SARS-CoV-2 Reverse Genetics Reveals a Variable Infection Gradient in the Respiratory Tract

Hou, Yixuan J.; Okuda, Kenichi; Edwards, Caitlin E.; Martinez, David R.; Asakura, Takanori; Dinnon, Kenneth H.; Kato, Takafumi; Lee, Rhianna E.; Yount, Boyd L.; Mascenik, Teresa M.; Chen, Gang; Olivier, Kenneth N.; Ghio, Andrew; Tse, Longping V.; Leist, Sarah R.; Gralinski, Lisa E.; Schäfer, Alexandra; Dang, Hong; Gilmore, Rodney; Nakano, Satoko; Sun, Ling; Fulcher, M. Leslie; Livraghi-Butrico, Alessandra; Nicely, Nathan I.; Cameron, Mark; Cameron, Cheryl; Kelvin, David J.; de Silva, Aravinda; Margolis, David M.; Markmann, Alena; Bartelt, Luther; Zumwalt, Ross; Martinez, Fernando J.; Salvatore, Steven P.; Borczuk, Alain; Tata, Purushothama R.; Sontake, Vishwaraj; Kimple, Adam; Jaspers, Ilona; O’Neal, Wanda K.; Randell, Scott H.; Boucher, Richard C.; Baric, Ralph S.

Summary The mode of acquisition and causes for the variable clinical spectrum of COVID-19 remain unknown. We utilized a reverse genetics system to generate a GFP reporter virus to explore SARS-CoV-2 pathogenesis and a luciferase reporter virus to demonstrate sera collected from SARS and COVID-19 patients exhibited limited cross-CoV neutralization. High-sensitivity RNA in situ mapping revealed the highest ACE2 expression in the nose with decreasing expression throughout the lower respiratory tract, paralleled by a striking gradient of SARS-CoV-2 infection in proximal (high) vs distal (low) pulmonary epithelial cultures. COVID-19 autopsied lung studies identified focal disease and, congruent with culture data, SARS-CoV-2-infected ciliated and type 2 pneumocyte cells in airway and alveolar regions, respectively. These findings highlight the nasal susceptibility to SARS-CoV-2 with likely subsequent aspiration-mediated virus seeding to the lung in SARS-CoV-2 pathogenesis. These reagents provide a foundation for investigations into virus-host interactions in protective immunity, host susceptibility, and virus pathogenesis.