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

PLoS Biol. 2021 Mar 17;19(3):e3001143. doi: 10.1371/journal.pbio.3001143. eCollection 2021 Mar.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Bronchi / pathology*
  • Bronchi / virology
  • COVID-19 / diagnosis*
  • COVID-19 / immunology
  • COVID-19 / pathology
  • COVID-19 / virology
  • Cells, Cultured
  • Epithelium / pathology
  • Epithelium / virology
  • Gene Expression*
  • Humans
  • Immunity, Innate
  • Longitudinal Studies
  • SARS-CoV-2 / genetics
  • SARS-CoV-2 / isolation & purification*
  • Single-Cell Analysis / methods*
  • Transcriptome
  • Viral Tropism