Single cell resolution of SARS-CoV-2 tropism, antiviral responses, and susceptibility to therapies in primary human airway epithelium

The human airway epithelium is the initial site of SARS-CoV-2 infection. We used flow cytometry and single cell RNAseq to understand how the heterogeneity of this diverse cell population contributes to elements of viral tropism and pathogenesis, antiviral immunity, and treatment response to remdesivir. We found that, while a variety of cell types are susceptible to infection, ciliated cells are a predominant cell target for SARS-CoV-2. Remdesivir treatment effectively inhibited viral replication across cell types, and blunted hyperinflammatory responses. We also found that heavily infected epithelial cells demonstrate impaired IFN signaling and express abundant IL-6, a potential mediator of COVID-19 pathogenesis. Basal layer of medium was replaced with infection media (DMEM with 2% FBS, 100 U/mL penicillin and streptomycin, 10 mM HEPES, 0.1 mM nonessential amino acids, 4 mM L-glutamate, and 1mM sodium pyruvate). Wells were left untreated, or treated with 100 ng of IFN-b or 0.1 mM remdesivir in the basal compartment for 1 hr prior to infection. For infection, SARS-CoV-2 strain 2019-nCoV/USA_WA1/2020 (provided by World Reference Center for Emerging Viruses and Arboviruses at the University of Texas Medical Branch) and icSARS-CoV-2-mNG, were added directly to the apical layer of cells for 1 hr at 37°C with rocking every 10 min. The virus was removed from the apical compartment and cells were incubated at 37°C until harvest.