Extended Data Fig. 5: Differential abundance testing, gene set enrichment analysis and clonal diversity analysis of T lymphoid compartment.

a, Box plots showing the proportion of cell types shown in Fig. 3a, n = 108 biologically independent samples. Boxes denote IQR with median shown as horizontal bars. Whiskers extend to 1.5x the IQR; outliers are shown as individual points. b, Volcano plots showing results of differential abundance testing. Abundance counts were modelled either comparing healthy vs. COVID-19, or as a function of severity. Hypothesis testing was performed using quasi-likelihood F-test comparing healthy controls to cases, or for either a linear or quadratic trend across disease severity. Differentially abundant cell types were determined using a 10% false discovery rate (FDR). c, Heatmaps showing mean expression levels across T cell subsets for suppressive (FOXP3), proliferating (MKI67) and exhaustion markers (PDCD1, HAVCR2, LAG3, TIGIT, TOX). Columns denote the mean log-normalised expression within each severity category and healthy controls. d, Volcano plot showing differential abundance testing according to time since symptom onset for the T cell populations. Differentially abundant (FDR 10%) points are shown in red. e, Gene set enrichment (Methods) in each T cell type based on differential gene expression (DGE) analysis was performed across COVID-19 disease severity groups, ordered from healthy > asymptomatic > mild > moderate > severe > critical. Statistically significant DE genes were defined with FDR < 1%. Significant enrichments were defined with 10% FDR. f, Bar plots showing percent (mean + /- SEM) of CD3⁺CD4⁺ (blue) and CD3⁺CD8⁺ (green) T cells expressing CD107a (left) and CD137 (right) in response to SARS-CoV-2 S peptide stimulation (n = 12 healthy, n = 10 mild, n = 17 moderate, n = 9 severe, and n = 5 critical biologically independent samples). Significance determined using Kruskal-Wallis with Dunn’s post-hoc corrected for multiple comparison. g, Box plots showing clone size distribution for each T cell subset (n = 9 asymptomatic, n = 19 mild, n = 29 moderate, n = 12 severe, n = 10 critical biologically independent samples). Boxes denote IQR with median shown as horizontal bars. Whiskers extend to 1.5x the IQR; outliers are shown as individual points. h, Box plots slowing clonal diversity for each T cell subset (n = 22 healthy, n = 12 asymptomatic, n = 22 mild, n = 31 moderate, n = 14 severe, n = 13 critical biologically independent samples). Boxes denote IQR with median shown as horizontal bars. Whiskers extend to 1.5x the IQR; outliers are shown as individual points.

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