An Investigation of Nirmatrelvir (Paxlovid) Resistance in SARS-CoV-2 M.

The high throughput YESS 2.0 platform was used to screen a large library of SARS-CoV-2 M variants in the presence of nirmatrelvir. Of the 100 individual most prevalent mutations identified in the screen and reported here, the most common were E166V, L27V, N142S, A173V, and Y154N, along with their various combinations.

High-Resolution Substrate Specificity Profiling of SARS-CoV-2 M; Comparison to SARS-CoV M.

The SARS-CoV-2 M protease from COVID-19 cleaves the pp1a and pp2b polyproteins at 11 sites during viral maturation and is the target of Nirmatrelvir, one of the two components of the frontline treatment sold as Paxlovid. We used the YESS 2.0 platform, combining protease and substrate expression in the yeast endoplasmic reticulum with fluorescence-activated cell sorting and next-generation sequencing, to carry out the high-resolution substrate specificity profiling of SARS-CoV-2 M as well as the related SARS-CoV M from SARS 2003.