Fig. 1: Characteristics of antigen-specific CD8⁺ T cells during acute and memory phases of SARS-CoV-2 infection.

a, Overview of study design. PBMC, peripheral blood mononuclear cell. b, Representative plots of CoV2-Dex staining. PE, Phycoerythrin. Numbers in the plots indicate percentage of parent population. c, Frequency of CoV2-Dex⁺ cells in healthy donors and patients with COVID-19 during acute infection and 6 months and 1 year after infection. Each dot represents an independent donor at the indicated timepoint (n = 10 healthy, n = 37 acute, n = 32 6 months, n = 29 1 year after infection). P values are shown. d, Linear regression of frequency of CoV2-Dex⁺ cells 6 months after infection as a function of CoV2-Dex⁺ cell frequencies during acute infection (n = 11). The P value was calculated with t-statistic. e, Uniform manifold approximation and projection (UMAP) plots of marker expression for up to 2,000 CD8⁺ T cells from each sample collected during acute infection (n = 37) analysed by spectral flow cytometry. Regions with high marker expression appear in red. An overlay of CoV2-Dex⁺ cells (red) and total CD8⁺ T cells (grey) is shown in the top left. f, Representative histograms showing expression of selected markers on CoV2-Dex^– and CoV2-Dex⁺ cells. g, Frequency of Ki-67⁺, HLA-DR⁺, granzyme B⁺, CX3CR1⁺ and CD127⁺ cells in CoV2-Dex^– (grey) and CoV2-Dex⁺ cells during acute infection and 6 months and 1 year after infection. Analysis was conducted on paired samples from acute infection versus 6 months and/or 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 were calculated using a Wilcoxon–Mann–Whitney test in c and g and corrected for multiple comparisons in g. All tests were performed two-sided.