Fig. 3: SARS-CoV-2 RNA⁺ single cells are enriched for phagocytic and endothelial cells.

a, b, Many SARS-CoV-2 RNA⁺ single cells do not express known SARS-CoV-2 entry factors. UMAP embedding of all 106,792 lung cells or nuclei (as in Fig. 2a), showing either a, only the 40,581 cells from seven donors containing any SARS-CoV-2 RNA⁺ cell, coloured by viral enrichment score (Supplementary Methods, red: stronger enrichment) and by SARS-CoV-2 RNA⁺ cells (black points), and marked by annotation and FDR of enrichment (legend) or b, all 106,792 cells/nuclei, coloured by expression of SARS-CoV-2 entry factors (co-expression combinations with at least 10 cells are shown). Dashed lines, major cell types. c, Reduction in SARS-CoV-2 RNA with prolonged symptom onset to death interval (Spearman ρ = −0.68, P < 0.005, two-sided test). Symptom onset to death (x axis, days) and lung SARS-CoV-2 copies per nanogram input RNA (y axis) for each donor (n = 16). d, Expression changes in SARS-CoV-2 RNA⁺ myeloid cells. Significantly differentially expressed (DE) host genes (log-normalized and scaled digital gene expression, rows; cutoff: FDR < 0.05 and log₂(fold change) > 0.5) across SARS-CoV-2 RNA⁺ (n = 158) and SARS-CoV-2 RNA⁻ myeloid cells (n = 790) (columns).