Performance of Three Common Hepatitis C Virus (HCV) Genotyping Assays for Identification of HCV Genotype 2/1 Chimeras

J Clin Microbiol. 2019 Jun 25;57(7):e00060-19. doi: 10.1128/JCM.00060-19. Print 2019 Jul.


Besides seven major hepatitis C virus (HCV) genotypes (GT), a number of intergenotypic recombinant strains have been described. These so-called chimeras combine genetic characteristics of different HCV genotypes. However, correct genotype classification is important, as choice and duration of direct-acting antiviral (DAA) treatment is mainly based on the viral genotype. Therefore, misclassification of chimeras might lead to suboptimal treatment of patients infected with these strains. For example, 2k/1b chimeras are typically described as HCV genotype 2 strains by commercially available hybridization assays, but real-time PCR-based tests recognizing another HCV region might be more suitable for correct chimera detection. In this study, the analytic capacity of the hybridization-assay Versant HCV Genotype 2.0 (LiPA 2.0) and the real-time PCR-based-assays cobas HCV GT and Abbott RealTime HCV Genotype II were tested in a selected cohort of 230 patients infected with HCV genotype 1 (n = 53) and 2 (n = 177) and 48 patients infected with HCV 2/1 chimeric strains. While the Versant HCV Genotype 2.0 (LiPA 2.0) assay failed to identify chimeras in all of the patients (48/48, 100%), cobas HCV GT and Abbott HCV Genotype II assays identified chimeras correctly in 90% (43/48) and 65% (31/48) of the cases, respectively. In conclusion, while the hybridization-based Versant HCV Genotype 2.0 (LiPA 2.0) assay seems to be unsuitable for detection of HCV 2/1 chimeras, use of the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II led to a higher rate of chimera detection.

Keywords: 2k/1b; assay; chimera; hepatitis C virus; recombinant.

Publication types

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

MeSH terms

  • Genotype
  • Genotyping Techniques / methods*
  • Hepacivirus / genetics*
  • Hepacivirus / isolation & purification*
  • Hepatitis C / diagnosis*
  • Humans
  • Molecular Diagnostic Techniques / methods*
  • Nucleic Acid Hybridization
  • RNA, Viral / blood
  • RNA, Viral / genetics
  • Reagent Kits, Diagnostic
  • Real-Time Polymerase Chain Reaction
  • Retrospective Studies
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Viral Proteins / genetics


  • RNA, Viral
  • Reagent Kits, Diagnostic
  • Viral Proteins