Fig. 1. Differential protein expression in plasma from patients with active SARS-CoV-2 infection.

The limma package was used to identify differentially expressed proteins (DEPs) from the single Olink panels and the combined dataset (893 unique proteins), which was defined as protein with more than 1.25-fold change with a P-value < 0.05 and FDR < 0.1. a Summary of the number of DEPs in each of the ten Olink panels used in the study. DEPs were used to calculate a score for each panel (refer to “Methods”), which was used for ROC curve analysis and the AUC under the ROC curves is stated for each panel. All ROC curves AUC had a P-value < 0.01. DeLong et al. method⁷⁰. b Unsupervised hierarchical clustering based on all proteins (a total of 893 unique proteins) assayed using the ten Olink panels showed a separation between patients with severe complications compared to mild cases and controls. The heatmap shows z-scores and clustering was done using correlation and average linkage. Principal component analysis (PCA) confirmed the separation of the severe cases based on the expression profiles of all proteins. c Volcano plots summarizing the DEPs across the patient groups. Differential expression analysis addressed severity as the main effect and included all factors, from obesity to SpO₂ (except for disease grading), to correct for the interaction of these factors with severity. The time between admission to blood collection was also considered for interaction with disease severity in the comparison between severe and mild cases (right volcano plot in c). The number and percentage of the DEPs relevant to all proteins assayed are stated in each panel. Similar analyses were carried out for each panel and shown in Supplementary Fig. 1.