Study population and eligibility criteria

Initially, this study involves the use of existing data and specimens from nine IDCRP ARI study protocols (Tables 1, 2, S1 Table). These protocols include: The Acute Respiratory Infection Consortium study (ARIC; IDCRP-045) [22,23]; the Immunogenicity of Novel H1N1 Vaccination among HIV-Infected Compared to HIV-Uninfected Persons (IDCRP-053) study [24]; the Epidemiology, Immunology and Clinical Characteristics of Emerging Infectious Diseases with Pandemic Potential study (EPICC, IDCRP-085) [14,15,25–39]); the Pragmatic Assessment of Influenza Vaccine Effectiveness in the DoD study (PAIVED, IDCRP-120) [40]; the COVID-19 Antibody Prevalence in Military Personnel Deployed to New York study (CAMP NYC, IDCRP-125; data only) [19]; the Prospective Assessment of SARS-CoV-2 Seroconversion study (PASS, IDCRP-126) [17,41,42]; the Seroprevalence of novel coronavirus antibodies among personnel deployed on the USNS Comfort during the COVID-19 pandemic study (COMFORT, IDCRP-128) [20]; The Observational Seroepidemiologic Study of COVID-19 at the United States Naval Academy study (TOSCANA, IDCRP-129) [43]; and the Prospective Investigation of SARS-CoV-2/ COVID-19 Epidemiology and Serology study (PISCES, IDCRP-130). Participant recruitment has been completed for all of these original studies, and results have been published from the original studies. Specimen laboratory data and/or additional longitudinal data is still being collected for the EPICC and PAIVED studies, and other protocols may be added to the ARI Repository Protocol in the future.

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Table 1. Contributing IDCRP Acute Respiratory Infection Protocol Study Characteristics (up to 27,230 total participants).

https://doi.org/10.1371/journal.pone.0317065.t001

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Table 2. Contributing Protocol Objectives.

https://doi.org/10.1371/journal.pone.0317065.t002

All studies included in the repository protocol have been conducted at military treatment facilities, in military training settings, within other DoD facilities, and/or in the context of DoD deployments related to the COVID-19 response. The overall population is therefore predominantly MHS beneficiaries, including (ADSM), retirees, and/or dependents. The nine studies included in this Repository protocol have had varying eligibility criteria (see S1 Table for inclusion and exclusion criteria) but generally fall under overarching repository eligibility criteria of MHS beneficiaries, including ADSM and those in congregate settings, who are infected by, exposed to, tested for, and/or vaccinated against ARI pathogens.

The majority of these studies, to date, are derived from a portfolio of studies established as part of COVID-19 research response. The EPICC study enrolled MHS beneficiaries 2020−2022 and with broad objectives to understand the epidemiology, immunology and clinical characteristics of COVID-19. This study has published multiple insights into the risk and risk factors of acute and long term complications of SARS-CoV-2 [14,28,44,45], COVID-19 clinical characteristics and symptomology [32], COVID-19 functional impact [15], COVID-19 diagnosis [46], SARS-CoV-2 immunology and vaccinology [33], and SARS-CoV-2 virology [35,47]. Data and specimens have been analyzed since March 2020, through to the present.

The PASS study examined SARS-CoV-2 seroconversions in a cohort of WRNMMC healthcare workers, in addition to licensed COVID-19 vaccine responses [42]. Enrollment commenced in August 2020 and last follow up occurred in June 2024. Data and specimens have been analyzed since August 2020 through the present. Analyses have included patterns and predictors of humoral, innate, and T cell immunity, including correlate of protection and variant escape analyses. Additionally, the PASS study has undertaken profiling of vaccine reactogenicity and COVID-19 symptomology across multiple years of the pandemic [17,34,41,48,49].

Two of the IDCRP COVID-19 studies focused on congregate settings or household transmissions. The TOSCANA study commenced enrollment of U.S Naval Academy midshipmen in 8/2020 with follow up through to 5/2021. TOSCANA examined the risk and risk factors of infection of SARS-CoV-2 in this congregate setting, including examining the ascertainment of infection by seroconversion compared to frequent population PCR testing [18]. Data and specimens were analyzed between 11/2021–1/2023. The PISCES study enrolled Uniformed Services University students and faculty, in addition to their respective households, to understand the risk and risk factors of SARS-CoV-2 infection and household transmission dynamics. Enrollment commenced in 2021/01/14 and concluded in 2021/06/17. Data and specimens were analyzed between 2021 and 2022.

The CAMP NYC enrolled military members who participated in the 2020 New York City Javitz Center COVID-19 clinical response. The study objectives focused on the risk and risk factors of SARS-CoV-2 infections (including infections ascertained by serology) and concluded that such risks were low in the context of high adherence to PPE [19]. Participants were enrolled in the CAMP-NYC study between 2020/03/24 and 2020/04/28; data and specimens were analyzed in 2020 and 2021. As similar conclusion was made with the COMFORT study which examined the seroepidemiology and SARS-CoV-2 infection risk in military members who deployed to New York City as part of the U.S.S Comfort COVID-19 medical response [19]. Participants were enrolled in the COMFORT study between 2020/05/09 and 2020/06/23; data and specimens were analyzed in 2020 and 2021

The PAIVED study was a large open-label Phase IV study of three licensed influenza vaccines (egg-derived inactivated, cell-derived inactivated influenza, and recombinant hemagglutinin) among MHS beneficiaries, enrolling between 11/7/2018 through 5/26/22. The primary objective was to examine clinical effectiveness of the three licensed vaccines, with multiple secondary immunological analysis and other objectives [21,40,50]. Data and specimens were analyzed from 2019 to present. Findings from the PAIVED study, to date, include (i) no major differences in vaccine effectiveness between egg-derived, cell-derived and recombinant-hemagglutinin influenza vaccines in the study sample [50]; (ii) similar A/H3N2 immunity elicited from egg and cell-based vaccines [40], and yet (iii) differential neuraminidase antibody responses elicited by egg and cell based vaccines [21].

The H1N1 vaccination study examined the immune responses to the pandemic H1N1 vaccine in those with and without HIV [51]. Participants were enrolled in the H1N1 study between 2009/11/09 and 2010/06/01; data and specimens were analyzed in 2010 through to 2017. This study contributed to our understanding of influenza vaccine immunogenicity between those with and without HIV infection, in addition to the role of vitamin D deficiency in H1N1 vaccine responses [24,51].

Finally, the ARIC study characterized the clinical outcomes and epidemiology of ARI across a multi-site cohort. Participants were enrolled in the H1N1 study between 2009/10/09 and 2019/04/12; data and specimens were analyzed from 2009 through to 2021. The ARIC study led to several insights into ARI in the MHS, including (i) similar influenza-like illness symptom severity and infection outcomes in those participants with and without HIV [23]; (ii) species, type and/or lineage-specific clinical phenotyping of influenza viruses, adenoviruses, rhinoviruses, and human coronaviruses [22,52–55]; (iii) patterns of influenza antiviral use [56] and; (iv) validation of quantitative symptom-scoring tool for influenza and other ARI [57,58].

Recruitment and consent

The IDCRP ARI Repository Protocol does not recruit or enroll new subjects. Data and specimens will only be used from participants who provided consent for secondary use of data and/or specimens, and who did not withdraw from, the original studies contributing to the repository.

Primary objective

The primary goal of the repository protocol is to create a curated, standardized dataset and biospecimen repository incorporating multiple IDCRP ARI protocols. This will permit answering further targeted scientific questions in pooled analyses and will serve as an on-demand repository for rapid assay development, sample size calculations, and observational study/clinical trial design (including those required as part of future rapid ARI pandemic research response).

Secondary objectives (supported and facilitated through the Primary Objective)

1. Compare the acute and chronic clinical outcomes and symptom phenotypes of ARI viral pathogens of importance to servicemembers and other MHS beneficiaries, including variant to variant comparison
2. Estimate predictors of acute and chronic clinical outcomes of ARI viral pathogens, including demographics, comorbidities, other host factors, and viral factors including infecting variant
3. Estimate and predict COVID-19, influenza, and adenovirus vaccine effectiveness in servicemembers and other MHS beneficiaries, as applicable
4. Identify predictors of optimal ARI vaccine immune responses (including those elicited by COVID-19 and influenza vaccines)
5. Estimate therapeutic effectiveness for licensed COVID-19 and influenza antivirals
6. Estimate effectiveness of non-pharmaceutical interventions, including masking and restriction of movement, against infection risk
7. Identify and evaluate prognostic and mechanistic viral and host biomarkers which correlate with the above secondary objectives
8. Evaluate the validity of current and future diagnostic and biomarker assays for the detection or prognostication of ARIs, including the support of new ARI diagnostic and biomarker assay development
9. Additional objectives as urgent DoD ARI research needs arise (e.g., during an outbreak or pandemic)

Sample size

Current sample size is up to 27,230 participants from at least nine existing IDCRP ARI Protocols (see Table 1). The sample size is fixed with the number of enrolled and eligible participants in the protocols being pooled. The observable effect sizes will vary by endpoints of specific pooled analyses (see Secondary Objectives) that will leverage this repository protocol.

Data curation

The repository protocol will only contain data and specimens from participants who approved future use of data and specimens in their consent. Data will be combined into a unified database, utilizing existing and newly created variables (overview shown in Fig 1). A Data Management Plan (DMP) and cross protocol data dictionary will be established, ensuring data and specimens are only included in those participants who indicated consent for future use (or for studies with a waiver of consent). This multi-relational database will be developed in Oracle and managed by the IDCRP Data Coordination Center (DCC) and will include clinical, demographic, and existing laboratory data.

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Fig 1. Schema showing the approach to data and specimen curation.

Protocols A, B, and C are notional illustrative protocols.

https://doi.org/10.1371/journal.pone.0317065.g001

Following data consolidation, a statistical analysis plan (SAP) will be developed for a preliminary assessment of the repository data to evaluate metadata structure including the total number of combined variables (and whether these are continuous, binary, or categorical), total number of combined observations, total number of common data variables (and respective number of observations) across two or more protocols, and total number of variables (and respective number of observations) which are similar enough to allow ontological cross-walking between two or more protocols. The overlap of laboratory assay data between protocols will also be evaluated, with assay type, performing laboratory, lab assay units, and measurement timepoints specified. Similarly, we will evaluate the overlap of similar specimen types (e.g., sera and PBMC) and timepoints of collection between protocols.

Documentation of these newly created common variables in the cross-protocol data dictionary will include: (i) common repository variable name, (ii) data type (e.g., continuous, categorical), (iii) any variable ontology cross-walking between protocols (iv) reference to the original variable names from individual protocols. The joint repository dataset will include a variable which defines the original IDCRP study in which the participant enrolled (the study population and eligibility criteria of which are summarized in S1 Table). This will provide context of how individual participants were selected for enrollment and therefore identify potential selection biases in cross protocol analyses. As other open protocols are updated with further specimens and data, data will also be updated in the master repository protocol.

Quality management

A Quality Management Plan (QMP, including a data Quality Assurance (QA)/Quality Control (QC) process) will be applied to ensure the accuracy, completeness, and acceptability of data/specimens from the contributing protocols. The QMP leverages data system checks, previously performed QM activities, and limited review of key protocol activities (informed Consent, data migration, and regulatory compliance). QM processes are designed to evolve during the lifecycle of this repository protocol, to continually mitigate previously- and newly identified risks.

Specimen curation

An inventory of all specimens will be created and verified (overview in Fig 1), with cross-linkage to FreezerWorks a specimen freezer inventory program (Dataworks Development, Inc; Mountlake Terrace, WA). An initial report will describe the demographic, clinical and laboratory characteristics, and specimen availability. Data and specimens will be updated in the master repository protocol as other open protocols are updated with further specimens and data.

Approach to analyses

After the scope and overlap of the data and specimens have been assessed, the consolidated data and/or specimens will be assessed to answer specific research questions as described in the secondary objectives with individual participant data and/or specimen results. In addition, the report will be used by the analysis team and collaborative investigators to help design new specific, hypothesis-driven questions that will be answered leveraging the repository protocol pooled data.

New analysis ideas will be vetted by an analysis working group (reflected by the byline authors of this paper). This is a collaborative framework in which (i) contributing principal investigators (PIs) have oversight on the use of specimens and data from their protocols and can be part of the joint scientific analysis enterprise, (ii) competing laboratory demands for specimens can be balanced early and often, (iii) lab and statistical analyses can be prioritized based on a consensus regarding the most impactful, specific study questions. New analysis ideas will be presented to the working group, and after consensus is reached, analyses will proceed if they are covered under the scope of the existing protocol.

The approach to individual participant-level data (IPD) pooled meta-analyses (secondary objectives) will be tailored to the specific scientific question. This will follow IPD analysis best-practices as described by Riley et al. [59] and IPD meta-analysis best practices for reporting results (further described in Riley et al [59]). Importantly, such ARI Repository IPD metanalyses will not necessarily occur across all contributing protocols. Consideration of the underlying sampled population, study design, and common variables will be incorporated into a DMP and SAP for each specific IPD metanalysis. The DMP and SAP for each IPD meta-analysis will include: analysis objectives (primary, secondary); analytic sample inclusion and exclusion criteria; dependent and independent variable definitions; approaches to poorly or incongruently defined endpoints and other variables across studies; assessment of dependent and independent variable normality and functional transformation as required for advanced analysis; effect size (e.g., risk ratio, odds ratio); causal inference approaches, including model fitting, model diagnostics and approach to repeated measures; approach to missing data; evaluation of patterns of missingness; subgroup analyses; and evaluation of effect modifiers. Specific statistical analysis approaches would be tailored to the study question, but may include linear regression, logistic regression, Cox-proportional hazard models, and mixed effects models.

Note that objectives such as in-vitro assay development and evaluation may be performed off relatively small number of biospecimens (in contrast to objectives which seek to evaluate sensitivity, specificity, likelihood ratios of established assays) [60,61].

Generation of additional laboratory data from the specimen repository

While no new enrollment or participant data collection occurs in this repository protocol, secondary laboratory data, aligned with the secondary objectives listed, may be generated by current and future laboratory science collaborators using the specimens reposed in the ARI repository protocol. These may include host response analyses (e.g., [16,29,45,62,63]), virological and viral genomic analyses (e.g., [47]), and diagnostic evaluation (e.g., [35,39,46]).

Ethics approval and consent to participate

Provisions related to future use of data and specimens for research purposes were included in the Informed Consent Documents and text of the original protocols being merged for this repository (with the stipulation that the future use would be under a protocol reviewed by the USU IRB). This ARI Repository Protocol (IDCRP-142) was approved by USU Institutional Review Board and originating protocols have had modifications which refer to the movement of data and specimens into IDCRP-142.

Disclaimer

Views expressed are those of the authors and do not reflect the official policy of the Uniformed Services University of the Health Sciences, the Department of the Army, the Department of the Navy, the Department of the Air Force, the Department of Defense, the Defense Health Agency, or the U.S. Government and the Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF). The investigators have adhered to the policies for the protection of human subjects as prescribed in 45 CFR 46.

E.D.L, D.R.T, M.P.S, A.M, A.F, K.P, E.C.G, K.M, R.O., T.H.B, and E.M are U.S. Government employees or military service members. This work was prepared as part of the author(s) official duties. Title 17 U.S.C. § 105 provides that ‘Copyright protection under this title is not available for any work of the United States Government.’ Title 17 U.S.C. §101 defines U.S. Government work as work prepared by a military service member or employee of the U.S. Government as part of that person’s official duties.