Extended Data Fig. 11: Entry factors in heart, kidney and liver COVID-19 tissues and differential gene expression in heart cell atlas.

a–c, SARS-CoV-2 entry factors are expressed in kidney, liver and heart cells. Average expression (dot colour) and fraction of expressing cells (colour, size) of SARS-CoV-2 entry factors (rows) across cell subsets (columns) in the kidney (a), liver (b) and heart (c). d–k, Genes and pathways differentially expressed between COVID-19 and healthy heart cells. d, log mean expression per cell (dot colour) and fraction of expressing cells (dot size) across cell types from healthy or COVID-19 heart (rows) for select genes (columns) that are differentially expressed between COVID-19 and healthy cells. e, Proportions of each cell type for COVID-19 (n = 15) and healthy (n = 28, two studies) samples (boxplots: middle line, mean; box bounds, first and third quartiles; whiskers, 1.5× the interquartile range; minima, smallest observed proportion; maxima, highest observed proportion). f, UMAP embedding of integrated COVID-19 and healthy snRNA-Seq profiles (dots) coloured by major cell types. Plot limited to a subset of 151,373 high-quality cells for visualization purposes. g–i, Cell-type-specific differentially expressed genes in COVID-19 versus healthy nuclei. Differential expression (log₂(fold change), x axis), and associated significance (−log₁₀(P), y axis; Supplementary Methods) for each gene (dot) between COVID-19 and healthy nuclei of cardiomyocytes (g), pericytes (h) and fibroblasts (i). Dashed line, FDR = 0.01. j, k, UMAP embedding of the meta-analysis atlas (as in f) but showing only COVID-19 (top) or healthy (bottom) nuclei profiles (dots) coloured by expression of PLCG2 (j) or AFDN (k). l, Low levels of viral UMIs in heart, liver and kidney, compared with lung. Cumulative viral read counts as a function of droplet UMI count. In lung (red) most virus-positive droplets are empty droplets (total UMI count approximately 100) with some virus-positive droplets that contain nuclei (UMI count > approximately 1,000), but in heart (green), liver (blue) and kidney (orange), most of the ‘virus-positive’ droplets have fewer than ten total UMI counts, indicating that these reads are not trustworthy.

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