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[Preprint]. 2022 Mar 10:rs.3.rs-1378671. [Version 1] doi: 10.21203/rs.3.rs-1378671/v1

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Extended Data Figure 4: — a) Volcano plot shows comparison of individuals recovered from non-severe (mild/moderate) and severe (severe/critical) COVID-19. Only individuals not hospitalized or discharged at day of sample collection are included. P-values were obtained from logistic regression, included correction for age and experiment and were corrected for multiple testing using Benjamini-Hochberg false discovery rate. Log2 fold change was calculated based on the mean of immune traits within non-severe and severe COVID-19 cases. P-values are shown as −log10.

b) Bar graph shows FDR-adjusted −log10 P-values for immune traits significantly different between non-severe and severe COVID-19 cases (cut-off for P-value < 0.012). Plot is similar to Extended Data Figure 3b but depicts P-values obtained with only individuals not hospitalized or released at day of sample collection. Bar on the left indicates the immune trait type. Color of bars indicate log2 fold change between non-severe and severe COVID-19 cases calculated as the ratio between the mean of immune traits between the two severity groups.

c) Comparison of stable immune traits between non-severe and severe COVID-19 cases including either all individuals (x-axis) or only individuals not hospitalized or released at day of sample collection (y-axis) is shown. Plot shows FDR-adjusted −log10 P-values for manually gated immune traits (N = 801). P-values were obtained by logistic regression and corrected for age and experiment batch. Size of symbols is based on −log10 P-values from analysis including all individuals. Color depicts the type of trait.

d) Venn graph depicts overlap of immune traits which differed between non-severe and severe COVID-19 group obtained from analysis including all (red circle, traits from Extended Data Fig. 3b) or only non-hospitalized individuals (blue circle, traits from Extended Data Fig. 4b).

e) Example flow cytometry data and gating of MAIT cells is shown (left) for one donor recovered from mild and severe COVID-19. Boxplot (right) shows frequency of MAIT cells per group. More detailed gating information is shown in Supplementary Data 3.

f) Boxplots show frequencies of CD4 (top) and CD8 (bottom) central memory (CM) cells of conventional CD4 and CD8 T cells, respectively, from all study groups.