Summary Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the cause of a present pandemic, infects human lung alveolar type 2 (hAT2) cells. Characterizing pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hAT2 cells limits the study. Here, we develop a feeder-free, long-term, three-dimensional (3D) culture technique for hAT2 cells derived from primary human lung tissue and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and proinflammatory genes in infected hAT2 cells, indicating a robust endogenous innate immune response. Further tracing of viral mutations acquired during transmission identifies full infection of individual cells effectively from a single viral entry. Our study provides deep insights into the pathogenesis of SARS-CoV-2 and the application of defined 3D hAT2 cultures as models for respiratory diseases. Graphical Abstract Highlights • Long-term 3D culture of primary hAT2 cells in chemically defined conditions • SARS-CoV-2 infects in vitro hAT2 models with substantial ultrastructural changes • Single-cell RNA-seq finds two cellular states of distinct innate immune phenotypes • Mutation analysis reveals single SARS-CoV-2 entry to a hAT2 cell for full infection To study infection response to SARS-CoV-2, Youk et al. developed a 3D culture model of human alveolar stem cells in chemically defined conditions. They reveal that SARS-CoV-2 productively infects alveolar type 2 cells, resulting in an innate immune response. Full infection of individual cells was exhibited from a single viral entry.
【저자키워드】 COVID-19, SARS-CoV-2, Infection, interferon, electron microscopy, single-cell RNA-seq, alveolar stem cells, human alveolar type 2 cells, 3D cultures, interferon-stimulating genes, 【초록키워드】 severe acute respiratory syndrome coronavirus 2, Transcriptome, stem cells, pathology, Vaccine, coronavirus, pandemic, Pathogenesis, innate immune response, Therapeutics, interferon, Transmission, severe acute respiratory syndrome Coronavirus, respiratory diseases, viral entry, RNA-Seq, Viral, Culture, cells, viral replication, human lung, single-cell RNA-seq, phenotype, respiratory, Viral mutations, change, single-cell, cellular, innate immune, Analysis, stem cell, acute respiratory syndrome, increased expression, acute respiratory syndrome coronavirus, SARS-CoV-2 entry, cellular physiology, human lung tissue, individual cells, proinflammatory genes, alveolar, viral mutation, pathogenesis of SARS-CoV-2, infect, limit, Cell, robust, defined, resulting, identify, lack, develop, exhibited, provide, condition, reveal, conditions, individual cell, proinflammatory gene, 【제목키워드】 Human, response, Model, STEM,