Fig. 6: Airway progenitor cells take part in the alveolar regeneration process after SARS-CoV-2 infection in hamsters.

a, b Quantification of cytokeratin 14 (CK14)⁺ airway basal cells (a) and secretoglobin 1a1 (SCGB1A1)⁺ club cells (b) within the whole alveolar space, airways, and within alveolar epithelial proliferation foci (ep. prol.). On the right, representative pictures of immunolabeling (brown signal) of CK14 (arrows) and SCGB1A1 in the alveoli and airways of SARS-CoV-2 and mock-infected hamsters at 112 days post infection (dpi). c Representative images of double immunofluorescence in an alveolar proliferation focus at 14 and 112 dpi. Cells are labeled with SCGB1A1 (green) and CK14 (red). In both pictures there are low to moderate numbers of CK14⁺SCGB1A1⁺ cells (arrows and inlets). The staining was performed in four animals/time-point with same results. d Quantification of ΔNP63⁺ airway basal cells within alveolar proliferation foci and representative picture of immunolabeling (brown signal, arrows) in an alveolar proliferation focus of a SARS-CoV-2-infected hamster at 6 dpi. e, f Heatmap of normalized expression values for genes associated with airway basal cells and club cells (Supplementary Table 1) at each dpi in mock- and SARS-CoV-2-infected hamsters. Expression values are scaled by row. Red indicates higher and blue lower relative expression levels. a, b, d quantification data are shown as box and whisker plots. The bounds of the box plot indicate the 25th and 75th percentiles, the bar indicates medians, and the whiskers indicate minima and maxima. Dots indicate individual values. Statistical analysis was performed by two-tailed Mann–Whitney U test. For multiple comparisons between time-points (quantification within alveolar proliferation foci), a Benjamini–Hochberg correction was applied. P- and q values ≤ 0.05 were considered significant. N = 8 animals/group for mock and SARS-CoV-2 respectively. Source data are provided as a Source Data file.