title: Comparison of line probe assay and DNA sequencing of 5' untranslated region for genotyping hepatitis C virus: description of novel line probe patterns.
abstract: We compared a commercial line probe assay (INNO-LiPA HCV II, Innogenetics, N.V., Ghent, Belgium, distributed by Bayer Diagnostics) to an in-house 5' untranslated region direct DNA sequencing method for genotyping hepatitis C virus (HCV). Initial evaluation demonstrated that the INNO-LiPA HCV II assay and sequencing assay assigned the same genotype for 110/132 (83.3%) patient specimens (98 subtype and 12 genotype only identifications). Following the initial evaluation, the INNO-LiPA HCV II assay was used routinely to genotype HCV from patient specimens submitted to our laboratory for genotyping (n = 1,739). During this second part of the study, novel line probe patterns have been noted and interpreted using the in-house direct sequencing assay. Reactivity at bands 1, 2, 3, 4, 5 and 8 (n = 4) or 1, 2, 3, 4, 6 and 7 (n = 2) represented HCV genotype 1. Reactivity at bands 1, 2, 5 and 9 (n = 1) represented HCV genotype 2. Reactivity at bands 1, 2, 5, 9 and 16 (n = 1) represented HCV genotype 4. Reactivity at bands 1, 2, 5, 9, 10, 11 (weak band) and 12 (n = 118) most likely represented HCV genotype 2b. This information should be of use to INNO-LiPA HCV II assay users.
authors.affiliation: Division of Clinical Microbiology, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: P Shawn
authors.initials: PS
authors.lastname: Mitchell
authors.forename: Lynne M
authors.initials: LM
authors.lastname: Sloan
authors.forename: David W
authors.initials: DW
authors.lastname: Majewski
authors.forename: Paul N
authors.initials: PN
authors.lastname: Rys
authors.forename: Paul J
authors.initials: PJ
authors.lastname: Heimgartner
authors.forename: Jon E
authors.initials: JE
authors.lastname: Rosenblatt
authors.forename: Franklin R
authors.initials: FR
authors.lastname: Cockerill
authors.forename: Thomas F
authors.initials: TF
authors.lastname: Smith
authors.forename: Robin
authors.initials: R
authors.lastname: Patel
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D015336:Molecular Probe Techniques; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D020121:5' Untranslated Regions