Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance

Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20509-13. doi: 10.1073/pnas.1105797108. Epub 2011 Dec 1.


The development of resistance to direct-acting antivirals (DAAs) targeting the hepatitis C virus (HCV) can compromise therapy. However, mechanisms that determine prevalence and frequency of resistance-conferring mutations remain elusive. Here, we studied the fidelity of the HCV RNA-dependent RNA polymerase NS5B in an attempt to link the efficiency of mismatch formation with genotypic changes observed in vivo. Enzyme kinetic measurements revealed unexpectedly high error rates (approximately 10(-3) per site) for G:U/U:G mismatches. The strong preference for G:U/U:G mismatches over all other mistakes correlates with a mutational bias in favor of transitions over transversions. Deep sequencing of HCV RNA samples isolated from 20 treatment-naïve patients revealed an approximately 75-fold difference in frequencies of the two classes of mutations. A stochastic model based on these results suggests that the bias toward transitions can also affect the selection of resistance-conferring mutations. Collectively, the data provide strong evidence to suggest that the nature of the nucleotide change can contribute to the genetic barrier in the development of resistance to DAAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antiviral Agents / pharmacology
  • Base Sequence
  • DNA Mutational Analysis*
  • Drug Resistance, Viral*
  • Genetic Variation
  • Genotype
  • Hepacivirus / genetics*
  • Kinetics
  • Models, Genetic
  • Models, Theoretical
  • Molecular Sequence Data
  • Mutation
  • Sequence Analysis, DNA
  • Stochastic Processes
  • Viral Nonstructural Proteins / genetics


  • Antiviral Agents
  • Viral Nonstructural Proteins
  • NS-5 protein, hepatitis C virus