(a) The UMAP plot shows the clustering of T and NK cells in BALFs (n = 11, HC2 and S3 excluded). (b) Heatmap showing the top 50 differentially expressed genes by various T and NK cell clusters in the BALFs. The gene names and their corresponding cell types were listed to the right. (c) The heatmap shows the expression levels of immune typing markers on different T and NK clusters. Doublets clusters were identified based on marker expression (CD68+CD3D+ and FCGR3B+CD3D+). (d)The bar plot shows the percentages of T and NK clusters in each studied subject. (e) The UMAP plots align the T and NK cell clusters across different groups of patients. (n = 3 for controls, n = 3 for moderate patients, n = 6 for severe/critical patients) (f) The volcano plot shows the selected DEGs of CD8+ T cells from moderate vs. severe/critical COVID-19 patients. Only genes specifically upregulated in T cells compared to macrophage cells are kept. And a gene is considered significant with adjust P < 0.05 (P-value adjusted by false discovery rate in MAST). Other indicates non-significant genes. (g) The GO-BP enrichment analysis of DEGs of CD8+ T cells between moderate vs. severe/critical COVID-19 patients shows enriched pathways (selected among pathways upregulated in moderate and severe/critical cases, adjust P < 0.05 (hypergeometric test, adjusted P-values obtained by Benjamini-Hochberg procedure). In (f-g), moderate: n = 3, severe: n = 5.