title: Evaluation of a new hepatitis C virus sequencing assay as a routine method for genotyping.
abstract: The determination of HCV genotypes, subtypes and isolates has been helpful in understanding the evolution and the epidemiology of the virus, and is an important factor in the pre-treatment evaluation. A new simpler and automated sequencing based system has been developed recently, the Visible Genetics TruGene Hepatitis C Assay. The aim of the study was to compare this new genotyping assay with reverse hybridization based Innogenetics INNO-LiPA HCV II assay that is used most commonly. Eighty-eight HCV-RNA positive patients were enrolled and divided in four groups: 26 hemodialysed patients, 30 untreated patients with chronic HCV hepatitis, 12 IFN non-responder patients with chronic HCV hepatitis, 20 asymptomatic HCV positive subjects. The 5'-UTR region was amplified by RT-PCR and the nucleotide sequences determined by the TruGene assay. In parallel, the amplicons were also tested by INNO-LiPA. Concordant results were obtained in 80 out of 88 cases (90.9%). The new assay allowed to genotype 2 samples not typed by LiPA as 1b and 2a/c. The new system also allowed the subtyping of 3 untypable samples, classified as genotype 1 by INNO-LiPA, as genotype 1b (1 sample) and, as genotype 4 (2 samples). The difference between these genotype 4 isolates and the closest genotype 1 isolate was 6 nucleotides. One LiPA genotype 1a sample was typed as 1b and 2 genotype 1b samples were all typed as 1a by the sequence analysis. In conclusion, the new assay is a sensitive and rapid method that is suitable for accurate large-scale genotyping.
authors.affiliation: Department of Health Sciences, University of Genoa, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Ansaldi
authors.forename: F
authors.initials: F
authors.lastname: Torre
authors.forename: B M
authors.initials: BM
authors.lastname: Bruzzone
authors.forename: A
authors.initials: A
authors.lastname: Picciotto
authors.forename: P
authors.initials: P
authors.lastname: Crovari
authors.forename: G
authors.initials: G
authors.lastname: Icardi
mesh_terms: D020121:5' Untranslated Regions / Q000032:analysis; D003001:Cloning, Molecular; D005821:Genetic Techniques; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017421:Sequence Analysis / Q000379:methods
chemical_list: D020121:5' Untranslated Regions