Viral RNAs were enriched in mononuclear phagocytic and endothelial lung cells, which induced specific host programs. Integrated computational analysis uncovered substantial remodelling in the lung epithelial, immune and stromal compartments, with evidence of multiple paths of failed tissue regeneration, including defective alveolar type 2 differentiation and expansion of fibroblasts and putative TP63 + intrapulmonary basal-like progenitor cells. Here we generated single-cell atlases of 24 lung, 16 kidney, 16 liver and 19 heart autopsy tissue samples and spatial atlases of 14 lung samples from donors who died of COVID-19. Nature volume 595, pages 107–113 ( 2021) Cite this articleĬOVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure 1, 2, 3, 4, but little is known about its pathophysiology. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets