title: Evaluation of the Abbott realtime HCV genotype II RUO (GT II) assay with reference to 5'UTR, core and NS5B sequencing.
abstract: BACKGROUND
  HCV genotyping is a critical tool for guiding initiation of therapy and selecting the most appropriate treatment regimen.
  
  
  OBJECTIVE
  To evaluate the concordance between the Abbott GT II assay and genotyping by sequencing subregions of the HCV 5'UTR, core and NS5B.
  
  
  METHODS
  The Abbott assay was used to genotype 127 routine patient specimens and 35 patient specimens with unusual subtypes and mixed infection. Abbott results were compared to genotyping by 5'UTR, core and NS5B sequencing. Sequences were genotyped using the NCBI non-redundant database and the online genotyping tool COMET.
  
  
  RESULTS
  Among routine specimens, core/NS5B sequencing identified 93 genotype 1s, 13 genotype 2s, 15 genotype 3s, three genotype 4s, two genotype 6s and one recombinant specimen. Genotype calls by 5'UTR, core, NS5B sequencing and the Abbott assay were 97.6% concordant. Core/NS5B sequencing identified two discrepant samples as genotype 6 (subtypes 6l and 6u) while Abbott and 5'UTR sequencing identified these samples as genotype 1 with no subtype. The Abbott assay subtyped 91.4% of genotype 1 specimens. Among the 35 rare specimens, the Abbott assay inaccurately genotyped 3k, 6e, 6o, 6q and one genotype 4 variant; gave indeterminate results for 3g, 3h, 4r, 6m, 6n, and 6q specimens; and agreed with core/NS5B sequencing for mixed specimens.
  
  
  CONCLUSIONS
  The Abbott assay is an automated HCV genotyping method with improved accuracy over 5'UTR sequencing. Samples identified by the Abbott assay as genotype 1 with no subtype may be rare subtypes of other genotypes and thus require confirmation by another method.
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA. Electronic address: melanie.mallory@aruplab.com.
authors.forename: Melanie A
authors.initials: MA
authors.lastname: Mallory
authors.affiliation: Abbott Molecular Inc., 1350 E. Touhy Avenue, Des Plaines, IL 60018, USA. Electronic address: danijela.lucic@abbott.com.
authors.forename: Danijela X
authors.initials: DX
authors.lastname: Lucic
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA. Electronic address: mitch.sears@gmail.com.
authors.forename: Mitchell T
authors.initials: MT
authors.lastname: Sears
authors.affiliation: Abbott Molecular Inc., 1350 E. Touhy Avenue, Des Plaines, IL 60018, USA. Electronic address: gavin.cloherty@abbott.com.
authors.forename: Gavin A
authors.initials: GA
authors.lastname: Cloherty
authors.affiliation: ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, 500 Chipeta Way, Salt Lake City, UT 84108, USA; University of Utah Department of Pathology, 15 North Medical Drive East, Salt Lake City, UT 84112, USA. Electronic address: hillyadr@aruplab.com.
authors.forename: David R
authors.initials: DR
authors.lastname: Hillyard
mesh_terms: D020121:5' Untranslated Regions; D057205:Automation, Laboratory / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods*; D016174:Hepacivirus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006526:Hepatitis C / Q000175:diagnosis* / Q000821:virology; D006801:Humans; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D017422:Sequence Analysis, DNA; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D020121:5' Untranslated Regions; D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase
keywords: DNA sequencing; Genotyping; Hepatitis C virus; Real-time PCR