title: Evidence for recombination in natural populations of dengue virus type 1 based on the analysis of complete genome sequences.
abstract: Recombination events are known to occur in non-segmented RNA viruses like polioviruses or alphaviruses. Analysis of the subgenomic sequences of dengue virus type 1 (DENV-1) structural genes has recently allowed the identification of possible recombination breakpoints. Because DENV is a major human pathogen, this discovery might have important implications for virus pathogenicity, vaccine safety and efficiency, or diagnosis and, therefore, requires clear confirmation. We report the complete sequence determination of one Asian and two African strains of DENV-1 isolated from human patients. Rigorous sequence analysis provided strong evidence for the occurrence of intragenomic recombination events between DENV-1 strains belonging to different lineages. Singapore S275/90 strain appears to be the evolutionary product of a recombination event between viruses belonging to two distinct lineages: one lineage includes an African strain isolated in Abidjan (Ivory Coast) and the other includes isolates from Djibouti and Cambodia. The 'Recombination Detection Program', bootscanning and analysis of diversity plots provided congruent results concerning the existence of a two-switch recombination event and the localization of recombination breakpoints. Thus, the 5' and 3' genomic ends of the Singapore S275/90 strain were inherited from a Djibouti/Cambodia lineage ancestor and an internal fragment located in the envelope/NS1 region originated from an Abidjan lineage ancestor.
authors.affiliation: Unité de Virologie Tropicale, Institut de Médecine Tropicale du Service de Santé des Armées, Unité des Virus Emergents, Université de la Méditerranée, BP 46, Parc du Pharo, 13998 Marseille Armées, France1.
authors.forename: H J G
authors.initials: HJG
authors.lastname: Tolou
authors.affiliation: Unité de Virologie Tropicale, Institut de Médecine Tropicale du Service de Santé des Armées, Unité des Virus Emergents, Université de la Méditerranée, BP 46, Parc du Pharo, 13998 Marseille Armées, France1.
authors.forename: P
authors.initials: P
authors.lastname: Couissinier-Paris
authors.affiliation: Unité de Virologie Tropicale, Institut de Médecine Tropicale du Service de Santé des Armées, Unité des Virus Emergents, Université de la Méditerranée, BP 46, Parc du Pharo, 13998 Marseille Armées, France1.
authors.forename: J-P
authors.initials: JP
authors.lastname: Durand
authors.affiliation: Unité de Virologie Tropicale, Institut de Médecine Tropicale du Service de Santé des Armées, Unité des Virus Emergents, Université de la Méditerranée, BP 46, Parc du Pharo, 13998 Marseille Armées, France1.
authors.forename: V
authors.initials: V
authors.lastname: Mercier
authors.affiliation: Laboratoire de Biologie Médicale, Hôpital Laveran, Marseille, France3.
authors.forename: J-J
authors.initials: JJ
authors.lastname: de Pina
authors.affiliation: Laboratoire de Virologie Moléculaire, Tropicale et Transfusionnelle, Faculté de Médecine, Unité des Virus Emergents, Université de la Méditerranée, Marseille, France2.
authors.forename: P
authors.initials: P
authors.lastname: de Micco
authors.affiliation: Laboratoire de Virologie Moléculaire, Tropicale et Transfusionnelle, Faculté de Médecine, Unité des Virus Emergents, Université de la Méditerranée, Marseille, France2.
authors.forename: F
authors.initials: F
authors.lastname: Billoir
authors.affiliation: Laboratoire de Virologie Moléculaire, Tropicale et Transfusionnelle, Faculté de Médecine, Unité des Virus Emergents, Université de la Méditerranée, Marseille, France2.
authors.forename: R N
authors.initials: RN
authors.lastname: Charrel
authors.affiliation: Laboratoire de Virologie Moléculaire, Tropicale et Transfusionnelle, Faculté de Médecine, Unité des Virus Emergents, Université de la Méditerranée, Marseille, France2.
authors.forename: X
authors.initials: X
authors.lastname: de Lamballerie
mesh_terms: D001483:Base Sequence; D002160:Cambodia; D007560:Cote d'Ivoire; D018076:DNA, Complementary / Q000235:genetics; D003716:Dengue Virus / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D019143:Evolution, Molecular; D008040:Genetic Linkage / Q000235:genetics; D016679:Genome, Viral; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment; D012846:Singapore; D014765:Viral Vaccines / Q000009:adverse effects / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D012367:RNA, Viral; D014765:Viral Vaccines