SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Sungnak, W.; Huang, N.; Becavin, C.; Berg, M.; Queen, R.; Litvinukova, M.; Talavera-Lopez, C.; Maatz, H.; Reichart, D.; Sampaziotis, F.; Worlock, K. B.; Yoshida, M.; Barnes, J. L.; Banovich, N. E.; Barbry, P.; Brazma, A.; Collin, J.; Desai, T. J.; Duong, T. E.; Eickelberg, O.; Falk, C.; Farzan, M.; Glass, I.; Gupta, R. K.; Haniffa, M.; Horvath, P.; Hubner, N.; Hung, D.; Kaminski, N.; Krasnow, M.; Kropski, J. A.; Kuhnemund, M.; Lako, M.; Lee, H.; Leroy, S.; Linnarson, S.; Lundeberg, J.; Meyer, K. B.; Miao, Z.; Misharin, A. V.; Nawijn, M. C.; Nikolic, M. Z.; Noseda, M.; Ordovas-Montanes, J.; Oudit, G. Y.; Pe'Er, D.; Powell, J.; Quake, S.; Rajagopal, J.; Tata, P. R.; Rawlins, E. L.; Regev, A.; Reyfman, P. A.; Rozenblatt-Rosen, O.; Saeb-Parsy, K.; Samakovlis, C.; Schiller, H. B.; Schultze, J. L.; Seibold, M. A.; Seidman, C. E.; Seidman, J. G.; Shalek, A. K.; Shepherd, D.; Spence, J.; Spira, A.; Sun, X.; Teichmann, S. A.; Theis, F. J.; Tsankov, A. M.; Vallier, L.; van den Berge, M.; Whitsett, J.; Xavier, R.; Xu, Y.; Zaragosi, L. -E.; Zerti, D.; Zhang, H.; Zhang, K.; Rojas, M.; Figueiredo, F.

doi:10.1038/s41591-020-0868-6

We investigated SARS-CoV-2 potential tropism by surveying expression of viral entry-associated genes in single-cell RNA-sequencing data from multiple tissues from healthy human donors. We co-detected these transcripts in specific respiratory, corneal and intestinal epithelial cells, potentially explaining the high efficiency of SARS-CoV-2 transmission. These genes are co-expressed in nasal epithelial cells with genes involved in innate immunity, highlighting the cells’ potential role in initial viral infection, spread and clearance. The study offers a useful resource for further lines of inquiry with valuable clinical samples from COVID-19 patients and we provide our data in a comprehensive, open and user-friendly fashion at www.covid19cellatlas.org.