Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2

Youk, Jeonghwan; Kim, Taewoo; Evans, Kelly V.; Jeong, Young-Il; Hur, Yongsuk; Hong, Seon Pyo; Kim, Je Hyoung; Yi, Kijong; Kim, Su Yeon; Na, Kwon Joong; Bleazard, Thomas; Kim, Ho Min; Fellows, Mick; Mahbubani, Krishnaa T.; Saeb-Parsy, Kourosh; Kim, Seon Young; Kim, Young Tae; Koh, Gou Young; Choi, Byeong-Sun; Ju, Young Seok; Lee, Joo-Hyeon

Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global 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 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 defined 3D hAT2 cultures as models for respiratory diseases.