOI: 10.1093/cid/ciab528.
2.
Suh M, Movva N, Jiang X, et al. Respiratory Syncytial Virus Is the Leading Cause 
of United States Infant Hospitalizations, 2009-2019: A Study of the National 
(Nationwide) Inpatient Sample. J Infect Dis 2022;226(Suppl 2):S154-S163. DOI: 
10.1093/infdis/jiac120.
3.
Sangare L, Curtis MP, Ahmad S. Hospitalization for respiratory syncytial virus 
among California infants: disparities related to race, insurance, and geography. J 
Pediatr 2006;149(3):373-7. DOI: 10.1016/j.jpeds.2006.04.063.
4.
Suh M, Movva N, Jiang X, et al. Respiratory Syncytial Virus Burden and 
Healthcare Utilization in United States Infants <1 Year of Age: Study of Nationally 
Representative Databases, 2011-2019. J Infect Dis 2022;226(Suppl 2):S184-
S194. DOI: 10.1093/infdis/jiac155.
5.
PATH. RSV Vaccine and mAb Snapshot. 
(https://www.path.org/resources/rsv- vaccine-and-mab-snapshot/).
6.
Simoes EAF, Madhi SA, Muller WJ, et al. Efficacy of nirsevimab against respiratory 
syncytial virus lower respiratory tract infections in preterm and term infants, and 
pharmacokinetic extrapolation to infants with congenital heart disease and chronic 
lung disease: a pooled analysis of randomised controlled trials. Lancet Child 
Adolesc Health 2023. DOI: 10.1016/S2352-4642(22)00321-2.
7.
Griffin MP, Yuan Y, Takas T, et al. Single-Dose Nirsevimab for Prevention of RSV 
in Preterm Infants. N Engl J Med 2020;383(5):415-425. DOI: 
10.1056/NEJMoa1913556.
8.
Keam SJ. Nirsevimab: First Approval. Drugs 2022. DOI: 10.1007/s40265-022-
01829- 6.
9.
Simoes EAF, Center KJ, Tita ATN, et al. Prefusion F Protein-Based Respiratory 
Syncytial Virus Immunization in Pregnancy. N Engl J Med 2022;386(17):1615-
1626. DOI: 10.1056/NEJMoa2106062.
10.
Larkin H. Investigational RSV Vaccine Given During Pregnancy Protects 
Newborns. JAMA 2022;328(22):2201. DOI: 10.1001/jama.2022.20032.
11.
Shapiro ED. Case-Control Studies to Assess the Effectiveness of Vaccines. 
J Pediatric Infect Dis Soc 2014;3(4):278-9. DOI: 10.1093/jpids/piu058.
12.
Oliveira CR, Ortiz AM, Sheth SS, Shapiro ED, Niccolai LM. Effectiveness of HPV 
vaccine by age at vaccination and number of doses: protocol for a population-based 
matched case-control study. BMJ Open 2021;11(4):e043093. DOI: 
10.1136/bmjopen- 2020-043093.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
46
13.
Johnson Jones ML, Gargano JW, Powell M, et al. Effectiveness of 1, 2, and 3 
Doses of Human Papillomavirus Vaccine Against High-Grade Cervical Lesions 
Positive for Human Papillomavirus 16 or 18. Am J Epidemiol 2020;189(4):265-276. 
DOI: 10.1093/aje/kwz253.
14.
Vazquez M, LaRussa PS, Gershon AA, et al. Effectiveness over time of 
varicella vaccine. JAMA 2004;291(7):851-5. DOI: 10.1001/jama.291.7.851.
15.
Oliveira CR, Massad C, Shapiro ED, Vazquez M. Clinical Effectiveness of Lyme 
Vaccine: A Matched Case-Control Study. Open Forum Infect Dis 
2021;8(8):ofab142. DOI: 10.1093/ofid/ofab142.
16.
Shioda K, de Oliveira LH, Sanwogou J, et al. Identifying signatures of the impact 
of rotavirus vaccines on hospitalizations using sentinel surveillance data from 
Latin American countries. Vaccine 2020;38(2):323-329. DOI: 
10.1016/j.vaccine.2019.10.010.
17.
Oliveira CR, Niccolai LM, Sheikha H, et al. Assessment of Clinical Effectiveness 
of BNT162b2 COVID-19 Vaccine in US Adolescents. JAMA Netw Open 
2022;5(3):e220935. DOI: 10.1001/jamanetworkopen.2022.0935.
18.
Prunas O, Weinberger DM, Pitzer VE, Gazit S, Patalon T. Waning Effectiveness 
of the BNT162b2 Vaccine Against Infection in Adolescents. medRxiv 2022. DOI: 
10.1101/2022.01.04.22268776.
19.
Patalon T, Gazit S, Pitzer VE, Prunas O, Warren JL, Weinberger DM. Odds 
of Testing Positive for SARS-CoV-2 Following Receipt of 3 vs 2 Doses of the 
BNT162b2 mRNA Vaccine. JAMA Intern Med 2022;182(2):179-184. DOI:
10.1001/jamainternmed.2021.7382.
20.
Pilishvili T, Fleming-Dutra KE, Farrar JL, et al. Interim Estimates of Vaccine 
Effectiveness of Pfizer-BioNTech and Moderna COVID-19 Vaccines Among Health 
Care Personnel - 33 U.S. Sites, January-March 2021. MMWR Morb Mortal Wkly 
Rep 2021;70(20):753-758. DOI: 10.15585/mmwr.mm7020e2.
21.
Moline HL, Whitaker M, Deng L, et al. Effectiveness of COVID-19 Vaccines in 
Preventing Hospitalization Among Adults Aged >/=65 Years - COVID-NET, 13 
States, February-April 2021. MMWR Morb Mortal Wkly Rep 2021;70(32):1088-
1093. DOI: 10.15585/mmwr.mm7032e3.
22.
Practices CACoI. Grading of Recommendations, Assessment, Development, and 
Evaluation (GRADE): Pfizer-BioNTech, Moderna, and Janssen COVID-19 booster 
doses. (https://www.cdc.gov/vaccines/acip/recs/grade/covid-19-booster-
doses.html).
23.
Marin M, Guris D, Chaves SS, et al. Prevention of varicella: recommendations of 
the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm Rep 
2007;56(RR-4):1-40. (https://www.ncbi.nlm.nih.gov/pubmed/17585291).
24.
Grubaugh ND, Cobey S. Of variants and vaccines. Cell 2021;184(26):6222-
6223. DOI: 10.1016/j.cell.2021.11.013.
25.
Grubaugh ND, Hanage WP, Rasmussen AL. Making Sense of Mutation: What 
D614G Means for the COVID-19 Pandemic Remains Unclear. Cell 
2020;182(4):794- 795. DOI: 10.1016/j.cell.2020.06.040.
26.
Kissler SM, Fauver JR, Mack C, et al. Viral Dynamics of SARS-CoV-2 Variants in 
Vaccinated and Unvaccinated Persons. N Engl J Med 2021;385(26):2489-2491. 
DOI: 10.1056/NEJMc2102507.
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025

APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025
IRB Protocol # 2000036550
                  Version 6.1 1/29/2025
[Type here][Type here][Type here]
47
27.
Lucas C, Vogels CBF, Yildirim I, et al. Impact of circulating SARS-CoV-2 variants 
on mRNA vaccine-induced immunity. Nature 2021;600(7889):523-529. DOI: 
10.1038/s41586-021-04085-y.
28.
Wyllie AL, Fournier J, Casanovas-Massana A, et al. Saliva or Nasopharyngeal 
Swab Specimens for Detection of SARS-CoV-2. N Engl J Med 2020;383(13):1283-
1286. DOI: 10.1056/NEJMc2016359.
29.
Kalinich CC, Jensen CG, Neugebauer P, et al. Real-time public health 
communication of local SARS-CoV-2 genomic epidemiology. PLoS Biol 
2020;18(8):e3000869. DOI: 10.1371/journal.pbio.3000869.
30.
Oliveira CR, Feemster KA, Ulloa ER. Pediatric COVID-19 Health Disparities and 
Vaccine Equity. J Pediatric Infect Dis Soc 2022;11(Supplement_4):S141-S147. 
DOI: 10.1093/jpids/piac091.
31.
Schmid P, Rauber D, Betsch C, Lidolt G, Denker ML. Barriers of Influenza 
Vaccination Intention and Behavior - A Systematic Review of Influenza 
Vaccine Hesitancy, 2005 - 2016. PLoS One 2017;12(1):e0170550. DOI:
10.1371/journal.pone.0170550.
32.
Jamison AM, Quinn SC, Freimuth VS. "You don't trust a government vaccine": 
Narratives of institutional trust and influenza vaccination among African 
American and white adults. Soc Sci Med 2019;221:87-94. DOI: 
10.1016/j.socscimed.2018.12.020.
33.
Varni JW, Seid M, Kurtin PS. PedsQL 4.0: reliability and validity of the Pediatric 
Quality of Life Inventory version 4.0 generic core scales in healthy and patient 
populations. Med Care 2001;39(8):800-12. DOI: 10.1097/00005650-
200108000- 00006.
34.
O'Neill RT. On sample sizes to estimate the protective efficacy of a vaccine. 
Stat Med 1988;7(12):1279-88. DOI: 10.1002/sim.4780071208.
35.
Centers for Disease C, Prevention. Newborn hepatitis B vaccination coverage 
among children born January 2003-June 2005--United States. MMWR Morb Mortal 
Wkly Rep 2008;57(30):825-8. (https://www.ncbi.nlm.nih.gov/pubmed/18668021).
APPROVED BY THE YALE UNIVERSITY IRB 2/24/2025