Genotyping of hepatitis C virus by Taqman real-time PCR

J Clin Virol. 2005 Oct;34(2):108-14. doi: 10.1016/j.jcv.2005.02.002.


Background: Genotype of hepatitis C virus (HCV) is of major importance for the outcome of treatment. The response rate is considerably lower for genotype 1, the predominant genotype in western countries.

Objectives: To develop and evaluate a new, simple method for genotyping of HCV based on real-time polymerase chain reaction (PCR) and Taqman probes targeting the 5' non-coding region.

Study design: The method was compared with Innolipa on 220 serum samples representing genotypes 1-4, and was applied on a further 614 clinical samples.

Results: Taqman typing of the 220 samples showed genotype 1 in 69, genotype 2 in 58, genotype 3 in 57 and genotype 4 in 19, while 17 were non-reactive. There was a complete concordance with Innolipa with the exception of seven samples, which were of genotype 1 by Taqman, but genotype 4 by Innolipa. Sequencing of these samples showed a subtype 4 variant which differed at two positions compared with subtypes 4b/c/d, which are targeted by the probe. By adding a modified probe, these genotype 4 variants could also be identified. Out of 614 consecutive clinical samples, 524 could be typed by the Taqman assay; 45.2% were genotype 1, 19.3% genotype 2, 33.8% genotype 3 and 1.7%, genotype 4.

Conclusion: The method was overall accurate and provides an attractive alternative for genotyping because processing time and costs are significantly reduced. Inclusion of probes targeting genotypes 5 and 6 is required for the method to be useful in areas where these genotypes are present.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions / genetics
  • DNA Primers
  • Genotype
  • Hepacivirus / classification*
  • Hepacivirus / genetics*
  • Humans
  • Phylogeny
  • Polymerase Chain Reaction / methods*
  • RNA, Messenger / genetics
  • RNA, Viral / genetics
  • Sensitivity and Specificity
  • Sequence Analysis, DNA


  • 5' Untranslated Regions
  • DNA Primers
  • RNA, Messenger
  • RNA, Viral