title: Genotyping of hepatitis C virus isolates by a new line probe assay using sequence information from both the 5'untranslated and the core regions.
abstract: The correct assessment of hepatitis C virus (HCV) genotypes and subtypes by commercial assays is of utmost importance mainly for the therapeutic management of patients suffering from HCV infections. In this study, the performance characteristics of a newly designed genotyping assay were evaluated that does not rely exclusively on sequence information derived from the 5'untranslated region but also takes into account part of the HCV core. One hundred and ten clinical specimens were tested by this new assay prior to its commercialisation. The obtained typing results were compared to those recorded by the 5'UTR-based Versant HCV Genotyping Assay, version 1, the core-related Gen-Eti K DEIA, and phylogenetic analyses of partial HCV core and NS5B sequences. The HCV genotypes and subtypes identified by the newly devised kit were completely in line with the assignments achieved by DEIA and phylogenetic analyses. In particular, all 64 HCV strains belonging to subtypes 1a or 1b were recognised correctly, and HCV 6e and 6f isolates were adequately assigned to subtypes 6c-l. Thus, the second generation of the Versant genotyping assay could overcome the drawbacks of its exclusively 5'UTR-based predecessor and will turn out to be a reliable tool for HCV typing in clinical laboratories.
authors.affiliation: Institute of Virology, National Reference Centre for Hepatitis C, Essen University Hospital, University of Duisburg-Essen, Essen, Germany. stefan.ross@uni-due.de
authors.forename: R S
authors.initials: RS
authors.lastname: Ross
authors.forename: S
authors.initials: S
authors.lastname: Viazov
authors.forename: M
authors.initials: M
authors.lastname: Roggendorf
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D000293:Adolescent; D000328:Adult; D000368:Aged; D002648:Child; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000453:epidemiology / Q000821:virology*; D006801:Humans; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology / Q000379:methods*; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization / Q000379:methods*; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase