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 ϭ 53) and 2 (n ϭ 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 . 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.

Pangenotypic direct‐acting antiviral agents for mixed genotype hepatitis C infection: A real‐world effectiveness analysis

“…26 The Cobas HCV GT assay using three different target regions in the HCV genome (50-UTR, Core, and NS5B) that was employed at our institution was demonstrated to have similar or slightly higher accuracy for mixed HCV genotype detection compared with other commercial methods. 27 Even though, genotype was indeterminate in 44% (48/108) of our patients. We performed in-house sequencing for core region for those with indeterminate results.…”