Figure 6. Tissue-resident memory CD8⁺ T cells are expanded post-COVID-19.

a, b. Unsupervised clustering of CD8⁺ T cells from adenoids and tonsils according to flow cytometric surface markers (a). Quantification of the effect of prior SARS-CoV-2 infection on CD8⁺ T cell clusters showing regression coefficients ± 95% confidence intervals (CI) and p values, estimated with a linear model controlling for age and sex (b). Significantly different clusters (p<0.05) between post-COV and UC groups are indicated with a star or highlighted in red. Adenoids post-COV n=12, UC n=35; tonsils post-COV n=15, UC n=42. c. Frequency of CD57⁺PD-1⁺ CD8⁺ T cells in post-COV and UC adenoids (post-COV n=17, UC n=42, p=0.044) and tonsils (post-COV n=18, UC n=46, p=0.030) d. Flow cytometry plots showing CD69, CD103, CXCR5 and CXCR3 expression on CD57⁺PD-1⁺ CD8⁺ T cells from one tonsil, representative of tonsils and adenoids from 26 donors. e. Adenoid from post-COV donor showing the location of CD57⁺PD-1⁺ CD8⁺ T in one GC, representative of 6 samples. GC is circled, magnification of square is in inset. CD8 is cyan, CD57 is yellow, PD-1 is pink. HLA-DR (blue) stains follicles, and Ki-67 (red) stains GC. 1:CD8⁺CD57⁺PD-1⁺; 2:CD8⁺CD57⁺ cells, scale bars 50μm (left), 10μm (right) f. Cytokine/cytotoxic factor combinations (involving granzyme B, IFN-γ, CD107a, IL-2 and TNF, analyzed by SPICE) produced by tonsillar CD8⁺ T cells from post-COV (n=13) and UC (n=13) donors following PMA and ionomycin stimulation. (Category 3: p=0.049, 10: p=0.051, 14: p=0.035, 18: p=0.020, 19: p=0.032, 22: p=0.007, 23: p=0.001, 26: p=0.017, 30: p=0.025). Sample list for panels a-c in Supplementary Table 2 and panels e-f in Supplementary Table 11. Each symbol represents one donor. Means ± S.D. are displayed in bar plots. Significance calculated using two-sided Mann-Whitney U test. *p<0.05.