title: Comparative performance evaluation of hepatitis C virus genotyping based on the 5' untranslated region versus partial sequencing of the NS5B region of brazilian patients with chronic hepatitis C.
abstract: BACKGROUND
  Genotyping of hepatitis C virus (HCV) has become an essential tool for prognosis and prediction of treatment duration. The aim of this study was to compare two HCV genotyping methods: reverse hybridization line probe assay (LiPA v.1) and partial sequencing of the NS5B region.
  
  
  METHODS
  Plasma of 171 patients with chronic hepatitis C were screened using both a commercial method (LiPA HCV Versant, Siemens, Tarrytown, NY, USA) and different primers targeting the NS5B region for PCR amplification and sequencing analysis.
  
  
  RESULTS
  Comparison of the HCV genotyping methods showed no difference in the classification at the genotype level. However, a total of 82/171 samples (47.9%) including misclassification, non-subtypable, discrepant and inconclusive results were not classified by LiPA at the subtype level but could be discriminated by NS5B sequencing. Of these samples, 34 samples of genotype 1a and 6 samples of genotype 1b were classified at the subtype level using sequencing of NS5B.
  
  
  CONCLUSIONS
  Sequence analysis of NS5B for genotyping HCV provides precise genotype and subtype identification and an accurate epidemiological representation of circulating viral strains.
authors.affiliation: Laboratório Central do Estado do Paraná, LACEN-PR, São José dos Pinhais, Paraná, Brazil.
authors.forename: Sueli M
authors.initials: SM
authors.lastname: Nakatani
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Santos
authors.forename: Irina N
authors.initials: IN
authors.lastname: Riediger
authors.forename: Marco A
authors.initials: MA
authors.lastname: Krieger
authors.forename: Cesar A B
authors.initials: CA
authors.lastname: Duarte
authors.forename: Maria
authors.initials: M
authors.lastname: do Carmo Debur
authors.forename: Flair J
authors.initials: FJ
authors.lastname: Carrilho
authors.forename: Suzane K
authors.initials: SK
authors.lastname: Ono
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D001938:Brazil; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000097:blood / Q000235:genetics* / Q000821:virology; D006801:Humans; D058889:Molecular Typing / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D010802:Phylogeny; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*; D017361:Viral Nonstructural Proteins / Q000097:blood* / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D017931:DNA Primers; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase