Summary
As the COVID-19 pandemic continues, there is an urgent need to better understand the illness and host
responses. In spring 2020, we established two cohorts of U.S. healthcare workers (HCW), a particularly hard-
hit frontline community, to understand the characteristics of the illness and to identify predictors of poor
outcomes, as well as of long-term sequelae. With the current study phase ending, extending follow-up activities
in these well-characterized cohorts is critical to monitor the evolution of the infection and its sequelae in a
rapidly evolving situation, which now includes vaccination and emergence of virus variants. In this time-
sensitive proposal, we extend the follow-up period for an additional 3 years, allowing us to answer important
epidemiological and mechanistic questions about infection, symptoms, long-term outcomes, and protective
immunity. In Aim 1, we will define biomarkers of SARS- CoV-2 symptom onset and severity, capitalizing on
serial biospecimens collected from cohort subjects prior to and during early stages of infection. We will test the
hypothesis that symptom onset and severity correspond to baseline differences in pre-existing factors,
including oral virome characteristics and peripheral blood transcriptome. We also will test whether, among
SARS-CoV-2+ individuals, progression of illness severity can be predicted by analysis of early biomarkers at
the time of diagnosis, including inflammatory biomarkers, immune cell populations, and organ-specific
biomarkers of dysfunction, such as cardiac enzymes and coagulation factors. In Aim 2, we will examine long-
term sequelae of asymptomatic and symptomatic COVID-19 infections. We will assess evidence of sustained
physiological dysregulation up to 3 years following SARS-CoV-2 infections of varying severity (including
asymptomatic), focusing on longitudinal biomarkers and pulmonary function. We will examine whether some
infected individuals have persistent abnormalities in immunologic, virologic, and end-organ biomarkers and
pulmonary function, compared to pre-infection biomarker and uninfected comparison subjects. We also will
assess whether persistent abnormalities in biomarkers are associated with prolonged convalescence and
reduced pulmonary function. In Aim 3, we will identify serum markers persisting after acute infection that may
confer protective immunity. Using sera from SARS-CoV-2+ individuals, we will characterize the spectrum and
functions of anti-SARS-CoV-2 antibodies and their relation to immune protection in the cohort as well as in an
innovative ex vivo lung slice model. We will specifically examine variation in magnitude, duration, function, and
spectrum of antibody responses in relation to severity of initial clinical infection. We will test the hypothesis that
anti-SARS-CoV-2 antibody concentrations and protective functions are associated with lower rates of
subsequent re-infection in cohort participants, as affected by vaccination status. The biospecimens (currently
>40,000) from these cohorts will be available for collaborative studies.