Development of a robust hepatitis C virus genotyping assay for effective clinical management

Abstract

Hepatitis C Virus (HCV) genotyping is an important tool in the initiation of therapy and the selection of the most appropriate treatment regime for hepatitis C. Here we developed an in-house HCV genotyping assay based on the real-time Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technology for the identification of the genotype and subtype of the virus. The real-time RT-PCR method targets both the 5’UTR and NS5B regions of the HCV genome than the conventionally used 5’UTR region for more accurate genotyping. We evaluated the performance of the inhouse genotyping assay by investigating the concordance with another commercially available genotyping assay, the inno-LiPa HCV II Reverse Hybridization Assay. 11 routine patient specimens were tested and the results were compared with the inno- LiPa HCV II Reverse Hybridization Assay. Among the 11 patient specimens, the inhouse HCV genotyping assay correctly identified 3 genotype 1a samples, 2 genotype 1b samples, 2 genotype 2 samples, 1 genotype 3 sample, 2 genotype 4 samples and 1 untyped sample. Therefore, genotype calls by both methods were 90.9% concordant. In conclusion, the in-house HCV genotyping assay based on real-time RT-PCR holds much promise in offering a more robust and accurate method than others for the identification of the genotypes and subtypes of the hepatitis C virus.