Fig. 1

Epithelial cell clusters in bronchoalveolar lavage fluid in patients with SARS-CoV-2 disease. A The 11 BaLF epithelial cells types. B Distribution of 11 BaLF epithelial cells types in healthy controls (HC) and patients with moderate (M) and severe (S) SARS-CoV-2 infection. C Component of epithelial cells in each sample. D Expression of ACE2 in epithelial cells in each group. E Histogram of ACE2 gene expression in epithelial cells. F Top marker gene dot plot of clusters 1–11. G Heat map of differential genes in cell-type clusters. H Violin plots showing distribution of expression for selected cluster marker genes.