Fig. 1: An atlas of peripheral immune cells in severe COVID-19 patients.
a Flowchart depicting the overall design of the study. Blood draws from patient P1 were performed at 2 time points (day 1 and day 5) and from P2 at 3 time points (day 1, day 5 and day 7). P1 on day 1 and P2 on day 1 and day 5 were positive based on a nucleic acid test of a throat swab specimen. P1 on day 5 and P2 on day 7 were negative based on a nucleic acid test of a throat swab specimen. Patients on day 1 were at the severe stage, and patients were in the remission stage on day 5 (P1 and P2); the day 7 blood draw for P2 (still in the remission stage) was performed based on a positive nucleic acid test on day 5. Note that the samples on day 1 were collected within 12 hours of tocilizumab treatment. b-d UMAP representations of integrated single-cell transcriptomes of 69,237 PBMCs, with 13,239 cells derived from our COVID-19 patients and 55,998 derived from the 10X Genomics official website16. Cells are colour-coded by clusters (b), disease state (c), and sample origin (d). Dotted circles represent cell types with a > 5% proportion within PBMCs in (b), and clusters significantly enriched in patients versus controls are shown in (c, d). Mono, monocyte; NK, natural killer cells; mDCs, myeloid dendritic cells; pDCs, plasmacytoid dendritic cells. e Violin plots of selected marker genes (upper row) for multiple cell subpopulations. The left column presents the cell subtypes identified based on combinations of marker genes.
