Evaluation of a new hepatitis C virus sequencing assay as a routine methodfor genotyping

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 automa ted sequencing based system has been developed recently, the Visible Geneti cs TruGene(TM) Hepatitis C Assay. The aim of the study was to compare this new genotyping assay with reverse hybridization based Innogenetics INNO-LiP A HCV II assay that is used most commonly. Eighty-eight HCV-RNA positive pa tients were enrolled and divided in four groups: 26 hemodialysed patients, 30 untreated patients with chronic HCV hepatitis, 12 IFN non-responder pati ents with chronic HCV hepatitis, 20 asymptomatic HCV positive subjects. The 5'-UTR region was amplified by RTPCR and the nucleotide sequences determin ed by the TruGene(TM) 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 Ib and 2a /c. The new system also allowed the subtyping of 3 untypable samples, class ified 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 cl osest genotype 1 isolate was 6 nucleotides. One LiPA genotype la sample was typed as Ib and 2 genotype Ib samples were all typed as la by the sequence analysis. In conclusion, the new assay is a sensitive and rapid method tha t is suitable for accurate large-scale genotyping. (C) 2001 Wiley-Liss, Inc .