Fig. 7: Comparison between blood (COMBAT) and lung (COSMIC) data.

a SCMAP matching heatmaps representing the Jaccard indices of similarity between COMBAT (blood)⁶ and COSMIC (lung) lymphocyte clusters. CD107a^- CD8 T cell and CD107a⁺ CD8 T cell in COSMIC matched to blood GZB^- CD8 T cells in COMBAT. IFN-γ⁺ CD4 T cells matched to COMBAT’s ‘activated CD4 T cells’. b SCMAP matching heatmaps representing the Jaccard indices of similarity between COMBAT (blood) and COSMIC (lung) myeloid clusters. Mono_CD31_ADJ and Mono_PAI-1_ADJ and all macrophage subsets matched with HLA DR^hi classical monocytes in the blood from COMBAT data. c UMAP representation of neutrophils from controls and COVID-19 infected patients (n = 2,776,928 single cells from n = 77 COVID-19 patients and 11 healthy volunteers (HV), down sampled to 100 000 cells per condition) obtained from COMBAT consortium, showing 8 subsets of neutrophils. d Heatmap showing median marker expression for genes (selected to match COSMIC’s key protein expression on neutrophils) on the 8 neutrophil subsets, demonstrating high similarity of marker expression in immature neutrophil 2 (iNeut2) in COMBAT (blood) with Neut_CD8_ADJ in COSMIC (lung) (See also Fig. 2f). e Abundance of the 8 neutrophil subsets in blood as % of total neutrophils, from healthy volunteers (HV), mild, severe and critical COVID-19 patients from the COMBAT consortium showing a progressive increase in immature 2 neutrophils with increasing COVID-19 disease severity. HV (n = 11), mild (n = 18), severe (n = 41), critical (n = 18) patients, n = 1 experiment. The boxplot is median, with IQR; whiskers are the range or 1.5*IQR (whichever is smaller). Composition analysis was performed using scCODA with inbuilt adjustment for multiple comparison⁷⁰. Credible compositional changes were identified comparing all groups to HV and FDR < 0.1 is marked with #. Source data are provided in Source Data File.