Fig 1: Single cell transcriptomes of COVID-19 patients show dynamic differences of activated B cell subpopulations at different stages after ICU admission.Peripheral blood activated/differentiated B cells (CD27high CD38high) were isolated and sorted by FACS for single cell sequencing (gating strategy in Supplementary Fig. 1a). a Percentage of CD27high CD38high cells among live B cells. Each sample is represented by a circle. The line indicates the median. Unpaired two-sided Mann–Whitney U test. b UMAP representation of 72,277 CD27high CD38high sorted B cells from 9 COVID-19 ICU patients and three healthy controls. Between 2416 and 11,229 cells were recovered per sample. Transcriptionally similar clusters were identified using shared nearest neighbor (SNN) modularity optimization (left). The combination of CD19, MS4A1, CD27, CD38, IFIT1, MIKI67, IRF4, and PRDM1 expression were used for annotation of the different activation/differentiation stages (right). c Heatmap of genes that resemble markers for the six different clusters. Depicted are genes with a p-value < 0.01 (two-sided Wilcoxon rank sum test) after Bonferroni correction, and an average absolute fold-change > log2(1.3). Shown are z-scores of the average expression. d UMAP representation of the expression levels of selected signature genes for activated/differentiated B cells. e UMAP representation of analyzed cells from one healthy control and two ICU patients, representing early (first week, patient #1) and late (>7days, patient #5) phase after ICU admission. f Percentage of cells belonging to a defined cluster among all sequenced B cells per donor. Each dot represents one time point from one single donor. Donors were grouped as “HC” for healthy controls (3 donors), “1st week” for patients within 7 days after ICU admission (six donors) and “Late” for patients who have been admitted to the ICU for more than a week at the time of analysis (eight donors). The line indicates the median. Significance was determined by using a two-sided analysis of varience (ANOVA) folowed by Tukey’s multiple comparison test with corrected p values as indicated in the figure.