title: Improvement of hepatitis C virus (HCV) genotype determination with the new version of the INNO-LiPA HCV assay.
abstract: Hepatitis C virus (HCV) isolates have been classified into six main genotypes. Genotyping methods, and especially the widely used line probe assay (LiPA), are frequently based on the 5'-untranslated region (5'UTR). However, this region is not appropriate for discriminating HCV strains at the subtype level and for distinguishing many genotype 6 samples from genotype 1. We investigated the capacity of a novel LiPA (Versant HCV Genotype 2.0 assay) based on the simultaneous detection of 5'UTR and Core regions for genotypes 1 and 6 to provide correct HCV genotypes (characterized with a phylogenetic analysis) in a set of HCV strains mainly encountered in Western countries. The improvement was assessed by comparing the results to those obtained with the previous version of the assay. Of the 135 tested samples, 64.7% were concordant for genotype group and subtype with sequencing reference results using the Versant HCV Genotype 2.0 assay versus 37.5% with the previous version. The yield was mainly related to a better characterization of genotype 1, since the accuracy, tested in 62 genotype 1 samples, increased from 45.2% with the first version to 96.8% with the new one. However, this new version necessitates a specific PCR and could no longer be used after 5'UTR PCR used for current HCV infection diagnosis. Moreover, the information provided by 5'UTR hybridization is not reliable for correctly identifying the diversity within genotypes 2 and 4. Thus, the Versant HCV Genotype 2.0 assay remains a useful tool for clinical practice when only the discrimination between major HCV genotypes is necessary.
authors.affiliation: Institut National de la Transfusion Sanguine, 6 Rue Alexandre-Cabanel, 75015 Paris, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Bouchardeau
authors.forename: Jean François
authors.initials: JF
authors.lastname: Cantaloube
authors.forename: Stéphane
authors.initials: S
authors.lastname: Chevaliez
authors.forename: Christine
authors.initials: C
authors.lastname: Portal
authors.forename: Annie
authors.initials: A
authors.lastname: Razer
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Lefrère
authors.forename: Jean Michel
authors.initials: JM
authors.lastname: Pawlotsky
authors.forename: Philippe
authors.initials: P
authors.lastname: De Micco
authors.forename: Syria
authors.initials: S
authors.lastname: Laperche
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods*; D011237:Predictive Value of Tests; D017422:Sequence Analysis, DNA; D014758:Viral Core Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics; D014773:Virology / Q000379:methods*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D014758:Viral Core Proteins; D017361:Viral Nonstructural Proteins; C069130:nucleocapsid protein, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase