Parallel detection of SARS‐CoV‐2 epitopes reveals dynamic immunodominance profiles of CD8 (+) T memory cells in convalescent COVID‐19 donors

OBJECTIVES: High‐magnitude CD8(+) T cell responses are associated with mild COVID‐19 disease; however, the underlying characteristics that define CD8(+) T cell‐mediated protection are not well understood. The antigenic breadth and the immunodominance hierarchies of epitope‐specific CD8(+) T cells remain largely unexplored and are essential for the development of next‐generation broad‐protective vaccines. This study identified a broad spectrum of conserved SARS‐CoV‐2 CD8(+) T cell epitopes and defined their respective immunodominance and phenotypic profiles following SARS‐CoV‐2 infection. METHODS: CD8(+) T cells from 51 convalescent COVID‐19 donors were analysed for their ability to recognise 133 predicted and previously described SARS‐CoV‐2‐derived peptides restricted by 11 common HLA class I allotypes using heterotetramer combinatorial coding, which combined with phenotypic markers allowed in‐depth ex vivo profiling of CD8(+) T cell responses at quantitative and phenotypic levels. RESULTS: A comprehensive panel of 49 mostly conserved SARS‐CoV‐2‐specific CD8(+) T cell epitopes, including five newly identified low‐magnitude epitopes, was established. We confirmed the immunodominance of HLA‐A*01:01/ORF1ab(1637–1646) and B*07:02/N(105–113) and identified B*35:01/N(325–333) as a third epitope with immunodominant features. The magnitude of subdominant epitope responses, including A*03:01/N(361–369) and A*02:01/S(269–277), depended on the donors' HLA‐I context. All epitopes expressed prevalent memory phenotypes, with the highest memory frequencies in severe COVID‐19 donors. CONCLUSION: SARS‐CoV‐2 infection induces a predominant CD8(+) T memory response directed against a broad spectrum of conserved SARS‐CoV‐2 epitopes, which likely contributes to long‐term protection against severe disease. The observed immunodominance hierarchy emphasises the importance of T cell epitopes derived from nonspike proteins to the overall protective and cross‐reactive immune response, which could aid future vaccine strategies.