Three-Dimensional Human Alveolar Stem Cell Culture Models Reveal Infection Response to SARS-CoV-2

Cell Stem Cell. 2020 Dec 3;27(6):905-919.e10. doi: 10.1016/j.stem.2020.10.004. Epub 2020 Oct 21.


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.

Keywords: 3D cultures; COVID-19; SARS-CoV-2; alveolar stem cells; electron microscopy; human alveolar type 2 cells; infection; interferon; interferon-stimulating genes; single-cell RNA-seq.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • COVID-19* / virology
  • Cell Culture Techniques
  • Culture Media
  • Humans
  • Interferons / metabolism
  • Models, Biological
  • Pulmonary Alveoli / metabolism
  • Pulmonary Alveoli / ultrastructure
  • Pulmonary Alveoli / virology*
  • SARS-CoV-2 / physiology*
  • SARS-CoV-2 / ultrastructure
  • Stem Cells / virology*
  • Transcriptome
  • Virus Internalization
  • Virus Replication


  • Culture Media
  • Interferons