Fig. 4: Strong clonal expansion of cytotoxic CD8⁺ T effector compartment in COVID-19 CVID patients.

a Heatmaps showing fold-change (baseline vs progression) of DEGs in CVID cohort, and non-CVID 1 cohort validated with non-CVID 2 cohort, for selected CD8⁺ T cell subsets. Genes are grouped by baseline expression comparison (equal, upregulated, or downregulated in CVID vs non-CVID). Gene clusters are labeled on the left, and cluster sizes are indicated on the right. b Table of selected significant GO categories for each cluster in (a). Clusters without significant enrichment are marked as NA. c Box plots showing ‘cytotoxic response’ score for selected CD8⁺ T cell subsets in CVID, non-CVID 1, and non-CVID 2 cohorts. Dots correspond to biological replicates from different subjects in the CVID group (BL: n = 5, PG: n = 5, CV: n = 5), the non-CVID 1 control group (BL: n = 6, PG_Mild: n = 4, CV_Mild: n = 5, PG_Severe: n = 5, CV_Severe: n = 5) and the non-CVID 2 control group (BL: n = 14, PG_Mild: n = 11, CV_Mild: n = 8, PG_Severe: n = 8, CV_Severe: n = 5). d Histograms and box plots showing levels of selected proteins in CD8⁺ T cell subsets, stratified by PID status and infection stage. Dots correspond to biological replicates from different subjects in the CVID group (BL: n = 3, PG: n = 4, CV: n = 4) and the non-CVID control group (BL: n = 4, PG: n = 6, CV: n = 4). Two-sided t-test was used (*p-value < 0.05). e UMAP depicting TCR clonal expansion in CVID patients by SARS-CoV-2 infection stages. Stacked barplot of TCR clonal expansion percentages across cell types and stages is indicated. Box plot whiskers denote minimum and maximum values (excluding outliers), with the box spanning Q1 to Q3 and a horizontal line for the median. BL baseline, PG progression, CV convalescence. Source data for panels are available in Source Data Fig. 4.