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 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, Tamás L. Horváth, Ellen F. Foxman, Richard W. Pierce, Anna Marie Pyle, David van Dijk, Craig B. Wilen
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.