Fig. 4: Longitudinal analysis of COVID-19 single-cell transcriptomes.

A UMAP representation of cell states (locations of cells in gene expression space) enriched or depleted over time in T, NK cells. A cell is colored orange if the proportion of Non-Progressor Mild1 cells (for example, top-left UMAP) in its immediate vicinity (300 nearest neighbors) increases over time, and blue if the proportion decreases. For comparison, the average scaled expression of all expressed genes related to type I IFN signaling is shown (type I IFN metagene). B Top 3 enriched GO terms of marker genes of cell states depleted over time in Non-Progressors (blue cells). C, D B cells, same as (A, B). E, F Myeloid cells, same as (A, B). G–I Prognostic type I IFN metagene z-score (normalized across all samples) of Mild Progressor (circles) and Non-Progressor (box-plots) samples, grouped by disease severity and duration. Horizontal dashed line: average type I IFN metagene z-score of the 5 asymptomatic (Asy) samples. In each PBMC sample, metagene z-scores were averaged across all T, NK cells (G), B cells (H), and myeloid cells (I). Filled circles: baseline samples of Progressors. Empty circles: second samples of Progressors. Box-and-whisker plots show the median (center line), 25th, and 75th percentile (lower and upper boundary), with a 1.5x inter-quartile range indicated by whiskers and outliers shown as individual data points. Source data are provided as a Source Data file.