Fig. 6: Cross-sectional cell state analysis to identify immune aberrations in severe COVID-19.

A UMAP representation of cell states (locations of cells in gene expression space) enriched or depleted with increasing COVID-19 severity. A cell is colored orange if the proportion of cells in its immediate vicinity (300 nearest neighbors) increases with increasing severity, and blue if the proportion decreases. Black outlines demarcate specific cell subtypes (clusters). B Left: Volcano plot of marker genes of CD4⁺ Tcm cell states enriched with increasing severity (orange Tcm cells vs all other Tcm cells). Middle: the top 3 corresponding enriched GO terms. Right: UMAP plot, each cell is colored by the average of the standardized gene expression values of the marker genes belonging to the most enriched GO term. C Same as B, for Cytotoxic CD8⁺ T-cell states that are depleted with increasing disease severity. D Same as A, for B cells. E Same as B, for memory B-cell states enriched with increasing severity. F Same as B, for naive B-cell states, depleted with severity. G Same as A, for myeloid cells. H Same as B, for CD14⁺ monocyte cell states enriched with increasing severity. I Same as B, for CD14⁺ monocyte cell states depleted with severity. Source data are provided as a Source Data file.