Fig 2: Surface protein abundance changes are observed in leukocyte subsets of patients with critical COVID-19.(A) Volcano plot of log fold change between COVID-19+ and healthy controls (x axis) versus -log10(P value) (y axis) in cM cells. Proteins that are significantly (FDR < 0.05) differentially abundant and have a log2(fold change) > 0.5 are highlighted. (B) Normalized (Norm.) LAIR1 and SIGLEC1 surface expression (exp.; y axis) at day 0 across eight cell types separated by case control status, severity, and presence of anti–IFN-a2 antibodies (x axis). Box plots show median and 25th and 75th percentile. (C) Normalized LAIR1 surface expression (y axis) in cMs over the course of disease for healthy controls, COVID-19- controls, and COVID-19+ cases. COVID-19- controls and COVID-19+ cases are separate by severity and the presence of anti–IFN-a2 antibodies. Insets show significant results of LMM testing for changes over time. (D) The bar plot shows correlation between the surface expression of 52 statistically significantly proteins to ISG-I score in cMs at day 0. Proteins are colored by their log2(fold change) expression between COVID-19+ cases and healthy controls. Red indicates higher expression in COVID-19+ cases. Blue indicates lower expression in COVID-19+ cases. (E) Scatter plot of normalized LAIR1 expression (y axis) versus the ISG-I score (x axis) for COVID-19+ cases colored by severity and anti–IFN-a2 status. *P < 0.05, **P < 0.01, and ***P < 0.001.

Fig 3: High expression of LAIR-1, PD-L1 and CD64 in neutrophils from children with COVID-19. (a) Frequency of LAIR-1 and PD-L1 positive cells in neutrophils from healthy (n = 20) and COVID-19 (n = 21). (b) Representative dot plots of LAIR-1 and PD-L1 expression in a donor from each cohort are shown. Numbers indicate the percentage of neutrophils positive for the expression of LAIR-1 or PD-L1. (c) Frequency of positive cells for CD16, CD32 and CD64 expression in neutrophils from healthy (n = 22) and COVID-19 (n = 56). (d) Representative dot plots of CD16 and CD64 expression are shown. Data show the percentages of positive cells in gated neutrophils. Median and min to max of n donors are shown in a and c. P values were determined by Kruskal-Wallis test with Dunn's posttest and Mann-Whitney U test: * p <0.05, ** p <0.01. Controls (white circle), COVID-19 (blue circle) (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.).