Extended Data Figure 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 heatmap. e. Correlations among various subsets of SARS-CoV-2-specific B cells (defined in Supplementary Fig.1-2) 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 heatmap. 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 c, 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