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Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia

Veasna Duong 1 Cameron Simmons 2 Laurent Gavotte 3 Alain Viari 4 Sivuth Ong 1 Ngan Chantha 5 Niall J. Lennon 6 Bruce W. Birren 6 Sirenda Vong 1 Jeremy J. Farrar 2 Matthew R. Henn 6 Vincent Deubel 1 Roger Frutos 7 Philippe Buchy 1, *
* Corresponding author
1 Institut Pasteur du Cambodge
2 Hospital for Tropical Diseases
3 UM2 - Université Montpellier 2 - Sciences et Techniques
4 BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
5 CNM - National Center of Parasitology
6 BROAD INSTITUTE - Broad Institute of MIT and Harvard
7 UMR INTERTRYP - Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides
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.
keyword : Dengue virus DENV-1 diversity Lineage dynamics genome sequence Cambodia
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CNRS | INRIA | CIRAD | RIIP | RIIP_CAMBODGE | BAMBOO | BIOENVIS | AGROPOLIS | IRD | UNIV-LYON1 | UDL

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Veasna Duong, Cameron Simmons, Laurent Gavotte, Alain Viari, Sivuth Ong, et al.. Genetic diversity and lineage dynamic of dengue virus serotype 1 (DENV-1) in Cambodia. Infection, Genetics and Evolution, Elsevier, 2011, N/A (N/A), pp.N/A. ⟨10.1016/j.meegid.2011.06.019⟩. ⟨pasteur-00805484⟩

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