Persistence of an Infectious Form of SARS-CoV-2 After Protease Inhibitor Treatment of Permissive Cells In Vitro

Reports have described severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rebound in coronavirus disease 2019 (COVID-19) patients treated with nirmatrelvir, a 3CL protease inhibitor. The cause remains a mystery, although drug resistance, reinfection, and lack of adequate immune responses have been excluded. We now present virologic findings that provide a clue to the cause of viral rebound, which occurs in approximately 20% of the treated cases. Persistence of infectious SARS-CoV-2 was experimentally documented in vitro after treatment with nirmatrelvir or another 3CL protease inhibitor, but not with a polymerase inhibitor, remdesivir. This infectious form decayed slowly with a half-life of approximately 1 day, suggesting that its persistence could outlive the treatment course to reignite SARS-CoV-2 infection as the drug is eliminated. Notably, extending nirmatrelvir treatment beyond 8 days abolished viral rebound in vitro. Our findings point in a particular direction for future investigation of virus persistence and offer a specific treatment recommendation that should be tested clinically.