Cell-type specific effects of SARS-CoV-2 P252L mutation on nirmatrelvir sensitivity

The SARS-CoV-2 main protease (NSP5) is the target of the FDA approved Nirmatrelvir (NTV) antiviral. Substitutions in NSP5, such as the P252L mutation, have been reported in clinical isolates and raise questions regarding its potential role in drug resistance. Here, we show that the P252L effect on NTV susceptibility is dependent on the culture model. The mutation arises spontaneously in VeroE6 cells without treatment but does not appear in Calu-3 cells. It becomes enriched under NTV pressure in both VeroE6 cells and Human Airway Epithelium (HAE) cultures but leads to a significant increase in EC₅₀ values only in VeroE6 cells. This discrepancy between allelic selection and functional resistance highlights the importance of using appropriate culture models when evaluating resistance mechanisms.