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

Abstract

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.

FIG 1

Percentage of chimeras identified by the hybridization-based assay Versant HCV Genotype 2.0 and the real-time PCR-based assays cobas HCV GT and Abbott RealTime HCV Genotype II.

FIG 2

(a) Overview of genotype and subtype determination by the hybridization-based assay Versant HCV Genotype 2.0 and the real-time PCR-based assay cobas HCV GT in comparison to that by population-based sequencing. If genotype or subtype were consistent with sequencing results, calls were termed consistent; otherwise, the subtype was refined by the sequencing analysis. (b and c) Detailed subtype determination by the hybridization-based assay Versant HCV Genotype 2.0 (b) and by the real-time PCR-based-assay cobas HCV GT (c) in comparison to that by population-based sequencing. If subtype was consistent with sequencing results, calls were termed consistent; otherwise, the subtype was refined by the sequencing analysis.

FIG 3

Schematic representation of viral recombination in HCV 2k/1b and targets for genotype typing/subtyping by the assays Versant HCV Genotype 2.0 (LiPA 2.0), cobas HCV GT, and Abbott RealTime HCV Genotype II. UTR, untranslated region; E, envelope protein; NS, nonstructural protein; gt, genotype.