Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

Jonathan Daniel Ip; Allen Wing-Ho Chu; Wan-Mui Chan; Rhoda Cheuk-Ying Leung; Syed Muhammad Umer Abdullah; Yanni Sun; Kelvin Kai-Wang To

doi:10.1016/j.ebiom.2023.104559

Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

EBioMedicine. 2023 May:91:104559. doi: 10.1016/j.ebiom.2023.104559. Epub 2023 Apr 14.

Authors

Jonathan Daniel Ip¹, Allen Wing-Ho Chu¹, Wan-Mui Chan¹, Rhoda Cheuk-Ying Leung¹, Syed Muhammad Umer Abdullah², Yanni Sun², Kelvin Kai-Wang To³

Affiliations

¹ State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
² Department of Electrical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon, Special Administrative Region, China.
³ State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China. Electronic address: kelvinto@hku.hk.

Abstract

Background: Nirmatrelvir-ritonavir (Paxlovid) and ensitrelvir are 3-chymotrypsin-like cysteine protease (3CL^pro) inhibitors which have been approved for the treatment of COVID-19 in 2021 and 2022, respectively. Previous studies have identified 3CL^pro mutations that are associated with reduced susceptibility to these antivirals. The aim of the current study was to estimate the global prevalence of 3CL^pro inhibitor-resistant SARS-CoV-2 strains.

Methods: We compiled a list of 3CL^pro mutations which have been associated with nirmatrelvir or ensitrelvir resistance based on either viral replication or 3CL^pro activity assays, and determined their prevalence among 13.4 million sequences deposited in GISAID as of December 14, 2022, about 1 year after the approval of nirmatrelvir-ritonavir. We analyzed the prevalence for different time periods, SARS-CoV-2 lineages and geographical locations.

Findings: Overall, 0.5% (67,095/13,446,588) of the sequences contained at least one mutation that was shown to affect the inhibitory activity of nirmatrelvir or ensitrelvir on viral replication or 3CL^pro activity. We did not observe any increasing trend of resistance after the widespread clinical use of nirmatrelvir-ritonavir. G15S (2070 per million) and T21I (1386 per million) were the most prevalent mutations, and these mutations were dominant in some SARS-CoV-2 lineages. E166V and S144E, previously shown to affect the inhibitory activity of nirmatrelvir on viral replication or protease activity by > 100-folds, were found in <1 per million sequences.

Interpretation: Our data suggest that 3CL^pro inhibitor resistance is currently rare. However, continuous global genotypic and phenotypic surveillance would be crucial in the early detection of resistant mutants.

Funding: Richard and Carol Yu, May Tam Mak Mei Yin, The Shaw Foundation Hong Kong, Michael Tong, Marina Lee, Government Consultancy Service, the Emergency Key Program of Guangzhou Laboratory (See acknowledgements for full list).

Keywords: Antiviral resistance; COVID-19; Ensitrelvir; Nirmatrelvir; Protease inhibitor; SARS-CoV-2.

MeSH terms

Antiviral Agents / pharmacology
Antiviral Agents / therapeutic use
COVID-19* / epidemiology
Endopeptidases
Humans
Mutation
Peptide Hydrolases*
Prevalence
Ritonavir
SARS-CoV-2 / genetics

Substances

Peptide Hydrolases
nirmatrelvir and ritonavir drug combination
Ritonavir
ensitrelvir
Endopeptidases
Antiviral Agents