title: Naturally occurring genotype 2b/1a hepatitis C virus in the United States.
abstract: BACKGROUND
  Hepatitis C Virus (HCV) infected patients are frequently repeatedly exposed to the virus, but very few recombinants between two genotypes have been reported.
  
  
  RESULTS
  We describe the discovery of an HCV recombinant using a method developed in a United States clinical lab for HCV genotyping that employs sequencing of both 5' and 3' portions of the HCV genome. Over twelve months, 133 consecutive isolates were analyzed, and a virus from one patient was found with discordant 5' and 3' sequences suggesting it was a genotype 2b/1a recombinant. We ruled out a mixed infection and mapped a recombination point near the NS2/3 cleavage site.
  
  
  CONCLUSIONS
  This unique HCV recombinant virus described shares some features with other recombinant viruses although it is the only reported recombinant of a genotype 2 with a subtype 1a. This recombinant represents a conundrum for current clinical treatment guidelines, including treatment with protease inhibitors. This recombinant is also challenging to detect by the most commonly employed methods of genotyping that are directed primarily at the 5' structural portion of the HCV genome.
authors.affiliation: University of Wisconsin-Madison, School of Medicine and Public Health, Department of Medicine, Madison, WI 53706, USA.
authors.forename: Dipankar
authors.initials: D
authors.lastname: Bhattacharya
authors.forename: Molly A
authors.initials: MA
authors.lastname: Accola
authors.forename: Israr H
authors.initials: IH
authors.lastname: Ansari
authors.forename: Rob
authors.initials: R
authors.lastname: Striker
authors.forename: William M
authors.initials: WM
authors.lastname: Rehrauer
mesh_terms: D024509:3' Flanking Region; D024506:5' Flanking Region; D001483:Base Sequence; D060085:Coinfection; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics; D016679:Genome, Viral; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000235:genetics* / Q000821:virology; D006801:Humans; D008969:Molecular Sequence Data; D058889:Molecular Typing / Q000379:methods*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D016865:Reassortant Viruses / Q000235:genetics / Q000302:isolation & purification; D011995:Recombination, Genetic; D014481:United States
chemical_list: D017931:DNA Primers