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Updated: Mar 14, 2026
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
Protease Inhibitor Resistance Remains Even After Mutant Strains Become Undetectable by Deep Sequencing
Hiromi Kan1,2, Michio Imamura1,2, Takuro Uchida1,2
1Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences.
Background:
Although treatment-emergent NS3/4A protease inhibitor (PI)-resistant variants typically decrease in frequency after cessation of PI therapy in patients with chronic hepatitis C virus (HCV) infection, HCV susceptibility to PIs in patients who have not responded to previous PI therapy has not been addressed.
Methods:
Patients with chronic HCV genotype 1 infection were treated either with simeprevir plus interferon or with daclatasvir plus asunaprevir. Frequencies of drug-resistant mutations among patients with treatment failure were analyzed by deep sequencing. Human hepatocyte chimeric mice were injected with serum samples obtained from either treatment-naive patients or nonresponders to treatment with daclatasvir plus asunaprevir and then were treated with simeprevir and sofosbuvir.
Results:
Virological response to daclatasvir plus asunaprevir treatment was significantly lower in patients with simeprevir treatment failure as compared to those without previous treatment. Deep-sequencing analysis showed that the frequency of PI treatment-emergent NS3-D168 mutations gradually decreased and were completely replaced by wild-type genes after cessation of therapy. However, mice injected with serum obtained from a patient with PI treatment failure rapidly developed NS3-D168 mutations at significantly higher frequencies following either simeprevir or sofosbuvir treatment.
Conclusions:
The virological response to daclatasvir plus asunaprevir treatment was low in patients with simeprevir treatment failure. PI resistance remains even after disappearance of mutant strains by deep sequencing.
Insights
Hepatitis C virus (HCV) protease inhibitor (PI) resistance persists in nonresponders, even when resistant mutations are undetectable. This highlights the need for effective treatment strategies for patients with prior PI treatment failure.
Area of Science:
- Hepatology
- Virology
- Molecular Biology
Background:
- Hepatitis C virus (HCV) protease inhibitor (PI) resistance typically declines after therapy cessation.
- Limited data exists on HCV susceptibility to PIs in patients with prior treatment failure.
Purpose of the Study:
- To investigate HCV susceptibility to PIs in patients with prior treatment failure.
- To analyze the persistence of PI-resistant mutations in chronic HCV genotype 1 infection.
Main Methods:
- Patients with chronic HCV genotype 1 received simeprevir/interferon or daclatasvir/asunaprevir.
- Deep sequencing analyzed drug-resistant mutation frequencies in treatment failures.
- Chimeric mice models assessed viral response to PI treatment after inoculation with patient serum.
Main Results:
- Lower virological response to daclatasvir/asunaprevir observed in patients with prior simeprevir failure.
- PI-resistant NS3-D168 mutations decreased post-therapy but rapidly re-emerged in mice from PI-experienced patients.
- Mice models showed rapid development of NS3-D168 mutations with simeprevir or sofosbuvir treatment.
Conclusions:
- HCV virological response is poor in patients with prior simeprevir treatment failure.
- Protease inhibitor resistance persists in HCV, detectable even after deep sequencing shows disappearance of mutant strains.
