title: Transcription-mediated amplification linked to line probe assay as a routine tool for HCV typing in clinical laboratories.
abstract: Typing of hepatitis C virus (HCV) isolates is currently a prerequisite for adequate tailoring of antiviral combination therapy. In many diagnostic laboratories, there seems to be a tendency toward convenient and time-saving procedures utilizing amplification products, which are already available from preceding qualitative or quantitative HCV ribonucleic acid (RNA) assays. In this context, we evaluated the performance characteristics of a combination of techniques, i.e., transcription-mediated amplification-line probe assay (TMA-LiPA), which links highly sensitive TMA of HCV RNA to the VERSANT HCV Genotype Assay (version 1). A total of 100 clinical samples were genotyped by TMA-LiPA. The obtained results were compared to those recorded by the original, nested reverse transcription (RT)-polymerase chain reaction (PCR)-based VERSANT assay, the core-related GEN-ETI-K DEIA, and phylogenetic analyses of partial sequences from the HCV core and NS5B regions. TMA-LiPA assigned the correct genotype to all 100 HCV isolates. For subtyping of genotype 1 and 2 isolates, TMA-LiPA only showed discriminatory powers of 82% and 53%, respectively. Thus, TMA-LiPA in our hands turned out as a convenient and time-saving routine procedure for HCV typing which currently provides sufficient information for clinical purposes. Like all 5'untranslated region (UTR)-based assays, the technique is limited, however, in its potentials to resolve the complexity of existing HCV subtypes.
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: S S
authors.initials: SS
authors.lastname: Kpakiwa
authors.forename: M
authors.initials: M
authors.lastname: Roggendorf
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001483:Base Sequence; D005260:Female; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D006526:Hepatitis C / Q000175:diagnosis / Q000821:virology; D006801:Humans; D008297:Male; D008875:Middle Aged; D008969:Molecular Sequence Data; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral