Fig. 3: Transition of antigen-specific CD8⁺ T cells to TCF1⁺CD45RA⁺ effector memory cells at 1 year.

a, Representative plots of CD45RA and CCR7 staining on CoV2-Dex^– and CoV2-Dex⁺ cells during acute infection and 6 months and 1 year after infection. Numbers in the plots indicate percentage of parent population. b, Percentages of T_naive, T_SCM, T_CM, T_effector/T_EM and T_EMRA cells in CoV2-Dex^– and CoV2-Dex⁺ cells during acute infection (n = 28). c, Percentages of T_naive, T_SCM, T_CM, T_effector/T_EM and T_EMRA CoV2-Dex⁺ cells in acute infection and 6 months and 1 year after infection (n = 28 acute, n = 24 6 months, n = 29 1 year). The grey lines connect individual donors sampled at different timepoints. P values are also shown. d, Expression of CD45RA (left) and CCR7 (right) determined by TotalSeq in individual CD8⁺ T cell clones in acute infection versus 6 months after infection (n = 41). e–g, Geometric mean fluorescence intensity (gMFI) of selected markers on T_effector/T_EM and T_EMRA CoV2-Dex⁺ cells in acute infection (e), and 6 months (f) and 1 year (g) after infection. Phenotypes were evaluated only in patients with more than 5 T_effector/T_EM and T_EMRA CoV2-Dex⁺ cells per sample (n = 24 acute, n = 24 6 months, n = 26 1 year). h, Percentages of TCF1⁺, T-BET⁺, EOMES⁺ and TOX⁺ CoV2-Dex^– and CoV2-Dex⁺ cells during acute infection (n = 28). i, Percentages of TCF1⁺, T-BET⁺, EOMES⁺ and TOX⁺ CoV2-Dex⁺ cells in acute infection, and 6 months and 1 year after infection (n = 28 acute, n = 24 6 months, n = 29 1 year). P values were calculated using a Wilcoxon signed-rank test in b, d–g, and a Wilcoxon–Mann–Whitney test with a correction for multiple comparisons using the Holm method in c and i. All tests were performed two-sided.