Fig. 3: ISG^hi naive CD4⁺ T cells are increased in SARS-CoV-2 infected infants.

a UMAP plots representing CD4⁺ T cell subclusters (SCs; n = 4) and patient groups (G1, G2, G3 or pHC). b Heat map representing scaled expression values of selected marker genes. c Boxplot comparing the proportion of each CD4⁺ T cell SC (n = 4) across the individuals (n = 40). pCoV patient groups (G1, G2 and G3) are shown in purple, and pHC in green. P values were calculated using a two-sided t-test comparing the mean (G1, G2 or G3) with mean (pHC). ns: non-significant. The upper and lower bounds represent the 75% and 25% percentiles, respectively. d Heat map representing scaled expression values of the most significant genes in CD4⁺ T cells from acutely infected (G2 and G3) infants, compared with healthy controls. e UMAP plot representing memory CD4⁺ T cell subsets. f Density plot, generated by the Nebulosa⁵¹ package, showing the expression of selected marker genes. g As in (c) in memory CD4⁺ T cell SCs. h As in (f) in Tregs. i As in (g) in Tregs.