title: The need for a sequencing-based assay to supplement the Abbott m2000 RealTime HCV Genotype II assay: a 1 year analysis.
abstract: BACKGROUND
  Hepatitis C (HCV) genotyping is important for treatment planning. The Abbott m2000 RealTime HCV Genotype II assay is a PCR-based assay targeting specific regions of the 5'NCR gene for genotypes 1-6, and the NS5b gene for subgenotypes 1a/1b. However, not all genotypes can be resolved, with results being reported as: 'indeterminate', 'mixed', 'genotype X reactivity with Y', or just the major genotype 1 alone.
  
  
  OBJECTIVE
  To assess the supplementary testing required for these unresolved HCV genotypes, these samples were tested further using an in-house core/E1 sequencing assay. The resulting genotypes/subgenotypes were assigned using phylogenetic analysis with reference HCV genotype sequences. Additional testing was conducted using the INNO-LiPA HCV II assay for truly mixed genotypes.
  
  
  RESULTS
  Out of 1052 samples tested, 89 (8.5%) underwent further sequencing to determine the HCV genotype: 16 that were 'indeterminate' on the m2000, were mostly genotype 2s and 3s by sequencing; 12 that were 'mixed', were mostly one of the genotypes reported in the mixture; 7 that were 'X reactivity with Y', were usually genotype X; 54 that gave just a major genotype 1 result were mostly 1a, with some 6 and 1b, and a few 1c. For three truly mixed genotypes, additional testing using the VERSANT(®) HCV Genotype Assay (LiPA) 2.0, showed two mixed 1 and 3, and one indistinguishable 6c-6l genotypes.
  
  
  CONCLUSIONS
  The Abbott m2000 RealTime HCV Genotype II assay can resolve most (∼90%) HCV genotypes. However in 9-10% of cases, to fully resolve the genotype, additional testing is required.
authors.affiliation: Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
authors.forename: Marlin
authors.initials: M
authors.lastname: Benedet
authors.affiliation: Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
authors.forename: Dena
authors.initials: D
authors.lastname: Adachi
authors.affiliation: Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada.
authors.forename: Anita
authors.initials: A
authors.lastname: Wong
authors.affiliation: Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada.
authors.forename: Sallene
authors.initials: S
authors.lastname: Wong
authors.affiliation: Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada.
authors.forename: Kanti
authors.initials: K
authors.lastname: Pabbaraju
authors.affiliation: Alberta Provincial Laboratory for Public Health, Calgary, Alberta, Canada; Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
authors.forename: Raymond
authors.initials: R
authors.lastname: Tellier
authors.affiliation: Alberta Provincial Laboratory for Public Health, Edmonton, Alberta, Canada; Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada. Electronic address: jwtang49@hotmail.com.
authors.forename: Julian W
authors.initials: JW
authors.lastname: Tang
mesh_terms: D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics*; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology*; D006801:Humans; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011933:Reagent Kits, Diagnostic / Q000592:standards; D017422:Sequence Analysis, DNA; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D011933:Reagent Kits, Diagnostic; D014764:Viral Proteins