Project 2: Serologic and molecular determinants of COVID-19 severity and immune protection

Project 2 Summary PROJECT 2. Serologic and molecular determinants of COVID-19 severity and immune protection. Unresolved scientific questions remain about how the type, kinetics and duration of SARS-CoV-2 serologic responses correlate with patient age, disease severity, protective immunity, and risk of spread to close contacts. Our overall goal is to utilize the well-annotated STOP-COVID data sets and longitudinal samples collected from the first-responder cohort (at high-risk for re-exposure) and family contacts (Project 1, Core B) to advance understanding of the specific host and viral factors that underlie long-lasting and protective serologic responses. Our three highly interactive aims include: to identify differences in virus neutralizing (VN) antibody isotypes and their target viral proteins/peptides/epitopes; to assess cross-protective immunity versus disease exacerbation by antibodies to common cold CoVs; and to probe, by virus-host transcriptome analysis, how SARS-CoV titer or sequence and initial immune response at mucosal sites or blood interrelate with disease outcomes and the above serologic responses. Aim 1: Define immunoglobulin isotypes, titer, target proteins and viral neutralization activity of SARS-CoV-2 specific Abs and their correlations with disease severity and protection: We will utilize VN assays (VNA) and a luciferase immunoprecipitation assay to identify VN antibody isotype specificities and their immunodominant and unique target viral proteins/peptides/epitopes relevant to disease severity and protection. Expected outcomes include data that delineate the temporal antibody isotypes and viral targets to refine protocols for serologic testing that align with protective immunity. Aim 2: Determine the impact of common cold CoVs (CCCoV) and SARS-CoV-2 specific antibodies on COVID-19 protection and disease severity in a high-exposure risk cohort of first responders and their household contacts. Diagnostic serum samples will be used in innovative ELISA platforms directed against unique and conserved CCCoV peptides, and Spike pseudotyped CCCoV to assess CCCoV antibody responses. Expected outcomes include original data on whether pre-existing CCCoV antibodies relate to COVID-19 clinical symptoms, severity or strain specificity of SARS-CoV-2 infection (Aim 3), or re-infection risk. Aim 3. Correlate patterns of mucosal and serologic immune responses with virus and host genetics. We will utilize a novel targeted host-SARS-CoV-2 RNA sequencing assay (CoV-DXVX) to assess whether virus titer or functional alterations in SARS-CoV-2 S1, S2, N proteins or other ORFs impact disease presentation, progression and outcome. Host response measured by the profile and strength of mucosal or blood immune gene induction will be correlated with the duration, type and protective ability of these serologic responses and with the ones above. Once vaccines are deployed to our first-responder cohort, all 3 aims will pivot to analyze how the above serologic response profiles and host immune gene induction differ in vaccinated SARS-CoV-2 seronegative and seropositive individuals compared with the naturally-infected individuals.