Extended Data Fig. 7: TCR repertoire diversity is lower in SARS-CoV-2-P samples complicated by superinfection or VAP.

(a) Number of patients contributing BAL samples for TCR-seq analysis (n = 130 samples; NPC [n = 13], OP [n = 16], SARS-CoV-2-P [n = 73], and OVP [n = 28]). (b) Proportion of TCR-seq samples grouped by T cell subset and diagnosis. (c) Number of TCR-seq samples grouped by early (≤48 hours following intubation) and late (>48 hours following intubation) timing of BAL sampling relative to intubation. (d) Box plot of the mean Sequential Organ Failure Assessment (SOFA) scores on the day of BAL sample. Nonsignificant after pairwise Wilcoxon rank-sum tests with FDR correction. (e) Proportion of discharged versus deceased status patients. Nonsignificant after pairwise χ² tests for homogeneity of proportions with FDR correction. (f) Proportion of sex (pairwise χ² tests for homogeneity of proportions with FDR correction. (g) TCR richness analysis showing Chao 1 values in combined BAL CD4⁺ and CD8⁺ T cells by diagnosis. (q < 0.05, pairwise Wilcoxon rank-sum tests with FDR correction). (h) As in g, grouped by early (≤48 hours following intubation) and late (>48 hours following intubation) timing of BAL sampling relative to intubation. (i) As in g, grouped by discharged versus deceased status. (j) Pearson correlation analysis between TCR richness (Chao 1 values) and patient age in combined BAL CD4⁺ and CD8⁺ T cells in SARS-CoV-2-P samples (left) and NPC, OP, and OVP samples (right). Shaded area represents 95% CI. (k) As in j, correlated with the duration of mechanical ventilation. (l) Richness analysis showing Chao 1 values in SARS-CoV-2-P samples grouped by discharged versus deceased status in primary SARS-CoV-2 infection only (top), bacterial superinfection (middle), and VAP (bottom). Wilcoxon rank sum tests.