Extended Data Fig. 5: Phenotyping of expanded CD4⁺ T cell populations.

a,b. Correlation between frequency of CD57⁺PD-1^hi CD4⁺ T cells and frequency of GC B cells in adenoids (a, n = 59) and tonsils (b, n = 64). c,d. Intracellular cytokine and cytotoxic factor expression in various CD4⁺ T cell subsets gated on CD57 and PD-1 from post-COV adenoids (c, n = 13) and tonsils (d, n = 13) after PMA/ionomycin stimulation. Mean cell frequency shown in heat map. e. Correlations among various subsets of SARS-CoV-2-specific B cells (defined in Supplementary Figs. 1) and significantly different tissue CD4⁺ T cell clusters (clusters 3, 6, 9 shown as % of CD4⁺ T cells) from unsupervised analysis. f. Percentage of CD25⁺CXCR5⁺PD-1^hi cells among CD4⁺ T cells in post-COV and UC adenoids and tonsils (p = 0.031). g. Cytokine production by CD25⁺ and CD25⁻ CXCR5⁺PD-1^hi CD4⁺ T cells in tonsils (n = 26) and adenoids (n = 26) following PMA/ionomycin stimulation, all p < 0.0001. h. Correlation between frequency of CD25⁺CXCR5⁺PD-1^hi CD4⁺ T cell and GC B cell frequencies in tonsils (n = 64). i. Frequency of CXCR3⁺CCR6⁻ cells among pre-T_FH cells (PD-1^intCXCR5⁺ conventional CD4⁺ T) in post-COV and UC adenoids (p = 0.042) and tonsils. j,k. Intracellular cytokine/cytotoxic factor expression in different pre-T_FH cell subsets gated on CXCR3 and CCR6 from post-COV adenoids (j, n = 13) and tonsils (k, n = 13) after PMA/ionomycin stimulation. Mean cell frequency shown in heat map. l. Comparison of IFN-γ production by CD4⁺ T cells in adenoids and tonsils following PMA/ionomycin stimulation (n = 26 including 13 post-COV and 13 UC samples of each tissue, p < 0.0001). For panels, f, and i: adenoids post-COV n = 17, UC n = 42; tonsils post-COV n = 18, UC n = 46. Each symbol represents one donor. Means ± S.D. displayed on bar plots. Significance calculated with two-sided Mann–Whitney U-test to compare two groups and Spearman’s rank test for correlations (r is Spearman’s coefficient). *p < 0.05, ****p < 0.0001.

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