Large scale analysis of the SARS-CoV-2 main protease reveals marginal presence of nirmatrelvir-resistant SARS-CoV-2 Omicron mutants in Ontario, Canada, December 2021-September 2023.

Abstract

In response to the COVID-19 pandemic, a new oral antiviral called nirmatrelvir-ritonavir (PaxlovidTM) was authorized for use in Canada in January 2022. In vitro studies have reported mutations in Mpro protein that may be associated with the development of nirmatrelvir resistance. To survey the prevalence, relevance and temporal patterns of Mpro mutations among SARS-CoV-2 Omicron lineages in Ontario, Canada. A total of 93,082 Mpro gene sequences from December 2021 to September 2023 were analyzed. Reported in vitro Mpro mutations were screened against our database using in-house data science pipelines to determine the nirmatrelvir resistance. Negative binomial regression was conducted to analyze the temporal trends in Mpro mutation counts over the study time period. A declining trend was observed in non-synonymous mutations of Mpro sequences, showing a 7.9% reduction (95% CI: 6.5%-‬9.4%; p<0.001) every 30 days. The P132H was the most prevalent mutation (higher than 95%) in all Omicron lineages. In vitro nirmatrelvir-resistant mutations were found in 3.12% (n=29/929) Omicron lineages with very low counts, ranging from one to 19. Only two mutations, A7T (n=19) and M82I (n=9), showed temporal presence among the BA.1.1 in 2022 and the BQ.1.2.3 in 2022, respectively. The observations suggest that, as of September 2023, no significant or widespread resistance to nirmatrelvir has developed among SARS-CoV-2 Omicron variants in Ontario. This study highlights the importance of creating automated monitoring systems to track the emergence of nirmatrelvir-resistant mutations within the SARS-CoV-2 virus, utilizing genomic data generated in real-time.