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. 2020 Dec 9;6(50):eabe3024. doi: 10.1126/sciadv.abe3024

Fig. 5. Single-cell gene expression analyses of PBMCs from COVID-19–infected, influenza-infected, and healthy participants demonstrate profound differences in the relative abundance and transcriptional activity of cell subsets across conditions.

Fig. 5

(A) Uniform Manifold Approximation and Projection (UMAP) plots depict transcriptional clusters, which (B) vary transcriptionally as a function of condition despite the presence of nearly all subsets across various conditions, as evidenced in (C). (D) Violin plots demonstrate significant down-regulation of HLA-DRA among all cells from COVID-19–infected patients compared to influenza-infected patients (with healthy controls included for reference). Asterisks indicate significance at Bonferroni-corrected P values < 0.001. (E) GSEA analysis of gene expression differences between COVID-19 and influenza groups across major cell subsets. In direct comparison to cells from influenza-infected patients, transcriptional patterns among cells from COVID-19–infected patients reveal significant up-regulation (red bars) of metabolic pathways, stress pathways, and glucocorticoid signaling pathways across major cell subsets, particularly monocytes/macrophages. In contrast, interferon pathways were significantly down-regulated (blue bars) among subsets from COVID-19–infected patients compared to those from influenza-infected patients. Gray bars indicate that tests for enrichment did not meet statistical significance for a particular subset. (F) Violin plots demonstrate significant down-regulation of STAT1, STAT2, and STAT3 among monocytes/macrophages from COVID-19–infected patients compared to influenza-infected patients (with healthy controls included for reference). Asterisks (***) indicate significance at Bonferroni-corrected P values of <0.001.