Fig. 2: Enhanced interferon response across immune cell populations defines protective immunity in SARS-CoV-2 infection.

a Tempora based analysis of longitudinally alternating gene pathways across cell clusters of pneumonic and non-pneumonic patients yielding “Type I Interferon signaling pathway” as a temporally significantly regulated pathway, non-pneumonic clusters are depicted in green, pneumonic clusters are in red, timepoints are chronologically set throughout the inferred time axis and depicted in the cluster names, statistical test conducted using the Tempora method. b, c Volcano plots of differentially regulated genes in CD4⁺ T cells and NK cells of pneumonic compared to non-pneumonic samples. Genes enriched in pneumonic samples have negative log(FC), genes enriched in non-pneumonic samples have positive log(FC). The color scale underneath emphasizes this (red pneumonic, green non-pneumonic) d Violin plots of expression of IFI44L and IFITM1 in CD4⁺ T cells and NK cells for pneumonic and non-pneumonic samples. e Volcano plot of differentially regulated genes in B cells of pneumonic compared to non-pneumonic samples. f Violin plots of expression of MX1, XAF1, and IFI44L in B cells for pneumonic and non-pneumonic samples. g Volcano plot of differentially regulated genes in monocytes of pneumonic compared to non-pneumonic samples. h Violin plots of expression of IFI44L, IFI44, LY6E, ISG15, and IFI6 in monocytes for pneumonic and non-pneumonic samples. b, c, e, g Red annotations are significantly upregulated (adj p val < 0.05), yellow ones are non-significantly differentially expressed. Positive fold change signifies higher expression in the non-pneumonic group. Line denotes adj p val < 0.05. Statistical testing for volcano plots described in methods. b–h Longitudinal samples are pooled if not otherwise indicated.