a, The clustering of BALF-derived T cells in patients with COVID-19 (n = 8, S3 excluded). The dotted lines partition the UMAP into CD4+ T cells (upper), CD8+ T cells (lower), innate T cells (left) and proliferating T cells (right). b, UMAP projection of clonally expanded T cells from patients with COVID-19. c, Clonal expansion status of T cell subsets in patients with moderate and severe/critical infection. Clonotype counts (left) and cell counts (right) are shown. d, Tissue-resident signature score by the expanded versus nonexpanded BALF CD8+ T cells in patients wuth moderate infection and by CD8+ T cells in patients with moderate versus severe/critical infection. In b–d, moderate was n = 3 and severe was n = 5.