This research was funded by a Berlin Institute of Health (BIH) grant to G.N., a German Federal Ministry of Aldoxorubicin Education and Research, Germany (BMBF) grant to M.W., grant number CAPSyS (01ZX1604B), and by a German Research Foundation (DFG) grant to J.T. subtypes, by strong and early expression of anti-viral, pro-inflammatory, and T cell recruiting genes. Recruitment of cytotoxic T cells as well as emergence of IgM antibodies precede viral clearance at day 5 post contamination. Investigating SARS-CoV-2 infected Syrian hamsters thus identifies cell type-specific effector functions, providing detailed insights into pathomechanisms of COVID-19 and informing therapeutic strategies. and transcripts were elevated only early at 2 and 3?dpi in alveolar and monocytic macrophages, and alveolar macrophages and (also known as CD126) and ((((and (Fig.?4a, Supplementary Fig.?5a). Blood transcriptome analysis recapitulated this early transcriptional activity at 2?dpi (Fig.?4b, Supplementary Fig.?5b), but declined by 5?dpi, whereas the signature persisted in the lungs until 14?dpi (Supplementary Fig.?5a, b). Open in a separate window Fig. 4 Transcriptional response to SARS-CoV-2 infection is strong in myeloid and moderate in epithelial cells.a, b Dotplot of differentially expressed genes in lungs (a) and blood (b). Shown are genes that are in at least one cell Aldoxorubicin type among the top four most changing genes as ranked by adjusted in blood and lungs from naive animals and 2?dpi. Bottom, boxplots of gene expression values of cells positive for expression. Significance levels were calculated using two-sided generalized linear mixed-effects models for bar plots and a two-sided Wilcoxon rank-sum test on all cells (i.e., not only the ones expressing the gene) for Aldoxorubicin boxplots. ?(left) and (right). For all bar plots, data display means??SD, ((Fig.?4c, Supplementary Fig.?5c), indicating that activation and acquisition of effector function occurred in lungs. Although AT2 cells are a main target of SARS-CoV-2 in lungs23, they displayed weaker and later transcriptional changes upon infection compared to monocytic macrophages (Figs.?4a, d, S5a, d). Notably, at 14?dpi differential transcriptional responses related to defense resolved in blood and lung cells. Instead, we observed upregulation of Fgfr1 cell cycle proliferation genes in AT2 cells including ((((was substantially overlapping (Supplementary Fig.?5f). To test whether hamster tissue responses are representative of infected human epithelial cells, we next referred to our scRNA-Seq dataset derived from Aldoxorubicin nasopharyngeal swabs of 19 COVID-19 patients and 5 healthy controls27. Here again, human and hamster epithelial cells derived from infected individuals and animals, respectively, showed a similar, moderate induction of most inflammatory mediators (Supplementary Fig.?6a, b). As notable difference, strong induction of neutrophil-recruiting chemokines targeting CXC chemokine receptor (CXCR) 2, such as ((and (~4C22%), as did a smaller proportion of AT2 cells (~3C5%) (Supplementary Table?3). By in situ-hybridization, we visualized SARS-CoV-2 RNA in bronchial epithelial cells (Fig.?5b), and AT1 (Fig.?5c, arrowhead) and AT2 (Fig.?5c, arrow) cells, whereas endothelial cells were consistently devoid of virus (Fig.?5b, hash). Importantly, viral RNA was detected in high numbers of intrabronchial and intraalveolar macrophages (Fig.?5d, arrows) at early time points. A fraction of macrophages contained high loads of virus without cell debris, pointing toward uptake of cell-free virus (Fig.?5d, inset). For comparison, a control staining section of alveoli is shown (Fig.?5e). Open in a separate window Fig. 5 Virus RNA in monocytic macrophages leads to dose-dependent activation of pro-inflammatory cytokines by TLR signaling.a Feature plots of entry factor expression in Uniform manifold approximation and projection (UMAP) projection. Coloration indicates expression values of indicated genes. bCe Detection of viral RNA by in situ-hybridization. Labeled are supposed endothelium (b, hash), Aldoxorubicin bronchial epithelial cells (b, arrowhead), AT1 (c, arrowhead) and AT2 (c, arrow). (d, inset), macrophages containing viral RNA and cell debris (arrowhead), and an example of high levels of viral RNA without cell debris in the inset (arrow). For bCe red signals viral RNA and blue hemalaun counterstain. Time points: b, c from 2?dpi, d from 3?dpi, e staining control. Bars: b, d, e?=?50?m, c?=?100?m, Inset in d?=?20?m. Micrographs representative of (h) and (i) gene expression in AT2 and monocytic macrophages along, comparing cells.