Extended Data 4: Severe COVID-19 is defined by the lack of a concerted IFN response across multiple cell types.

a. Frequencies of the MPC subsets among all MPC across control (n=14), SARS-CoV-2 negative (n=11) and SARS-CoV-2 positive (n=21) individuals. b. UMAP visualization of the 19,289 MPC colored (left) and split by (right) by disease severity. c. Frequencies of the classical monocytes, cycling monocytes, non-classical monocytes and C1Q+ non classical monocytes among all MPC across SARS-CoV-2 negative (M/M, n=6; severe, n=5) and SARS-CoV-2 positive (M/M, n=11; severe, n=10) individuals split it by disease severity. d. Overlay of previously described (39) glycolytic and oxidative phosphorylation gene signature on mononuclear phagocytic cells (MPC) from UMAP plot in FigS3b. e. Volcano plot showing results of differential gene expression (DGE) analysis performed on all MPC between mild/moderate (right) and severe (left) patients. f. Correlation matrix using Spearman Rank Correlation between the frequency of all neutrophils and monocytes subtypes in all SARS-CoV-2 negative (n=11) and SARS-CoV-2 positive patients (n=21). g. Scatter plot between neutrophil and CD4 T cell ISG positive subsets patient by patient (M/M, n=11; severe, n=10; COVID-, n=11). Statistical significance was assessed using a two-way ANOVA test with multiple comparisons. * p.value < 0.05; ** p.value < 0.01; *** p.value < 0.001; **** p.value < 0.0001. Boxplot center, median; box limits, 25th and 75th percentile; whiskers, min. and max. data point.