A Longitudinal Molecular and Cellular Lung Atlas of Lethal SARS-CoV-2 Infection in K18-hACE2 Transgenic Mice

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic, resulting in about 500 million cases of infection and 6 million deaths. Numerous investigations have been carried out to investigate the pathophysiology of SARS-CoV-2. However, the most of studies, based solely on patients' peripheral blood mononuclear cells, were unable to provide detailed mechanistic insights into SARS-CoV-2 pathophysiology in inflamed tissue. Furthermore, COVID-19 animal models are unable to accurately reproduce the severe SARs-CoV-2 infection shown in patients, highlighting a critical demand for more relevant animal system-based research. Hence, we performed single-cell RNA sequencing with lung tissues from K18-hACE2 mice during SARS-CoV-2 infection. Upon SARS-CoV-2 infection, we observed severe lung pathologies such as acute pneumonia, alveolar collapse, and immune cell infiltration in lung tissue from K18-hACE2 TG mice. The 36 different types of cells identified by scRNA-seq dynamically orchestrate SARS-CoV-2-induced pathologies. In the myeloid compartment, SPP1+ macrophages were identified as the key driver of severe lung inflammation associated with fibrosis in K18-hACE2 TG mice. Furthermore, dynamic receptor-ligand interaction across many cell types, including immunological and bronchial cells, defined the enhanced TGFβsignaling pathway associated with delayed tissue regeneration, severe lung injury, and fibrotic processes. Overall, our study gives complete insights into SARS-CoV-2 pathogenesis in lung tissue, which may inform the development of innovative COVID-19 diagnostics and therapies.Funding Information: This research was supported by the National research foundation of Korea (NRF) grant funded by the Korea government (MSIT) (2020M3A9I2109027, 2021R1A2C2004501). Some figures were Created with BioRender.com.Declaration of Interests: The authors declare no conflicts of interest.Ethics Approval Statement: All protocols were approved by the Institutional Animal Care and Use Committee of the Seoul National University Bundang Hospital (IACUC number BA 2008-301-071-05). All animals were cared for in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals, eighth Edition. The Seoul National University Bundang Hospital Institutional Biosafety Committee approved the procedures for sample handling, inactivation, and transfer from Animal Biosafety Level 3 (ABSL-3) containment.