title: Serendipitous identification of natural intergenotypic recombinants of hepatitis C in Ireland.
abstract: BACKGROUND
  Recombination between hepatitis C single stranded RNA viruses is a rare event. Natural viable intragenotypic and intergenotypic recombinants between 1b-1a, 1a-1c and 2k-1b, 2i-6p, respectively, have been reported. Diagnostically recombinants represent an intriguing challenge. Hepatitis C genotype is defined by interrogation of the sequence composition of the 5' untranslated region [5'UTR]. Occasionally, ambiguous specimens require further investigation of the genome, usually by interrogation of the NS5B region. The original purpose of this study was to confirm the existence of a suspected mixed genotype infection of genotypes 2 and 4 by clonal analysis at the NS5B region of the genome in two specimens from two separate individuals. This initial identification of genotype was based on analysis of the 5'UTR of the genome by reverse line probe hybridisation [RLPH].
  
  
  RESULTS
  The original diagnosis of a mixed genotype infection was not confirmed by clonal analysis of the NS5B region of the genome. The phylogenetic analysis indicated that both specimens were natural intergenotypic recombinant forms of HCV. The recombination was between genotypes 2k and 1b for both specimens. The recombination break point was identified as occurring within the NS2 region of the genome.
  
  
  CONCLUSIONS
  The viral recombinants identified here resemble the recombinant form originally identified in Russia. The RLPH pattern observed in this study may be a signature indicative of this particular type of intergenotype recombinant of hepatitis C meriting clonal analysis of NS2.
authors.affiliation: Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, Clinical Sciences Building, Cork University Hospital, Cork, Ireland. i.moreau@ucc.ie
authors.forename: Isabelle
authors.initials: I
authors.lastname: Moreau
authors.forename: Susan
authors.initials: S
authors.lastname: Hegarty
authors.forename: John
authors.initials: J
authors.lastname: Levis
authors.forename: Patrick
authors.initials: P
authors.lastname: Sheehy
authors.forename: Orla
authors.initials: O
authors.lastname: Crosbie
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Kenny-Walsh
authors.forename: Liam J
authors.initials: LJ
authors.lastname: Fanning
mesh_terms: D000595:Amino Acid Sequence; D005838:Genotype; D016174:Hepacivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D007494:Ireland; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D011995:Recombination, Genetic; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017361:Viral Nonstructural Proteins / Q000737:chemistry / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase
chemical_list: D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; C400562:HVR1 protein, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase