Fig. 1: Multi-stage single-cell analysis of PBMCs from CVID and non-CVID individuals with or without COVID-19.

a Overview of the participants included in this study, the samples collected and the data generated. Created in BioRender. Ballestar, E. (2024) https://BioRender.com/o27q186. b UMAP visualization showing different immune cell populations identified and cell-specific marker gene expression in the non-CVID 1 cohort (n = 6 for baseline, n = 5 for progression mild, n = 5 for progression severe, n = 5 for convalescence mild and n = 5 for convalescence severe) and in the CVID cohort (n = 5 paired samples at baseline, progression and convalescence). The number of captured cells in each cohort is indicated in brackets. The B cell compartment includes naïve B cells, memory B cells and plasmablasts. The T cell compartment includes CD4⁺ naïve T cells, CD4⁺ memory T cells, CD4⁺ cytotoxic CTL (only in sample P3), regulatory T cells (Treg), gamma-delta T (γδT) cells, CD8⁺ naïve T cells, CD8⁺ memory T cells, CD8⁺ NKT-like cells, mucosal-associated invariant T (MAIT) cells, and proliferating T cells. The NK cell compartment includes NK CD56^bright and NK CD56^dim cells. The myeloid cell compartment includes classical and non-classical monocytes, as well as conventional dendritic cells (cDC) and plasmacytoid dendritic cells (pDCs). In addition, we captured hematopoietic stem cells (HSC) and platelets. c Violin plots showing the gene expression levels of selected markers. d Stacked barplot showing cell cluster frequencies in each group. Source data for panels in this figure are provided in the Source Data Fig. 1 file.