scRNA-seq analysis at 28 days after influenza infection shows that Sox2 lineage-traced cells can generate bona fide AT2 cells, as indicated by expression of canonical AT2 markers such as Sftpc and Lamp3, but with very low levels of secretory cell markers such as Scgb1a1 (Fig. 4f, g, and Supplementary Fig. 4f). This evidence concerns the gene SOX2 and influenza.