ABSTRACT The lung epithelium forms the first barrier against respiratory pathogens and noxious chemicals; however, little is known about how &gt;90% of this barrier – made of alveolar type 1 (AT1) cells – responds to injury, in contrast to our accumulating knowledge of epithelial progenitor and stem cells whose importance lies in their ability to restore the barrier. Using Sendai virus to model natural infection in mice, we combine 3D imaging, lineage-tracing, and single-cell genomics to show that AT1 cells have an intermediary role by persisting in areas depleted of alveolar type 2 (AT2) cells, mounting an interferon response, and receding from invading airway cells. Sendai virus infection mobilizes airway cells to form alveolar SOX2+ clusters without differentiating into AT1 or AT2 cells, as shown in influenza models. Intriguingly, large AT2-cell-depleted areas remain covered by AT1 cells, which we name “AT2-less regions”, and are replaced by SOX2+ clusters spreading both basally and luminally around AT1 cell extensions. AT2 cell proliferation and differentiation are largely confined to topologically distal regions – the end of airspace that could be in the periphery or middle of the lung – and form de novo alveolar surface, with limited contribution to in situ repair of AT2-less regions. Time course single-cell RNA-seq and AT1-cell interactome analyses suggest enhanced recognition of AT1 cells by immune cells and altered growth signals. Our comprehensive spatiotemporal and genome-wide study highlights the hitherto unappreciated role of AT1 cells during Sendai virus infection and possibly other injury-repair processes.

Intermediary role of lung alveolar type 1 cells in epithelial repair upon Sendai virus infection