SARS-CoV-2 escapes CD8 T cell surveillance via mutations in MHC-I restricted epitopes [10x]

CD8+ T cell immunity to SARS-CoV-2 has been implicated in COVID-19 severity and virus control. Here, we identified non-synonymous mutations in MHC-I restricted CD8+ T cell epitopes after deep sequencing of 747 SARS-CoV-2 virus isolates. Mutant peptides exhibited diminished or abrogated MHC-I binding, which was associated with a loss of recognition and functional responses by CD8+ T cells isolated from HLA-matched COVID-19 patients. Our findings highlight the capacity of SARS-CoV-2 to subvert CD8+ T cell surveillance through sporadically emerging escape mutations in MHC- I restricted viral epitopes. Single-cell RNA-sequencing (10x Genomics Immune Profile 5') of expanded T cells from two patients. Four separate samples were collected per patient and pooled after labelling with hashtag oligos: WT YLQ-, WT YLQ+, MUT YLQ-, MUT YLQ+. *** Raw sequence data submission to the European Genome-Phenome Archive (EGA) to protect patient privacy - in progress.