Performance of three common HCV genotyping assays for identification of HCV genotype 2/1 chimeras

Besides six major HCV genotypes a number of inter-genotypic 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 antivirals (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), the real-time PCR-based-assays cobas® HCV GT and Abbott® Realtime HCV-Genotype-II were tested in a selected cohort of 230 HCV genotype 1 (n=53) and 2 (n=177) infected patients 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.