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Journal articles
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
4
BAMBOO - An algorithmic view on genomes, cells, and environments
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
Veasna Duong 1
Author
Cameron Simmons 2
Author
Laurent Gavotte 3
Mail :
Author IdHAL : lgavotte
Alain Viari 4
Mail :
Author IdHAL : alain-viari ORCID : https://orcid.org/0000-0002-1329-7777
Roger Frutos 7
Author
Philippe Buchy 1
Mail :
Correspondent author
1
Institut Pasteur du Cambodge (BP 983 - 5 , Boulevard Monivong, Phnom Penh - Cambodia)
- RIIP - Réseau International des Instituts Pasteur (25, rue du Dr Roux 75724 Paris Cedex 15 - France)
2
Hospital for Tropical Diseases (Ho Chi Minh City - Vietnam)
- OUCRU - Oxford University Clinical Research Unit [Ho Chi Minh City] (190 Ben Ham Tu, District 5, Ho Chi Minh City - Vietnam)
3
UM2 - Université Montpellier 2 - Sciences et Techniques (Place Eugène Bataillon - 34095 Montpellier cedex 5 - France)
4
BAMBOO - An algorithmic view on genomes, cells, and environments (Laboratoire de Biométrie et Biologie Évolutive. UMR CNRS 5558 Campus de La Doua - Université Claude Bernard - Lyon 1 Bâtiment Grégoire Mendel - 16 rue Raphael Dubois 69 100 Villeurbanne -- INRIA Grenoble - Rhône-Alpes Inovallée 655 avenue de l'Europe -Montbonnot 38 334 Saint Ismier Cedex France - France)
- Inria Grenoble - Rhône-Alpes (Inovallée
655 avenue de l'Europe
38330 Montbonnot - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (43 Bld du 11 Novembre 1918 69622 VILLEURBANNE CEDEX - France)
- UCBL - Université Claude Bernard Lyon 1 (43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex - France)
- Université de Lyon (92 rue Pasteur - CS 30122, 69361 Lyon Cedex 07 - France)
- Inria - Institut National de Recherche en Informatique et en Automatique (Domaine de Voluceau Rocquencourt - BP 105 78153 Le Chesnay Cedex - France)
- VAS - VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (Université de Lyon, VetAgro Sup, 69280 Marcy l'Etoile (campus vétérinaire); Université de Clermont, VetAgro Sup, 63370 Lempdes (campus agronomique) - France)
- CNRS - Centre National de la Recherche Scientifique : UMR5558 (France)
- UCBL - Université Claude Bernard Lyon 1 (43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex - France)
5
CNM - National Center of Parasitology (National Center for Parasitology, Entomology and Malaria Control #372 Monivong Blvd (Corner St.322) - Cambodia)
- National Malaria Center [Phnom Penh] (372 boulevard Monivong, Phnom Penh - Cambodia)
6
BROAD INSTITUTE - Broad Institute of MIT and Harvard (Cambridge, MA 02142 - United States)
- HMS - Harvard Medical School [Boston] (25 Shattuck Street Boston, MA 02115 - United States)
- MIT - Massachusetts Institute of Technology (77 Massachusetts Ave, Cambridge, MA 02139 - United States)
- Massachusetts General Hospital [Boston] (55 Fruit Street Boston, MA 02114 - United States)
7
UMR INTERTRYP - Interactions hôtes-vecteurs-parasites-environnement dans les maladies tropicales négligées dues aux trypanosomatides (Campus International de Baillarguet TA A-17/G 34398 Montpellier cedex 5 - France)
- Cirad - Centre de Coopération Internationale en Recherche Agronomique pour le Développement : UMR17 (Siège 42, rue Scheffer 75116 Paris - France)
- UCBL - Université Claude Bernard Lyon 1 (43, boulevard du 11 novembre 1918, 69622 Villeurbanne cedex - France)
- Université de Lyon (92 rue Pasteur - CS 30122, 69361 Lyon Cedex 07 - France)
- IRD - Institut de Recherche pour le Développement : UMR177 (Siège Le Sextant 44, bd de Dunkerque CS 90009 13572 Marseille cedex 02 - France)
- UB - Université de Bordeaux (35, place Pey Berland - 33076 Bordeaux - France)
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.
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https://hal-riip.archives-ouvertes.fr/pasteur-00805484
Contributor : Philippe Buchy <>
Submitted on : Thursday, March 28, 2013 - 9:10:46 AM
Last modification on : Tuesday, February 11, 2020 - 10:10:29 AM
Document(s) archivé(s) le : Sunday, April 2, 2017 - 9:24:15 PM
Contributor : Philippe Buchy <>
Submitted on : Thursday, March 28, 2013 - 9:10:46 AM
Last modification on : Tuesday, February 11, 2020 - 10:10:29 AM
Document(s) archivé(s) le : Sunday, April 2, 2017 - 9:24:15 PM
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Identifiers
- HAL Id : pasteur-00805484, version 1
- DOI : 10.1016/j.meegid.2011.06.019
- PUBMED : 21757030
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Citation
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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