Fig. 5: Dissection of inflammatory and antiviral response pathways in all monocyte (CD14⁺ and CD16⁺) subsets from the discovery set.

a, ICA representation of CD14⁺ monocytes derived from all severity groups (n = 22,690 cells). IC1 and IC2 components allowed the separation of CD14⁺ monocytes according to severity. b, Heatmap representation of the top 50 unique genes contributing to either IC1 or IC2 in the CD14⁺ monocytes subset; z-scores of average expression levels are colour-coded. c, Violin plot distribution of enrichment score values of enriched pathways in the top 50 genes contributing to either IC1 or IC2; severity groups are colour-coded, each dot represents a cell and the horizontal line displays the mean value of the enrichment score of each given pathway. The violin plots were designed using the total CD14⁺ monocyte subsets from the discovery set, obtained from n = 2 HC, n = 4 moderate and n = 6 severe samples. Comparative analysis was performed using the two-sided Wilcoxon rank-sum test. P values were adjusted to multiple testings using ‘Bonferroni’ correction. Asterisks above severe indicate P values for severe versus control; asterisks above moderate indicate significance of moderate versus control. *P < 0.05, **P < 0.01, ***P < 0.001. d, Dot plot of in-house constructed antiviral effector molecule modules across CD14⁺ monocytes and severity groups. Expression levels are colour-coded, and the percentage of cells expressing the respective gene is size-coded. e, UMAP representation of CD16⁺ monocytes (n = 866 cells) labelled according to severity group. f, Heatmap representation of top 50 DEGs among the three groups from the CD16⁺ monocytes subset; z-scores of average expression levels are colour-coded.