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

• Published in: PLoS biology Vol. 19; no. 3; p. e3001143
• Main Authors: Ravindra, Neal G, Alfajaro, Mia Madel, Gasque, Victor, Huston, Nicholas C, Wan, Han, Szigeti-Buck, Klara, Yasumoto, Yuki, Greaney, Allison M, Habet, Victoria, Chow, Ryan D, Chen, Jennifer S, Wei, Jin, Filler, Renata B, Wang, Bao, Wang, Guilin, Niklason, Laura E, Montgomery, Ruth R, Eisenbarth, Stephanie C, Chen, Sidi, Williams, Adam, Iwasaki, Akiko, Horvath, Tamas L, Foxman, Ellen F, Pierce, Richard W, Pyle, Anna Marie, van Dijk, David, Wilen, Craig B
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17-03-2021; Public Library of Science (PLoS)
• Subjects: Adult; Analysis; Biology and life sciences; Bronchi - pathology; Bronchi - virology; Cells, Cultured; Coronaviruses; COVID-19; COVID-19 - diagnosis; COVID-19 - immunology; COVID-19 - pathology; COVID-19 - virology; Epithelial cells; Epithelium; Epithelium - pathology; Epithelium - virology; Gene Expression; Gene sequencing; Humans; Immunity, Innate; Infections; Longitudinal Studies; Medicine and health sciences; Methods; Middle East respiratory syndrome; Mortality; Nucleocapsids; Polymerase chain reaction; Public health; Respiratory diseases; RNA sequencing; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Single-Cell Analysis - methods; Target recognition; Transcriptome; Transcriptomes; Tropism; Viral diseases; Viral Tropism; Virus diseases; United States; United States > US
• ISSN: 1545-7885; 1544-9173; 1545-7885
• DOI: 10.1371/journal.pbio.3001143

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.