Evaluation of the TRUGENE HCV 5 ′ NC Genotyping Kit with the New GeneLibrarian Module 3.1.2 for Genotyping of Hepatitis C Virus from Clinical Specimens

Abstract

The TRUGENE HCV 5NC genotyping kit (GeneLibrarian modules 3.1.1 and 3.1.2) and VERSANT HCV genotyping assay were compared by using 96 hepatitis C virus (HCV) RNA-positive patient specimens, including HCV genotypes 1, 2, 3, 4, 5, 6, and 10. The TRUGENE HCV 5NC genotyping kit (GeneLibrarian module 3.1.2) yielded the most accurate genotyping results.Hepatitis C virus (HCV) has been classified into at least six distinct genotypes that can be further differentiated into multiple subtypes (12, 13). Recent anti-HCV treatment algorithms suggest that tailoring antiviral therapy based on HCV genotype as well as HCV RNA titer can optimize therapeutic outcome (2, 7). While sequence variability is found throughout the HCV genome, the 5Ј noncoding (5ЈNC) region remains highly conserved and is the target of choice for detection by reverse transcription-PCR (RT-PCR) (5,14,15). Despite the limited sequence diversity found within the HCV 5ЈNC region compared to that of a highly diversified genomic target such as the nonstructural (NS) 5B region, practical considerations have made the 5ЈNC region the preferred target for HCV genotyping in most diagnostic laboratories (3,6,8). Several HCV genotyping assays are currently commercially available, including the TRUGENE HCV 5ЈNC genotyping kit (TRUGENE 5ЈNC; Bayer HealthCare LLC, Berkeley, Calif.) and the VERSANT HCV genotype assay (LiPA; Bayer HealthCare LLC). Recently, there have been several published comparisons of these two assays (1,8,10), in addition to several other evaluations of the TRUGENE 5ЈNC (4, 11). To date, none of these comparisons has evaluated the TRUGENE 5ЈNC in conjunction with the new HCV 5ЈNC GeneLibrarian module 3.1.2 (GL 3.1.2; Bayer HealthCare LLC). The GL 3.1.2 is a new 5ЈNC sequence database validated by phylogenetic analysis of the 5ЈNC and corresponding NS5B sequences from over 250 HCV strains collected worldwide and is designed for use with the TRUGENE 5ЈNC

Genotyping hepatitis C virus from hemodialysis patients in Central Brazil by line probe assay and sequence analysis

“…However, the genotyping methods employed in those studies, which were based on 5' noncoding (5'NC) region analyses, did not permit the correct identification of HCV subtypes (10)(11)(12)(13)(14)(15)(16)(17). To our knowledge, the present study is the first to analyze Brazilian HCV samples using two genotyping methods: line probe assay (LiPA, based on the 5'NC region) and the nucleotide sequencing analysis of the nonstructural 5B (NS5B) region, which has been used as a reference method for accurate genotyping (10)(11)(12)(13)(14)(15)(16)(17). Thus, our objective was to determine which HCV genotypes and subtypes occur in hemodialysis patients in Central Brazil and also to compare the genotyping efficiency of LiPA and direct sequencing of the NS5B region.…”

“…On the other hand, this region does not contain sufficient information for the recognition of all different types and subtypes. Thus, in the present study we chose the NS5B region for sequence analysis since this region appears to be much more accurate for identifying variations in the nucleotide sequences (10)(11)(12)(13)(14)(15)(16)(17).…”

HCV-Core Region: Its Significance in HCV-Genotyping and Type Dependent Genomic Expression

“…Earlier, the determination of HCV-genotypes was done by methods, such as automated reverse hybridization [33] and semi automated sequencing [34,35]. These methods need a previously amplified genomic product as starting material.…”

Hepatitis C virus quasispecies in HIV-infected women: Role of injecting drug use and highly active antiretroviral therapy (HAART)

“…For women found to be viremic, we determined HCV genotype using the NC TRUGENE HCV 5Ј NC Genotyping Kit (Bayer HealthCare LLC, Tarrytown, NY) as recommended by the manufacturer and as described. 34 Reverse-Transcription PCR. We extracted RNA from 100 L serum by means of a modified guanidinium thiocyanate-phenol/chloroform technique using a commercially available kit (Triazol, Gibco) and dissolved it in 20 L water.…”