Typing of Hepatitis C Virus by a New Method Based on Restriction Fragment Length Polymorphism

Abstract

A new restriction fragment length polymorphism (RFLP) analysis has been developed for hepatitis C virus (HCV) typing in the viral 5′ non-coding region and contiguous core region. These genomic sequences were chosen for the relative nucleotide homology among different genotypes and for the presence of polymorphic sites. By employing two endonucleases (AccI and MboI) and, in some instances, a third one (EcoRII), we can unambiguously and reproducibly distinguish between genotypes and subtypes 1a, 1b, 1c, 2a, 2c, 2b, 3a, 3b, 4a, 5a and 6a. The method was applied for diagnosing two Italian groups of HCV-infected individuals reflecting a randomly collected population and a group of intravenous drug users. The accuracy of this method has been validated by comparison with INNOLiPA and by sequencing. Our approach represents an improvement over previous RFLP methods, since typing is accurate and simpler.

Determination of HCV genotype by direct sequence analysis of quantitative PCR products

“…Several alternative HCV typing procedures have therefore been suggested, usually based on the analysis of PCR products by hybridization with genotype-specific probes [Stuyver et al, 1996;Viazov et al, 1997], or restriction length polymorphism [Thiers et al, 1997;Buoro et al, 1999].…”

Distribution Pattern of Hepatitis C Virus Genotypes and Correlation with Viral Load and Risk Factors in Chronic Positive Patients

“…The limitations of the test INNOLiPA are well known, especially concerning its inability to correctly discriminate the subtypes 2a and 2c of the genotype 2 and subtype 1c of genotype 1, as demonstrated using a restriction fragment length polymorphism (RFLP) analysis [32]. Anyway, its degree of specificity is similar to that of RFLP analysis and, as previously reported, comparable to that of the direct sequencing test Trugene, with an accuracy of 76 and 74%, respectively, even though the INNOLiPA confirms its less subtype discriminating power in subtyping genotype 2 [33,34].…”

Interspousal transmission of hepatitis C in Thailand

“…It is possible to further distinguish the variants, using a third restriction enzyme (MboI), into genotypes 6a and 3a. 31 Unfortunately, we did not perform these additional tests. We were not able to determine the final result for genotype in specimens 1B, 3B, and 4A (not determined).…”