Resistance Potential of the HLA-A2-restricted Immunodominant SARS-CoV-2 Specific CD8+ T Cell Receptor Repertoire to Antigenic Drift
A major concern of COVID-19 is immune escape. While T cells are implicated in protection against severe disease, direct evaluation of their capacity to specifically target SARS-CoV-2 variants remains limited. We aim to narrow this gap by profiling the ability of CD8+ T cells to recognize SARS-CoV-2 mutations after vaccination and observe a high degree of phenotype and repertoire diversity. To better understand the breadth of antigen repertoire coverage, we interrogate the ability of SARS-CoV-2 specific TCRs to bind all point mutations of the immunodominant HLA-A2:S269-277 epitope. While mutation space coverage is surprisingly vast, specific substitutions are not recognized by the vaccine-elicited repertoire. Structural analyses reveal a TCR sequence-based antigen recognition limitation intrinsic to vaccination. Further investigation reveals that this repertoire 'hole' is not present in the naive repertoire, suggesting future immune escape through these potential escape mutations could be relieved by modifications to vaccines. Overall design: To understand the viral mutation coverage of vaccine-elicited T cell receptor repertoires in individuals that have received COVID-19 mRNA vaccines, we multiplexed DNA-barcoded pMHC multimers with single cell T cell receptor and RNA sequencing before and after vaccination. In vitro expanded antigen specific T cell receptors were also isolated using single cell amplicon VDJ sequencing.