Fig. 3: Phenotypic diversity of epitope-specific CD8⁺ T cells after diverse SARS-CoV-2 exposures.

a, Uniform manifold approximation and projection (UMAP) of all SARS-CoV-2 epitope-specific CD8⁺ T cells based on gene expression (GEX). Coloring shows the results of graph-based unsupervised clustering performed with the Seurat package. b, Density plot of CCR7 and CD45RA surface expression (measured by CITE-seq) in GEX clusters. c, Bubble plot of representative differentially expressed genes for each cluster. Size of the circle shows the percentage of cells in a cluster expressing a certain gene; color scale shows the gene expression level. d, Distribution of epitope-specific T cells in gene expression clusters between study groups. e, Proportion of spike-specific T cells is significantly increased in cluster 1 after vaccination of previously infected individuals, compared to the pre-vaccination time point (P < 0.0001, two-sided Fisher exact test). f, Proportion of spike-specific cells in EMRA (cluster 1) across study groups for samples with more than ten spike-specific cells (Kruskal–Wallis H test P = 0.028; inf, n = 8; inf-vax1, n = 8; inf-vax2, n = 13; vax2, n = 10; vax2-inf, n = 4). Boxes represent the median and 25th to 75th percentiles, and whiskers indicate the minimum to maximum values but no further than 1.5 times the IQR. g, Expression of classical cytotoxic and memory markers across study groups and T cell specificities. Size of the circle shows percentage of cells in a cluster expressing a certain gene; color scale shows the gene expression level. h, Clone size distribution within GEX clusters. Fractions of cells from the ten most abundant clonotypes in each cluster are shown with colors, and all other clonotypes are shown in gray. i, Number of cells in cluster 7 (exhausted) and cluster 10 (cycling) in samples are strongly correlated (Spearman rank correlation ρ = 0.79, two-sided test P < 2.2 × 10⁻¹⁶). The line shows the linear fit, and the shaded area shows the 95% confidence interval for the linear fit. j,k, T cell repertoire diversity of spike-specific (j) and non-spike-specific (k) repertoires across study groups (P = 0.63 for spike, P = 0.17 for non-spike, Kruskal–Wallis H test). Normalized Shannon entropy of TCRβ is plotted for samples with more than three unique TCRβ clonotypes (for spike: inf, n = 10; inf-vax1, n = 9; inf-vax2, n = 21; vax2, n = 13; vax2-inf, n = 7 and for non-spike: inf, n = 13; inf-vax1, n = 9; inf-vax2, n = 18; vax2-inf, n = 6). Boxes represent the median and 25th to 75th percentiles, and whiskers indicate the minimum to maximum values but no further than 1.5 times the IQR.