Evaluation of in-house and commercial genotyping assays for molecular typing of hepatitis C virus in Hong Kong

Abstract

This study aims to evaluate genotyping assays for hepatitis C virus (HCV). An in-house nucleic acid sequencing method is performed in parallel with the Roche Linear Array HCV genotyping test on 73 HCV-positive (66 clinical samples and seven proficiency testing quality control samples) and 12 HCV-negative samples (11 clinical samples and one proficiency testing sample). The performance of the in-house method was comparable with that of the Roche assay (concordance rate: 89.4%). Discordant results included four mixed infections missed by the in-house method, two false-negatives with the Roche assay, and three discrepant results. The in-house method exhibited a higher resolution (subtype vs. genotype level) at a lower running cost (25% of the commercial assay). The in-house method was also used to genotype 375 HCV clinical isolates to determine the genotypic distribution of HCV in Hong Kong between 2005 and 2008. A total of 441 (52.8%) clinical isolates proved to be genotype 1, which shows a poorer response to interferon therapy. Genotype 6 was the next most common (32.0%). Prevalence of genotypes 2 and 3 was 7.7% and 6.6%, respectively, and prevalence of genotypes 4 and 5 was 0.9% and 0%, respectively. Although the in-house nucleic acid sequencing method failed to detect a few cases of mixed HCV infection, its high resolution and low running cost make it suitable for surveillance and outbreak investigation.

Utilization of a Duplex HybProbe Real-Time PCR to Detect and Estimate IL-28B Polymorphisms Prevalence among HIV/HCV Co-infected Patients in Hong Kong

“…Conversely the prevalence of HCV genotype 1, 3 and 6 were roughly similar, which was inconsistent with previous local studies, suggesting that the HIV/HCV co-infection might predominantly affect intravenous drug users with distinct epidemiological and transmission pattern. [10,12].…”

“…For assay evaluation, IL-28B polymorphisms of 46 samples were further confirmed by Sanger sequencing. HCV viral load was quantitated by Abbott m2000 RealTime HCV assay (Abbott Laboratories, USA) while HIV-1 and HCV genotypes were confirmed by our in-house methods [9,10]. Statistical analysis was performed by Graphpad Prism version 6(Graphpad software, California, US).…”

Laboratory Methods in Liver Pathology Diagnosis

“…Assays targeting other regions in addition to the 5′UTR have been nowasays developed for the proper discriminate between subtypes 1a and 1b. [27] From another scientific perspective, the Abbott RealTime HCV Genotype II (Abbott Molecular) targets the 5'UTR and NS5B regions. This assay is based on a single-step real-time RT-PCR with labeled genotype-/subtype-specific probes with a god end reffering to the minimizes contamination but with amplified products.…”

Hepatitis C virus: Virology, diagnosis and treatment

“…HCV genotyping assays approved for in vitro diagnostic use are also commercially available [23,49] . The Linear Array HCV Genotyping Test (Roche Molecular Systems) targets the 5'UTR [71] . This assay is based on conventional PCR amplification followed by reverse hybridization onto membrane strips containing specific probes.…”