Abstract

Nirmatrelvir, an oral antiviral agent that targets a SARS-CoV-2 main protease (3CLpro), is clinically useful against infection with SARS-CoV-2 including its omicron variants. Since most omicron subvariants have reduced sensitivity to many monoclonal antibody therapies, potential SARS-CoV-2 resistance to nirmatrelvir is a major public health concern. Several amino acid substitutions have been identified as being responsible for reduced susceptibility to nirmatrelvir. Among them, we selected L50F/E166V and L50F/E166A/L167F in the 3CLpro because these combinations of substitutions are unlikely to affect virus fitness. We prepared and characterized delta variants possessing Nsp5-L50F/E166V and Nsp5-L50F/E166A/L167F. Both mutant viruses showed decreased susceptibility to nirmatrelvir and their growth in VeroE6/TMPRSS2 cells was delayed. Both mutant viruses showed attenuated phenotypes in a male hamster infection model, maintained airborne transmissibility, and were outcompeted by wild-type virus in co-infection experiments in the absence of nirmatrelvir, but less so in the presence of the drug. These results suggest that viruses possessing Nsp5-L50F/E166V and Nsp5-L50F/E166A/L167F do not become dominant in nature. However, it is important to closely monitor the emergence of nirmatrelvir-resistant SARS-CoV-2 variants because resistant viruses with additional compensatory mutations could emerge, outcompete the wild-type virus, and become dominant.

Resistance to nirmatrelvir, an oral antiviral agent that targets SARS-CoV-2 and is clinically useful against infection with Omicron variants, is currently not well understood. In this study, the authors characterize mutant viruses with reduced sensitivity to nirmatrelvir in vitro and in vivo.

Details

Title
In vitro and in vivo characterization of SARS-CoV-2 strains resistant to nirmatrelvir
Author
Kiso, Maki 1 ; Furusawa, Yuri 2 ; Uraki, Ryuta 2   VIAFID ORCID Logo  ; Imai, Masaki 3 ; Yamayoshi, Seiya 3   VIAFID ORCID Logo  ; Kawaoka, Yoshihiro 4   VIAFID ORCID Logo 

 University of Tokyo, Division of Virology, Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X) 
 University of Tokyo, Division of Virology, Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); National Center for Global Health and Medicine Research Institute, The Research Center for Global Viral Diseases, Tokyo, Japan (GRID:grid.45203.30) (ISNI:0000 0004 0489 0290) 
 University of Tokyo, Division of Virology, Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); National Center for Global Health and Medicine Research Institute, The Research Center for Global Viral Diseases, Tokyo, Japan (GRID:grid.45203.30) (ISNI:0000 0004 0489 0290); University of Tokyo, International Research Center for Infectious Diseases, Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X) 
 University of Tokyo, Division of Virology, Institute of Medical Science, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); National Center for Global Health and Medicine Research Institute, The Research Center for Global Viral Diseases, Tokyo, Japan (GRID:grid.45203.30) (ISNI:0000 0004 0489 0290); The University of Tokyo Pandemic Preparedness, Infection and Advanced Research Center, Tokyo, Japan (GRID:grid.26999.3d) (ISNI:0000 0001 2151 536X); University of Wisconsin–Madison, Department of Pathobiological Sciences, School of Veterinary Medicine, Madison, USA (GRID:grid.14003.36) (ISNI:0000 0001 2167 3675) 
Pages
3952
Publication year
2023
Publication date
2023
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2832906406
Copyright
© The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.