Figure 4.

Impaired antigen presentation distinguishes the immune response to SARS-CoV-2 versus other respiratory pathogens

(A) Comparison of immune features derived from each leukocyte subpopulation between experimental groups. A dot plot displaying the ES calculated in HAP versus COVID-19s (x axis; threshold 0.4) compared with the ES calculated in COVID-19m versus COVID-19s (y axis; threshold 0.3). Each dot represents one immunological feature. The red box highlights immune features, which are different in COVID-19s and HAP, with a focus on changes within the monocyte and DC fraction.

(B and C) Median expression of HLA-DR (B) or CD86 (C) within classical monocytes of HCs shown in gray, HAP patients in blue, and COVID-19m and COVID-19s patients across TPs 1–5 shown in red.

(D and E) Correlation between median expression of HLA-DR (D) or CD86 (E) in monocytes or DCs (TPs 1 and 2 pooled) against the severity grade of COVID-19 patients.

(F) Heatmap depicting the Z score of each monocyte and DC related immune feature (highlighted in A) compared with HCs for every TP. Both negative and positive changes are visualized by intensity of red color scale.

(G and H) Median expression and the 25th and 75th percentiles of HLA-DR (G) or CD86 (H) in FlowSOM-generated monocyte and DC immune cell clusters.

^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.001, and ^∗∗∗∗p < 0.0001, Mann-Whitney test, BH correction. See also Figure S4.