title: Natural non-homologous recombination led to the emergence of a duplicated V3-NS5A region in HCV-1b strains associated with hepatocellular carcinoma.
abstract: BACKGROUND
  The emergence of new strains in RNA viruses is mainly due to mutations or intra and inter-genotype homologous recombination. Non-homologous recombinations may be deleterious and are rarely detected. In previous studies, we identified HCV-1b strains bearing two tandemly repeated V3 regions in the NS5A gene without ORF disruption. This polymorphism may be associated with an unfavorable course of liver disease and possibly involved in liver carcinogenesis. Here we aimed at characterizing the origin of these mutant strains and identifying the evolutionary mechanism on which the V3 duplication relies.
  
  
  METHODS
  Direct sequencing of the entire NS5A and E1 genes was performed on 27 mutant strains. Quasispecies analyses in consecutive samples were also performed by cloning and sequencing the NS5A gene for all mutant and wild strains. We analyzed the mutant and wild-type sequence polymorphisms using Bayesian methods to infer the evolutionary history of and the molecular mechanism leading to the duplication-like event.
  
  
  RESULTS
  Quasispecies were entirely composed of exclusively mutant or wild-type strains respectively. Mutant quasispecies were found to have been present since contamination and had persisted for at least 10 years. This V3 duplication-like event appears to have resulted from non-homologous recombination between HCV-1b wild-type strains around 100 years ago. The association between increased liver disease severity and these HCV-1b mutants may explain their persistence in chronically infected patients.
  
  
  CONCLUSIONS
  These results emphasize the possible consequences of non-homologous recombination in the emergence and severity of new viral diseases.
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Le Guillou-Guillemette
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Adeline
authors.initials: A
authors.lastname: Pivert
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Elise
authors.initials: E
authors.lastname: Bouthry
authors.affiliation: Laboratoire de Virologie, CHU Clermont-Ferrand, France.
authors.forename: Cécile
authors.identifier: http://orcid.org/0000-0003-2859-6566
authors.initials: C
authors.lastname: Henquell
authors.affiliation: Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, Brest, France.
authors.forename: Odile
authors.identifier: http://orcid.org/0000-0001-8027-8333
authors.initials: O
authors.lastname: Petsaris
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Ducancelle
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Veillon
authors.affiliation: Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, Brest, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Vallet
authors.affiliation: Laboratoire de Virologie, CHU Limoges, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Alain
authors.affiliation: Laboratoire de Virologie, CHU Pitié-Salpêtrière, Paris, France.
authors.forename: Vincent
authors.identifier: http://orcid.org/0000-0001-6517-2901
authors.initials: V
authors.lastname: Thibault
authors.affiliation: Laboratoire de Virologie, CNR VHE, Inserm U1043, CHU Purpan, Toulouse, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Abravanel
authors.affiliation: AP-HP, GHU Cochin, Laboratoire de Virologie, Université Paris Descartes, Paris, France.
authors.forename: Arielle A
authors.initials: AA
authors.lastname: Rosenberg
authors.affiliation: Laboratoire de Virologie, CHU Hôtel Dieu, Nantes, France.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: André-Garnier
authors.affiliation: Laboratoire de Virologie, CHU, Dijon, France.
authors.forename: Jean-Baptiste
authors.initials: JB
authors.lastname: Bour
authors.affiliation: Laboratoire de Virologie, CHU Avicenne, Bobigny, France.
authors.forename: Yazid
authors.initials: Y
authors.lastname: Baazia
authors.affiliation: Laboratoire de Virologie, Hôpital Pellegrin Tripode, CHU Bordeaux, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Trimoulet
authors.affiliation: Laboratoire de Virologie, Centre de Biologie Nord, Hôpital de la Croix Rousse, Lyon, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: André
authors.affiliation: Université François Rabelais, Inserm U966, CHU Tours, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Gaudy-Graffin
authors.affiliation: Laboratoire de Virologie, CHU Besançon, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Bettinger
authors.affiliation: Laboratoire de Virologie, UMI 3265 UJF-EMBL-CNRS, CHU, Unit of Virus Host Cell Interactions, Grenoble, France.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Larrat
authors.affiliation: Laboratoire de Virologie, UMI 3265 UJF-EMBL-CNRS, CHU, Unit of Virus Host Cell Interactions, Grenoble, France.
authors.forename: Anne
authors.initials: A
authors.lastname: Signori-Schmuck
authors.affiliation: Laboratoire de Bactériologie-Virologie, CHU Saint-Etienne, France.
authors.forename: Hénia
authors.initials: H
authors.lastname: Saoudin
authors.affiliation: Laboratoire de Bactériologie-Virologie, CHU Saint-Etienne, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Pozzetto
authors.affiliation: Laboratoire de Virologie, CHU Rennes, France.
authors.forename: Gisèle
authors.identifier: http://orcid.org/0000-0001-8784-1926
authors.initials: G
authors.lastname: Lagathu
authors.affiliation: Laboratoire de Virologie, CHU Rennes, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Minjolle-Cha
authors.affiliation: Institut de Virologie, CHU Strasbourg, Inserm U748, Strasbourg, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Stoll-Keller
authors.affiliation: Laboratoire de Virologie-Bactériologie, CHU Henri-Mondor, Créteil, France.
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Pawlotsky
authors.affiliation: Laboratoire de Virologie, CNR VHE, Inserm U1043, CHU Purpan, Toulouse, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Izopet
authors.affiliation: Département de Bactériologie-Virologie-Hygiène Hospitalière et Parasitologie-Mycologie, CHRU, LUBEM, Brest, France.
authors.forename: Christopher
authors.identifier: http://orcid.org/0000-0001-7321-4593
authors.initials: C
authors.lastname: Payan
authors.affiliation: Laboratoire de Virologie, CHU Angers, France.|HIFIH Laboratory, UPRES 3859, SFR 4208, LUNAM University, Angers, France.
authors.forename: Françoise
authors.initials: F
authors.lastname: Lunel-Fabiani
authors.affiliation: IRHS, Université d'Angers, SFR4207 QUASAV, Angers, France.
authors.forename: Christophe
authors.initials: C
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mesh_terms: D001499:Bayes Theorem; D006528:Carcinoma, Hepatocellular / Q000821:virology; D015331:Cohort Studies; D019143:Evolution, Molecular; D020440:Gene Duplication; D056426:Genetic Loci; D016174:Hepacivirus / Q000235:genetics*; D006526:Hepatitis C / Q000821:virology; D054884:Host-Pathogen Interactions; D006801:Humans / Q000821:virology; D008113:Liver Neoplasms / Q000821:virology; D009154:Mutation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011995:Recombination, Genetic; D014759:Viral Envelope Proteins / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase
chemical_list: D014759:Viral Envelope Proteins; D017361:Viral Nonstructural Proteins; C087035:E1 protein, Hepatitis C virus; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase