title: Determination of HCV genotype by direct sequence analysis of quantitative PCR products.
abstract: Hepatitis C virus (HCV) genotyping, combined with quantitative evaluation of HCV RNA, may be beneficial for the management of chronic hepatitis C and in the selection of candidates for interferon treatment. In this study, the COBAS AMPLICOR HCV MONITOR test, a commercially available quantitative assay for HCV RNA, was used. Amplification products obtained from HCV-positive cases were subjected to direct sequencing and genotyping based on seven phylogenetically informative regions within the 5'UTR. Results were compared with those obtained by INNO-LiPA assay. Typing results yielded by both methods were in complete accordance for type and subtype assignment. Twenty-nine of 500 specimens (5.8%) were unclassifiable and belonged to samples with a titer of <70.000 IU, as determined by quantitative assay. Despite this limitation, the overall gain in efficiency, the low rate of test failure and a better resolution of mixed genotypes all constitute a considerable advantage of this system over the commercial hybridization technique for routine clinical laboratory use.
authors.affiliation: Laboratory of Virology, Spedali Civili, Brescia, Italy. gargiulo@bshosp.osp.unibs.it
authors.forename: Franco
authors.initials: F
authors.lastname: Gargiulo
authors.forename: Maria Antonia
authors.initials: MA
authors.lastname: De Francesco
authors.forename: Gabriele
authors.initials: G
authors.lastname: Pinsi
authors.forename: Caterina
authors.initials: C
authors.lastname: Pollara
authors.forename: Luigina
authors.initials: L
authors.lastname: Terlenghi
authors.forename: Francesca
authors.initials: F
authors.lastname: Perandin
authors.forename: Nino
authors.initials: N
authors.lastname: Manca
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D005838:Genotype; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000175:diagnosis* / Q000821:virology; D006801:Humans; D009693:Nucleic Acid Hybridization / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000097:blood*; D011933:Reagent Kits, Diagnostic; D017422:Sequence Analysis, DNA
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic