Sci Rep.: co-auth.: I. Xenarios

Sci Rep. 2016 Jul 25;6:30316. doi: 10.1038/srep30316.

Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors.

Author information

  • 1Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium.
  • 2Emergency Center for Transboundary Animal Diseases (ECTAD), Food and Agriculture Organization of the United Nations, Hanoi, Viet Nam.
  • 3Department of Animal Husbandry &Dairying, Government of Haryana, India.
  • 4Earth and Life Institute (ELI), Université catholique de Louvain (UCL), Louvain-la-Neuve, Belgium.
  • 5Department of Geography, Université de Namur, Namur, Belgium.
  • 6Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Seibersdorf, Austria.
  • 7Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro (Padua), Italy.
  • 8Swiss-Prot &Vital-IT group, Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
  • 9Center for Integrative Genomics (CIG), University of Lausanne, Lausanne, Switzerland.
  • 10Department of Animal Health, Epidemiology Division, Ministry of Agriculture and Rural Development, Hanoi, Viet Nam.
  • 11Emergency Center for Transboundary Animal Diseases (ECTAD), FAO Regional Office for Asia and the Pacific (FAO-RAP), Bangkok, Thailand.
  • 12Animal Production and Health Division (AGAH), Food and Agriculture Organization of the United Nations (FAO), Rome, Italy.
  • 13Fonds National de la Recherche Scientifique, Brussels, Belgium.


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.

PMID: 27453195