title: Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia.
abstract: In Cambodia, dengue virus (DENV) was first isolated in 1963 and has become endemic with peak epidemic during raining season. Since 2000, the Dengue National Control Program has reported from 10,000 to 40,000 cases per year with fatality rates ranging from 0.7 to 1.7. All four dengue serotypes are found circulating in Cambodia with alternative predominance of serotypes DENV-2 and DENV-3. The DENV-1 represents from 5% to 20% of all circulating viruses, depending upon the year. In this work, 79 clinical strains of DENV-1 were isolated between 2000 and 2009 and their genome fully sequenced. Four distinct lineages with different dynamics were identified. The main evolutionary drive was negative selective pressure but each lineage was characterized by the presence of specific mutations acquired through evolution. Coexistence, extinction and replacement of lineages occurred over the 10-year period. Lineages 1, 2 and 3 were all detected since 2000-2002 and disappeared in 2003, 2004-2005 and 2007, respectively. Lineages 1 and 2 displayed different dynamics. Lineage 1 was very diverse whereas lineage 2 was very homogeneous. Lineage 4 which derived from lineage 3 in 2003 remained the only one at the end of the sampling period in 2008-2009 owing to a selective sweep. The lineages dynamic of DENV-1 viruses and consequences for molecular epidemiology are discussed.
authors.affiliation: Institut Pasteur in Cambodia, Réseau International des Instituts Pasteur, 5 Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia.
authors.forename: Veasna
authors.initials: V
authors.lastname: Duong
authors.forename: Cameron
authors.initials: C
authors.lastname: Simmons
authors.forename: Laurent
authors.initials: L
authors.lastname: Gavotte
authors.forename: Alain
authors.initials: A
authors.lastname: Viari
authors.forename: Sivuth
authors.initials: S
authors.lastname: Ong
authors.forename: Ngan
authors.initials: N
authors.lastname: Chantha
authors.forename: Niall J
authors.initials: NJ
authors.lastname: Lennon
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.forename: Sirenda
authors.initials: S
authors.lastname: Vong
authors.forename: Jeremy J
authors.initials: JJ
authors.lastname: Farrar
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Henn
authors.forename: Vincent
authors.initials: V
authors.lastname: Deubel
authors.forename: Roger
authors.initials: R
authors.lastname: Frutos
authors.forename: Philippe
authors.initials: P
authors.lastname: Buchy
mesh_terms: D000293:Adolescent; D000328:Adult; D002160:Cambodia / Q000453:epidemiology; D002648:Child; D002675:Child, Preschool; D003715:Dengue / Q000453:epidemiology*; D003716:Dengue Virus / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D005814:Genes, Viral; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D007223:Infant; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D011110:Polymorphism, Genetic; D019655:Quantitative Trait, Heritable; D012367:RNA, Viral / Q000235:genetics; D012641:Selection, Genetic; D055815:Young Adult
chemical_list: D012367:RNA, Viral