Extended Data Fig. 2: Identification of HLA-A2-restricted T cell epitopes and activation of CD8 T cells by epitopes from SARS-CoV-2.

(a) Exemplary flow cytometry result of CD8 T cell activation marker CD69 and CD137 expression after cocultivation with T2 cells loaded with distinct set of peptides (n = 4 per experiment). Variant strain IDs indicate mixed ancestral or mutant epitopes from the corresponding variant strain in Fig. 2a that were used in each experiment. CD69 and CD137 expression was detected by flow cytometry 16 hours after cocultivation. A: ancestral; M: mutant. Paired ancestral and mutant epitopes are placed adjacently. (b) Representative FACS plots of specific CD8 T cells recognized by tetramers containing SARS-CoV-2 epitope peptides. CD8 T cells from healthy donors were co-cultivated with T2 cells loaded with various peptides for activation for 16 hours. The cells were stained with corresponding tetramer containing ancestral or mutated epitope, and compared before (Day 0, top row) and after (Day 7, bottom row) stimulation. (c) Representative FACS plots of specific CD8 T cells recognized by tetramers containing SARS-CoV-2 epitope peptides. CD8 T cells from healthy donors were co-cultivated with T2 cells loaded with tetramers prepared using SARS-CoV-2 epitope S269-277. The cells were stained with corresponding tetramer containing ancestral or mutated epitope, and compared before (Day 0; top row) and after (Day 7; bottom row) stimulation. (d) Epitope-specific CD8 T cell quantification (n = 3) before (day 0) and after 7 days of stimulation by distinct pair of ancestral and mutant SARS-CoV-2 epitopes. P-values are determined by two-sided T-test. (e) Representative data for detection of epitope-specific CD8 T cells in the HLA-A2⁺ healthy donors after second doses (Day 7 and Day 50) of inactivated SARS-CoV-2 vaccine with tetramers prepared using SARS-CoV-2 epitope S269-277 for. Cells were sitmulated for 16 hours before staining. (f) Comparison of epitope-specific CD8 T cells between HLA-A2⁺ healthy young (n = 5) and old (n = 5) donors, 7 (top row) and 50 (bottom row) days after second doses of inactivated SARS-CoV-2 vaccine. Specific CD8 T cells were stained with tetramers prepared using ancestral (S269-277) and mutant (P272L) SARS-CoV-2 epitopes individually. Data are summarized as mean ± SD. Paired ancestral and mutant epitopes are listed adjacently on the x-axis. P-values are determined by two-sided T-test.