title: [Hepatitis C virus genotyping: comparison of the Abbott RealTime HCV Genotype II assay and NS5B sequencing].
abstract: OBJECTIVE
  Hepatitis C virus genotyping is needed for treatment decision and monitoring. The results of a genotyping assay based on real-time PCR and TaqMan chemistry were compared with the results of NS5B region sequencing.
  
  
  METHODS
  One hundred and two sera (genotypes 1-6) were tested. Amplification and detection of viral RNA were performed with the Abbott RealTime HCV Genotype II assay targeting 5'non-coded region (5'NC) for the identification of genotypes 1 to 6 and NS5B, for 1a and 1b subtypes detection. Sequencing of 5'NC fragment was used to resolve discrepant results.
  
  
  RESULTS
  No indeterminate results were obtained. Concordance with NS5B sequencing was 93% (95 on 102), 96% at the genotype level (98 on 102) and 93% for genotype 1 subtyping (40 on 43). Discordant genotyping results were a 2f subtype identified as 5, a 6a typed as 1, a 3a identified as a 1-3 co-infection and a 4r identified as a 1-4 co-infection. Discordant subtyping results were 2 1b subtypes only typed as 1 and a 1e identified as 1a.
  
  
  CONCLUSIONS
  Abbott RealTime HCV Genotype II assay is a rapid, automated and simple to interpret method for HCV genotyping. It allows the detection of possible mixed infections which might have a negative impact on therapeutic response. However, the discrepant results found in this small series underline the need for assay optimization.
authors: Département de virologie, hôpital Paul-Brousse, AP-HP, 12, avenue Paul-Vaillant-Couturier, 94800 Villejuif, France.
authors: P
authors: P
authors: Vaghefi
authors: E
authors: E
authors: Marchadier
authors: E
authors: E
authors: Dussaix
authors: A-M
authors: AM
authors: Roque-Afonso
mesh_terms: D003199:Computer Systems; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000097:blood / Q000821:virology; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D011446:Prospective Studies; D012367:RNA, Viral / Q000097:blood / Q000235:genetics* / Q000302:isolation & purification; D011933:Reagent Kits, Diagnostic; D017423:Sequence Analysis, RNA / Q000379:methods*; D019914:Taq Polymerase; D013997:Time Factors; D014766:Viremia / Q000821:virology
chemical_list: D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic; D019914:Taq Polymerase