Fig. 2: Compositional changes and CD55 expression in T cells subpopulations of COVID-19 patients.

A UMAP representation of 31,763 Τ cells coloured by cell type and B cluster assignment. C UMAP representation of all the T cells analysed across different disease states as indicated (healthy group: 11,180 cells, mild disease group: 13,687 cells, severe disease group: 2470 cells and critical disease group: 4426 cells). D Stacked bar plot representing T cell cluster quantitative changes (%) in each disease state as indicated, E Pearson correlation plot of scaled expression values followed by hierarchical clustering, for the most variable genes identified in the T cell subpopulations integrated. Colour spectrum represents positive correlations in red, to no correlation in white, to negative correlation in blue. F scRNA-seq heatmap showing the average scaled expression for selected marker genes of each subpopulation; mean expression is colour coded as indicated. G Feature plots showing CD55 gene expression in the T cell subpopulation UMAP space. H Dot plot depicting expression levels of CD55 in all T cell clusters across disease state; the dot size represents the fraction of cells in the clusters, mean expression is colour coded as indicated. I Matrix plot depicting differential expression of CD55 across the different T cell subpopulations depending on the disease state; mean CD55 expression levels and disease states, are colour coded, as indicated. J CD55 expression levels in each T cell cluster, in healthy and severe donors as indicated. Mean expression bar plots, with error bars representing the 95% bootstrapped confidence intervals around the mean. Statistical analysis performed by the Wilcoxon rank sum test *p < 0.05, **p < 0.01, ****p < 0.0001. K Side-by-side plots of flow cytometry histograms showing CD55 expression in CD4⁺ (top panel) and CD8⁺ T (lower panel) cell populations; severe disease patient sample (blue histogram), critical disease patient sample (red histogram) and healthy control sample (grey histogram). L Bar plots depicting quantitation of CD55 protein expression levels in CD4⁺ and CD8⁺ T cells determined by flow cytometric analysis in severe (n = 20) and critical (n = 20) COVID-19 patient cohorts (mean ± SD); Statistical analysis was performed by one-way ANOVA testing for more than two groups comparisons. Post-hoc analysis was performed by Fisher’s least significant difference test. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001.