Nucleotide polymorphisms in the 5'-UTR region of HCV can affect the ability of two widely used assays to assign an HCV genotype

J Virol Methods. 2013 Oct;193(1):205-8. doi: 10.1016/j.jviromet.2013.06.002. Epub 2013 Jun 19.


Determination of hepatitis C virus genotype is crucial for establishing the duration of antiviral therapy and predicts response to treatment. In this study, consecutive serum samples collected from two patients with chronic hepatitis C infection were tested by two assays used widely, the Abbott RealTime HCV Genotype II and the Versant HCV Genotype 2.0 assays, in order to assign a genotype to the virus. The obtained results were verified by phylogenetic analysis of the NS5B region and sequencing of the 5'-UTR of the viral genome. Testing of the serum samples from both patients gave an indeterminate result with the Abbott assay. By contrast, the Versant assay gave an indeterminate result for one patient and identified an HCV-2b subtype in the other patient. Phylogenetic analysis of the NS5B region confirmed the presence of HCV-2b in this latter patient and disclosed the presence of HCV-3h in the other patient. Sequencing of the 5'-UTR revealed the presence of nucleotide changes at positions -166 and -119 of HCV-2b, and at positions -138, -108 and -99 of HCV-3h. Nucleotide mutations located in the 5'-untraslated region of hepatitis C virus may impair the ability of commercial assays to assign an HCV genotype.

Keywords: HCV genotyping; HCV polymorphisms; HCV real-time; InnoLipa.

Publication types

  • Case Reports
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions*
  • Aged
  • Female
  • Genotype
  • Hepacivirus / classification*
  • Hepacivirus / genetics*
  • Hepatitis C, Chronic / diagnosis
  • Hepatitis C, Chronic / virology*
  • Humans
  • Male
  • Middle Aged
  • Molecular Diagnostic Techniques / methods*
  • Phylogeny
  • Polymorphism, Genetic*
  • Sequence Analysis, DNA
  • Viral Nonstructural Proteins / genetics
  • Virology / methods*


  • 5' Untranslated Regions
  • Viral Nonstructural Proteins
  • NS-5 protein, hepatitis C virus