Profiling of SARS-CoV-2 virus shedding, antibody neutralization and T cell receptor repertoires in a large, multi-center cohort of young adults with varied prior exposures

Background: The cellular and neutralizing antibody responses to SARS-CoV-2 infection are complex, particularly with multiple and heterogeneous exposures. We sought to understand the changes to the antibody and T cell repertoire elicited by mildly symptomatic or asymptomatic infections in young adults, and how immune responses to prior vaccination may interact with new viral exposures in this population. Additionally, profiling both aspects of humoral and cellular immunity from a single vial of blood is experimentally challenging. Methods: We developed a protocol to recover T cell receptor (TCR) repertoires from frozen blood clots, i.e. remnant material, retained after coagulation of whole blood for serum recovery and antibody analysis. The method was applied to a subset of participants in a COVID-19 vaccine trial (CoVPN 3006, n=209 participants). We sequenced TCR repertoires and measured anti-SARS-CoV-2 antibody responses from pre-exposure, post-vaccination, and post-breakthrough blood samples. Results: Clot material provided suitable genomic DNA for TCR profiling, with vaccination and infection leading to expansions in T cell responses. Consistent with prior studies, we found that hybrid immunological exposures (vaccination after infection) lead to the greatest antibody potency and spike TCR breadth. When the order of exposure was reversed, we observed evidence of attenuated disease severity (reduced shedding duration and lower peak nasal viral load) in post-vaccination versus primary infections. Discussion: The protocols described here for recovery of TCR repertoires from remnant coagulated material, will facilitate more common estimation of cellular and neutralizing antibody immune responses as potential correlates of protection in large clinical trial cohorts where peripheral blood mononuclear cell (PBMC) acquisition or analysis is otherwise infeasible.