Fig. 5: Tracking T cells across peripheral blood and BALFs in patients with COVID-19.

a The T cell data from two mild and five severe COVID-19 patients who had paired PBMC and BALF samples were integrated and presented on the UMAP. b The percentages of each T cell subset in paired BALF (B) and PBMC (P) of the same patient are compared. c Heatmaps display the selected DEGs in NK, CD4-Tm, and CD8-Tm cells in BALF (B) or PBMC (P) from the mild (M) or severe (S) COVID-19 patients. Cytokine-related genes are red marked (logFC > 0.41, adjusted P < 0.01). d The migration index in each T cell subset across paired PBMC and BALF from seven patients are shown (STARTRAC-migr indices). e TCR clonotypes were classified into five different types as indicated by different color bars (singleton indicates non-expanded TCR clonotype, multiplet indicates expanded TCR clonotype, dual-clone indicates those clonotype shared in paired PBMC and BALF samples). The bar plots show the percentages of different types of TCR clonotypes in different T cell subsets from paired PBMC and BALF samples. f The circus plot shows the degree of TCR clonotype sharing across different T cell subsets in PBMC and BALF from the mild and severe COVID-19 groups. g Heatmap shows the selected DEGs in each T cell clones derived from the top 13 TCR clonotypes shared across PBMC vs BALF compartments (logFC > 0.41, adjusted P < 0.01). h The V, J genes of the TCR α and β chains of the top 13 dual clonotypes are listed, and the amino acid sequences of their CDR3 are shown.