Single-cell transcriptome of bronchoalveolar lavage fluid reveals sequential change of macrophages during SARS-CoV-2 infection in ferrets

Abstract Few studies have used a longitudinal approach to describe the immune response SARS-CoV-2 infection. Here, we perform single-cell RNA sequencing of bronchoalveolar lavage fluid cells longitudinally obtained from SARS-CoV-2-infected ferrets. Landscape analysis lung microenvironment shows distinct changes in cell proportions and characteristics compared uninfected control, at 2 5 days post-infection (dpi). Macrophages are classified into 10 subpopulations with transcriptome among monocyte-derived infiltrating macrophages differentiated M1/M2 macrophages, notably dpi. Moreover, trajectory reveals gene expression toward M1 or M2 identifies macrophage subpopulation that has rapidly undergone SARS-CoV-2-mediated activation inflammatory responses. Finally, find show patterns modules downregulated by immune-modulatory drugs. Overall, these results elucidate fundamental aspects dynamics provoked