Fig. 3: Inferred differentiation pathways for epithelial cells from the upper respiratory tract.

a, UMAP displaying the subset of airway epithelial cells of all patients infected with SARS-CoV-2 used in this study (see Methods). b, Pseudo-time trajectory projected onto a UMAP of selected epithelial cells. Pseudo-time values are color coded. The red dot indicates the start point of the trajectory. Numbers in circles indicate three inferred differentiation paths c, Dot plot depicting the markers of the epithelial cell types. Expression levels are color coded; the percentage of cells expressing the respective gene is size coded. d, Cell density of airway epithelial cell clusters along inferred cellular trajectory reflecting epithelial cell differentiation. Cells are ordered by pseudo-time (cell-to-cell distance metric) as computed by reversed graph embedding approach of Monocle3 (left). Expression of specific genes along the cell trajectory important for the corresponding differentiation paths (right). The dots indicate the gene expression of individual cells colored by the epithelial cell type. The green lines approximate expression along the inferred trajectory by polynomial regression fits.