Fig. 2: Strong interferon response is observed in COVID-19 samples.

a Heatmap showing the top differentially expressed genes (logFC > 0.5, adjusted p-value < 0.05 calculated by Wilcoxon rank-sum test with Bonferroni correction for multiple comparisons) for each major cell type, comparing time-point A and B. The level of expression of these genes in control samples is shown as well. The upper part of the heatmap depicts genes that are increased at time-point A compared to B (marked “time-point A up”). b–g IFN-I scores were calculated based on the expression of 12 ISGs for each sample. b IFN-I score is markedly increased in all cell types in COVID-19 at time point A, relative to controls. c IFN-I score decreases from time-point A to B in nearly all cell types. d IFN-I score is higher in progressive vs stable COVID-19 patients, and at time-point, A (earlier blood draw) compared to time-point B (later one). ****p-value < 1E−300 calculated by Wilcoxon rank-sum test. e, f Viral load for each patient was calculated based on RT-qPCR analysis of nasopharyngeal swabs or saliva samples. e Shown is a scatter plot of scaled log viral load vs scaled IFN-I score for all COVID-19 samples. Correlation coefficient (R) and p-value are indicated. Error bands denote a 95% confidence interval. p-value was calculated based on an F-test for the significance of the regression model. f Shown is a violin plot depicting the IFN-I score for each sample, with the corresponding viral loads indicated below the plot. Arrows mark the time difference (in days) between paired samples (i.e., from the same patient) at two time-points: A (early/before tocilizumab treatment) and B (late/after tocilizumab). g Scatter plot for the 8 paired samples, showing a very high correlation between the time difference from sample A to B and the respective change in scaled IFN-I score during that time. Correlation coefficient (R) and p-value are indicated. Error bands denote a 95% confidence interval. p-value was calculated based on an F-test for the significance of the regression model. IFN interferon, ND not detectable. FC fold-change. Source data are provided as a Source Data file.