Fig. 2: Cellular tropism of SARS-CoV-2 infection.

a, Absolute abundance of S⁺ cells for lungs of patients without COVID-19 (grey) or with COVID-19 (red). b, Distribution of S⁺ cells across metaclusters in COVID-19. Inset displays intensity of KRT8/18 and S⁺ for single cells from non-COVID-19 (left) and COVID-19 (right) groups. c, Phenotype of alveolar epithelial cells in COVID-19, depending on levels of S. d, Intensity of differential markers between cells dependent on S levels. e, Distribution of S signal in a spatial context. Structural, cell-type-specific and functional markers are displayed alone or in combination. For the green channel in the images in the rightmost column, the S channel was multiplied with KRT8/18 or CD68 to highlight T cells that are positive for both markers. Scale bar, 200 μm (main panels), 50 μm (magnified images on right (unless otherwise indicated)). f, g, Differential interactions in healthy lung and lungs of patients with COVID-19 (f) or between early and late COVID-19 (g). h, Fibroblasts and macrophages from early and late COVID-19. Scale bars, 200 μm. i, j, Proportion of cleaved CASP3⁺ macrophages (left) or neutrophils (right) (i), and C5b–C9⁺ epithelial (left) or endothelial (right) cells (j), for each disease group. k, Deposition of C5b–C9 in epithelial cells in healthy lung and lungs from patients with COVID-19. Scale bars, 100 μm. In a, i, j, n = 237 images from 27 biologically independent samples; **P < 0.01; *P < 0.05, two-sided Mann–Whitney U test, pairwise between groups, Benjamini–Hochberg FDR adjustment. In f, g, P values are from two-sided Mann–Whitney U test with Benjamini–Hochberg FDR adjustment. Box plots show interquartile range (25th–75th percentiles); centre line is median (50th percentile).