RT Journal Article SR Electronic T1 Robust three-dimensional expansion of human adult alveolar stem cells and SARS-CoV-2 infection JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.07.10.194498 DO 10.1101/2020.07.10.194498 A1 Jeonghwan Youk A1 Taewoo Kim A1 Kelly V. Evans A1 Young-Il Jeong A1 Yongsuk Hur A1 Seon Pyo Hong A1 Je Hyoung Kim A1 Kijong Yi A1 Su Yeon Kim A1 Kwon Joong Na A1 Thomas Bleazard A1 Ho Min Kim A1 Natasha Ivory A1 Krishnaa T. Mahbubani A1 Kourosh Saeb-Parsy A1 Young Tae Kim A1 Gou Young Koh A1 Byeong-Sun Choi A1 Young Seok Ju A1 Joo-Hyeon Lee YR 2020 UL http://biorxiv.org/content/early/2020/07/10/2020.07.10.194498.abstract AB Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global pandemic, infects human lung alveolar cells (hACs). Characterising the pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hACs limits the study. Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for human alveolar type 2 (hAT2) cells, 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 pro-inflammatory genes in infected hAT2 cells, indicating 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 long-term 3D hAT2 cultures as models for respiratory diseases.Competing Interest StatementThe authors have declared no competing interest.