title: Genotyping hepatitis C viruses from Southeast Asia by a novel line probe assay that simultaneously detects core and 5' untranslated regions.
abstract: Hepatitis C viruses (HCVs) display a high level of sequence diversity and are currently divided into six genotypes. A line probe assay (LiPA), which targets the 5' untranslated region (5'UTR) of the HCV genome, is widely used for genotyping. However, this assay cannot distinguish many genotype 6 subtypes from genotype 1 due to high sequence similarity in the 5'UTR. We investigated the accuracy of a new generation LiPA (VERSANT HCV genotype 2.0 assay), in which genotyping is based on 5'UTR and core sequences, by testing 75 selected HCV RNA-positive sera from Southeast Asia (Vietnam and Thailand). For comparison, sera were tested on the 5'UTR based VERSANT HCV genotype assay and processed for sequence analysis of the 5'UTR-to-core and NS5b regions as well. Phylogenetic analysis of both regions revealed the presence of genotype 1, 2, 3, and 6 viruses. Using the new LiPA assay, genotypes 6c to 6l and 1a/b samples were more accurately genotyped than with the previous test only targeting the 5'UTR (96% versus 71%, respectively). These results indicate that the VERSANT HCV genotype 2.0 assay is able to discriminate genotypes 6c to 6l from genotype 1 and allows a more accurate identification of genotype 1a from 1b by using the genotype-specific core information.
authors.affiliation: Department of Virology, Erasmus Medical Center, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands.
authors.forename: Suwanna
authors.initials: S
authors.lastname: Noppornpanth
authors.forename: Erwin
authors.initials: E
authors.lastname: Sablon
authors.forename: Kathy
authors.initials: K
authors.lastname: De Nys
authors.forename: Xuan Lien
authors.initials: XL
authors.lastname: Truong
authors.forename: Jan
authors.initials: J
authors.lastname: Brouwer
authors.forename: Marianne
authors.initials: M
authors.lastname: Van Brussel
authors.forename: Saskia L
authors.initials: SL
authors.lastname: Smits
authors.forename: Yong
authors.initials: Y
authors.lastname: Poovorawan
authors.forename: Albert D M E
authors.initials: AD
authors.lastname: Osterhaus
authors.forename: Bart L
authors.initials: BL
authors.lastname: Haagmans
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D014758:Viral Core Proteins / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D014758:Viral Core Proteins