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

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.

Dynamic innate immune response determines susceptibility to SARS-CoV-2 infection and early replication kinetics

“…SARS-CoV-2 (USA-WA1/2020; BEI Resources) was generously provided by the Wilen laboratory (Yale University, New Haven, CT). Virus was cultured on Vero E6 cells, a filtered supernatant was used as the virus stock, and titer was determined by plaque assay as described previously ( Ravindra et al, 2021 ). We confirmed that the cell lysate/supernatant did not contain significant levels of IFN or other molecules that activate ISG expression by mock-inoculating BEAS2B cells with UV-inactivated stocks.…”

“…Innate immune responses such as the antiviral IFN response are often critical for curtailing early viral replication at mucosal surfaces; however, recent work shows that SARS-CoV-2 antagonizes and delays this response ( Banerjee et al, 2020b ; Blanco-Melo et al, 2020 ; Konno et al, 2020 ; Xia et al, 2020 ; Zhou et al, 2020 ; Martin-Sancho et al, 2021 ; Ravindra et al, 2021 ). Nonetheless, there is strong evidence that the IFN response protects against severe COVID-19, from both genetic and autoantibody studies, and from in vitro studies showing protection of cells using recombinant IFNs.…”

A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

“…Two single cell sequencing data sets representing infected and non-infected cells directly derived from human samples 31 and cultured human bronchial epithelial cells 32 (HBECs) were used to identify the areas of the COVID-19 PHARMACOME responding at gene expression level to SARS-CoV-2 infection. Details of the gene expression data processing and mapping are available in the supplementary material (see section “Gene expression data analysis”).…”

In Vitro Lung Models and Their Application to Study SARS-CoV-2 Pathogenesis and Disease

“…In addition to gas exchange, the human airway epithelium has been recognized to function as the main entry point for several pathogens. Notably, human airway epithelial cells represent a primary target of coronaviruses, including the highly transmissible and pathogenic Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) [ 4 , 5 , 6 ]. To defend itself from pathogens such as SARS-CoV-2, epithelial cells have adapted numerous strategies that include tightly packed epithelial cells forming tight junctions, mucosal epithelium trapping invading pathogens in the secreted mucus barrier and the expression of pattern-recognition receptors.…”