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03, 2021;19 (3): e3001143.

Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes.

Neal G Ravindra, Mia Madel Alfajaro, Victor Gasque, Nicholas C Huston, Han Wan, Klara Szigeti-Buck, Yuki Yasumoto, Allison M Greaney, Victoria Habet, Ryan D Chow, Jennifer S Chen, Jin Wei, Renata B Filler, Bao Wang, Guilin Wang, Laura E Niklason, Ruth R Montgomery, Stephanie C Eisenbarth, Sidi Chen, Adam Williams, Akiko Iwasaki, Tamas L Horvath, Ellen F Foxman, Richard W Pierce, Anna Marie Pyle, David van Dijk, Craig B Wilen
Author Information
  1. Neal G Ravindra: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America. ORCID
  2. Mia Madel Alfajaro: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America.
  3. Victor Gasque: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America. ORCID
  4. Nicholas C Huston: Department of Molecular Biophysics & Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America. ORCID
  5. Han Wan: Department of Molecular, Cellular, and Developmental Biology, Yale School of Medicine, New Haven, Connecticut, United States of America.
  6. Klara Szigeti-Buck: Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America.
  7. Yuki Yasumoto: Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America. ORCID
  8. Allison M Greaney: Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America. ORCID
  9. Victoria Habet: Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America.
  10. Ryan D Chow: Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America. ORCID
  11. Jennifer S Chen: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America. ORCID
  12. Jin Wei: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America. ORCID
  13. Renata B Filler: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America.
  14. Bao Wang: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America. ORCID
  15. Guilin Wang: Yale Center for Genome Analysis, Yale School of Medicine, New Haven, Connecticut, United States of America.
  16. Laura E Niklason: Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America.
  17. Ruth R Montgomery: Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America. ORCID
  18. Stephanie C Eisenbarth: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America.
  19. Sidi Chen: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America.
  20. Adam Williams: The Jackson Laboratory, Farmington, Connecticut, United States of America.
  21. Akiko Iwasaki: Department of Immunobiology, Yale University, New Haven, Connecticut, United States of America.
  22. Tamas L Horvath: Department of Comparative Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America.
  23. Ellen F Foxman: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America. ORCID
  24. Richard W Pierce: Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America.
  25. Anna Marie Pyle: Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America.
  26. David van Dijk: Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School Medicine, New Haven, Connecticut, United States of America. ORCID
  27. Craig B Wilen: Department of Laboratory Medicine, Yale University, New Haven, Connecticut, United States of America. ORCID
PMID: 33730024 DOI: 10.1371/journal.pbio.3001143

Abstract

There are currently limited Food and Drug Administration (FDA)-approved drugs and vaccines for the treatment or prevention of Coronavirus Disease 2019 (COVID-19). Enhanced understanding of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection and pathogenesis is critical for the development of therapeutics. To provide insight into viral replication, cell tropism, and host-viral interactions of SARS-CoV-2, we performed single-cell (sc) RNA sequencing (RNA-seq) of experimentally infected human bronchial epithelial cells (HBECs) in air-liquid interface (ALI) cultures over a time course. This revealed novel polyadenylated viral transcripts and highlighted ciliated cells as a major target at the onset of infection, which we confirmed by electron and immunofluorescence microscopy. Over the course of infection, the cell tropism of SARS-CoV-2 expands to other epithelial cell types including basal and club cells. Infection induces cell-intrinsic expression of type I and type III interferons (IFNs) and interleukin (IL)-6 but not IL-1. This results in expression of interferon-stimulated genes (ISGs) in both infected and bystander cells. This provides a detailed characterization of genes, cell types, and cell state changes associated with SARS-CoV-2 infection in the human airway.

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Grants

  1. T32 AI055403/NIAID NIH HHS
  2. /Wellcome Trust
  3. UL1 TR001863/NCATS NIH HHS
  4. /Howard Hughes Medical Institute
  5. R21 AI133440/NIAID NIH HHS
  6. K08 AI119139/NIAID NIH HHS
  7. R01 HL138540/NHLBI NIH HHS
  8. K08 AI128043/NIAID NIH HHS
  9. K08 HL136898/NHLBI NIH HHS
  10. F30 CA250249/NCI NIH HHS
  11. U19 AI089992/NIAID NIH HHS
  12. R01 AI141609/NIAID NIH HHS

MeSH Term

Adult
Bronchi
COVID-19
Cells, Cultured
Epithelium
Gene Expression
Humans
Immunity, Innate
Longitudinal Studies
SARS-CoV-2
Single-Cell Analysis
Transcriptome
Viral Tropism
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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