Fig. 1: Age-dependent changes in cell composition of the upper airways.
a, Nasal samples of children (n = 42) and adults (n = 44) were collected from individuals negative and positive (asymptomatic/mild/moderate COVID-19) for SARS-CoV-2 and subjected to scRNA-seq. b, Uniform manifold approximation and projection (UMAP) showing all identified individual immune and epithelial cell types and states. MC/basophil, mast cells or basophils; moMa, monocyte-derived macrophages; nrMa, non-resident macrophages; rMa, resident macrophages; mDC, myeloid dendritic cells; CD11c_mDC, CD11c-expressing mDC; pDCs, plasmacytoid dendritic cells; DNT, double-negative T cells; NK, natural killer cells; NKT, natural killer T cells; p_NKT, proliferating NKT cells; ag_T, aging T cells; CD8_Tm, memory CD8+ T cells; CTL1 and CTL2, type 1 and 2 cytotoxic T cells; IL-17A_CD8, IL-17A-expressing CD8 T cells; IL-17a_CD4, IL-17A expressing CD4+ T cells; p_T, proliferating T cells; Cil-diff, differentiating ciliated cells; Epi_low RNA, epithelial cells with low RNA; FOXN4, FOXN4+ cells. c, Scaled UMAPs displaying 45,000 cells per group reveal pronounced differences in the nasal cell composition of SARS-CoV-2-negative and -positive children and adults. d, Table showing all cell types/states significantly different between children and adults in non-infected individuals. Given are mean differences in percent; positive values indicate a higher number of cells of the respective cell population in children compared to adults. Comparisons were performed by Kruskal–Wallis test followed by Dunn’s two-sided post hoc comparison with Benjamini–Hochberg correction (***P < 0.001; Neutrophil, 5.54 × 10−7; CD8_Tm, 1.97 × 10−4; CTL2, 1.83 × 10−5; Basal, 6.96 × 10−5; Ciliated, 9.18 × 10−7; also see Extended Data Fig. 2a). e, Scatter plots representing changes of specific immune and epithelial cells over time. Depicted are the percentages of the respective cell type/state with respect to all cells for immune cells (left) or epithelial cells (right) of each individual. Individuals negative for SARS-CoV-2 are indicated in gray, individuals positive for SARS-CoV-2 in red. Lines represent curve fitting results by local polynomial regression (LOESS). The P values are from linear regression analysis (Benjamini–Hochberg adjusted two-tailed).
