Extended Data Fig. 3: Lower frequencies of SARS-CoV-2-specific T cells are found in PBMC samples.

a, CD69 expression on TNF−producing CD4⁺ and CD8⁺ T cells in PBMCs. b, CD69 expression on IFN-γ−producing CD4⁺ and CD8⁺ T cells in PBMCs. c,d, Percentage of TNF (c) or IFN-γ (d) production by CD4⁺ or CD8⁺ T cells after overnight stimulation of BAL, or overnight (ON) or 10 days (10d) expansion of PBMCs with SARS-CoV-2 peptide pools. e,f, Correlation of TNF (e) or IFN-γ (f) responses for CD4⁺ or CD8⁺ T cells in BAL vs PBMC after overnight peptide stimulation (ON). g,h, Correlation of TNF (g) or IFN-γ (h) responses for CD4⁺ or CD8⁺ T cells in BAL vs PBMC after 10 days peptide expansion (10d). a,b, floating bars indicate the mean, minimum and maximum values within the dataset; c,d bars at median. a,b, analysis on 4 biologically independent PBMC samples from donors that showed the highest frequencies of IFN-γ production in BAL; c-h, n = 10 biologically independent samples examined over one independent experiment; a-d, Kruskal-Wallis one-way ANOVA test and Dunn’s multiple comparison. e-h, Spearman correlation.

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