title: Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors.
abstract: The highly pathogenic avian influenza (HPAI) H5N1 virus has been circulating in Asia since 2003 and diversified into several genetic lineages, or clades. Although the spatial distribution of its outbreaks was extensively studied, differences in clades were never previously taken into account. We developed models to quantify associations over time and space between different HPAI H5N1 viruses from clade 1, 2.3.4 and 2.3.2 and agro-ecological factors. We found that the distribution of clades in the Mekong region from 2004 to 2013 was strongly regionalised, defining specific epidemiological zones, or epizones. Clade 1 became entrenched in the Mekong Delta and was not supplanted by newer clades, in association with a relatively higher presence of domestic ducks. In contrast, two new clades were introduced (2.3.4 and 2.3.2) in northern Viet Nam and were associated with higher chicken density and more intensive chicken production systems. We suggest that differences in poultry production systems in these different epizones may explain these associations, along with differences in introduction pressure from neighbouring countries. The different distribution patterns found at the clade level would not be otherwise apparent through analysis treating all outbreaks equally, which requires improved linking of disease outbreak records and genetic sequence data.
authors.affiliation: Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.
authors.forename: Jean
authors.initials: J
authors.lastname: Artois
authors.affiliation: Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam.
authors.forename: Scott H
authors.initials: SH
authors.lastname: Newman
authors.affiliation: Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.|Department of Animal Husbandry &Dairying, Government of Haryana, India.
authors.forename: Madhur S
authors.initials: MS
authors.lastname: Dhingra
authors.affiliation: Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.|Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium.
authors.forename: Celia
authors.initials: C
authors.lastname: Chaiban
authors.affiliation: Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.|Department of Geography, Université de Namur, Namur, Belgium.
authors.forename: Catherine
authors.initials: C
authors.lastname: Linard
authors.affiliation: Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Seibersdorf, Austria.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Cattoli
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy.
authors.forename: Isabella
authors.initials: I
authors.lastname: Monne
authors.affiliation: Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy.
authors.forename: Alice
authors.initials: A
authors.lastname: Fusaro
authors.affiliation: Swiss-Prot &Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.|Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland.
authors.forename: Ioannis
authors.initials: I
authors.lastname: Xenarios
authors.affiliation: Swiss-Prot &Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Robin
authors.initials: R
authors.lastname: Engler
authors.affiliation: Swiss-Prot &Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Robin
authors.initials: R
authors.lastname: Liechti
authors.affiliation: Swiss-Prot &Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Dmitri
authors.initials: D
authors.lastname: Kuznetsov
authors.affiliation: Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam.
authors.forename: Thanh Long
authors.initials: TL
authors.lastname: Pham
authors.affiliation: Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam.
authors.forename: Tung
authors.initials: T
authors.lastname: Nguyen
authors.affiliation: Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam.
authors.forename: Van Dong
authors.initials: VD
authors.lastname: Pham
authors.affiliation: Emergency Center for Transboundary Animal Diseases (ECTAD), FAO Regional Office for Asia and the Pacific (FAO-RAP), Bangkok, Thailand.
authors.forename: David
authors.initials: D
authors.lastname: Castellan
authors.affiliation: Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
authors.forename: Sophie
authors.initials: S
authors.lastname: Von Dobschuetz
authors.affiliation: Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
authors.forename: Filip
authors.initials: F
authors.lastname: Claes
authors.affiliation: Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
authors.forename: Gwenaëlle
authors.initials: G
authors.lastname: Dauphin
authors.affiliation: Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam.
authors.forename: Ken
authors.initials: K
authors.lastname: Inui
authors.affiliation: Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.|Fonds National de la Recherche Scientifique, Brussels, Belgium.
authors.forename: Marius
authors.initials: M
authors.lastname: Gilbert
mesh_terms: D000383:Agriculture; D000818:Animals; D002645:Chickens; D004196:Disease Outbreaks; D004372:Ducks; D005838:Genotype; D005843:Geography; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification* / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D010802:Phylogeny; D058974:Phylogeography; D011201:Poultry Diseases / Q000453:epidemiology / Q000821:virology; D012959:Socioeconomic Factors; D062206:Spatial Analysis; D014744:Vietnam / Q000453:epidemiology