Fig. 4: Transcriptional signature of antigen-specific CD8⁺ T cell clones persisting at 6 months.

a, Proportion of CoV2-Dex⁺ CD8⁺ T cell clones present during acute infection that were also detectable 6 months after infection. b, Clone size of persisting versus non-persisting CoV2-Dex⁺ CD8⁺ T cell clones (n = 41 persistent, n = 139 non-persistent). c, UMAP plot of persistent (red) versus non-persistent (green) CoV2-Dex⁺CD8⁺ T cell clones detected during acute infection. d, Gene set enrichment analysis showing enrichment of genes associated with cytokine signalling in persistent clones and mTOR signalling and proliferation in non-persistent CoV2-Dex⁺ T cell clones. Red dashed lines indicate minimal and maximal cumulative enrichment values. P value calculation was performed as detailed in the Method section. e, Expression of selected genes and CCR7 and CD45RA protein determined by Totalseq for persistent versus non-persistent CoV2-Dex⁺ T cell clones. P values were calculated using a Wilcoxon signed-rank test; a Bonferroni correction was applied for multiple comparisons. f, Expression level of selected genes in persistent versus non-persistent individual T cell clones; each dot represents one clone. g, Expression level of selected genes in cells from a single non-persistent clone compared to cells from a single persistent T cell clone; each dot represents one cell (n = 5 CASSQVIGNQPQHF, n = 16 CASSAPGPLTTQYF). In f, g, the white diamonds indicate median expression. For b, f, g, P values were calculated using a Wilcoxon–Mann–Whitney test. All tests were performed two-sided.