Construction and characterization of Genotype-3 hepatitis C virus replicon revealed critical genotype-3-specific polymorphism for drug resistance and viral fitness

Mingzhe Guo; Jie Lu; Tianyu Gan; Xiaogang Xiang; Yongfen Xu; Qing Xie; Jin Zhong

doi:10.1016/j.antiviral.2019.104612

Construction and characterization of Genotype-3 hepatitis C virus replicon revealed critical genotype-3-specific polymorphism for drug resistance and viral fitness

Antiviral Res. 2019 Nov:171:104612. doi: 10.1016/j.antiviral.2019.104612. Epub 2019 Sep 19.

Authors

Mingzhe Guo¹, Jie Lu², Tianyu Gan³, Xiaogang Xiang², Yongfen Xu⁴, Qing Xie², Jin Zhong⁵

Affiliations

¹ CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China; Shanghai Tech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
² Department of Infectious Disease, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
³ CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
⁴ CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China.
⁵ CAS Key Laboratory of Molecular Virology and Immunology, Unit of Viral Hepatitis, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China; Shanghai Tech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: jzhong@ips.ac.cn.

PMID: 31542377
DOI: 10.1016/j.antiviral.2019.104612

Abstract

Hepatitis C virus (HCV), a major causative agent of chronic hepatitis, is a positive-stranded RNA virus and has a high degree of genetic diversity due to its error-prone RNA-dependent RNA polymerase. Development of direct-acting antiviral agents (DAAs) has greatly improved the therapeutic outcome of chronic hepatitis C patients. However, naturally existing resistance-associated variants (RAVs) or occurrence of resistance-associated substitutions (RASs) in the HCV genome may impose a challenge to the long-term success of the DAA-based therapies. Genotype-3 HCV is the most difficult genotype to treat by DAAs, but the underlying molecular mechanisms remain to be explored. Here we developed a novel genotype-3a subgenomic replicon PR87A7 by screening a HCV cDNA pool amplified from a patient serum RNA. PR87A7 replicon displayed strong resistance to anti-NS3 DAAs, mainly owing to a genotype-3-specific polymorphism 168Q in NS3. Introduction of NS3 168Q into a genotype-2a JFH1 strain rendered resistance to anti-NS3 DAAs while greatly diminished the viral replication, and yet this fitness defect can be rescued by additional genotype-3-specific polymorphism. In conclusion, we developed a novel genotype-3a subgenomic replicon by a functional screening approach, and revealed genotype-3-specfic amino acid residues that confer resistance to anti-NS3 DAAs while retaining viral fitness.

Keywords: Antiviral resistance; Direct-acting antiviral agents; Genotype-3; Hepatitis C virus; Replicon.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Substitution
Cell Line, Tumor
Dose-Response Relationship, Drug
Drug Resistance, Viral*
Genetic Fitness
Genome, Viral
Genotype*
Hepacivirus / classification
Hepacivirus / drug effects*
Hepacivirus / genetics*
Hepatitis C / drug therapy
Hepatitis C / virology*
Humans
Phylogeny
Polymorphism, Genetic*
Viral Nonstructural Proteins / genetics
Virus Replication / drug effects*

Substances

NS3 protein, hepatitis C virus
Viral Nonstructural Proteins