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Viruses 2015, 7(6), 3310-3328; doi:10.3390/v7062773

Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks

1
Environmental and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait City, Safat 13109, Kuwait
2
Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MA 55108, USA
3
Department of Evolution and Ecology, Center for Population Biology, University of California Davis, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Eric O. Freed
Received: 7 April 2015 / Revised: 2 June 2015 / Accepted: 16 June 2015 / Published: 23 June 2015
(This article belongs to the Section Animal Viruses)
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Abstract

Previous Bayesian phylogeographic studies of H5N1 highly pathogenic avian influenza viruses (HPAIVs) explored the origin and spread of the epidemic from China into Russia, indicating that HPAIV circulated in Russia prior to its detection there in 2005. In this study, we extend this research to explore the evolution and spread of HPAIV within Europe during the 2005–2010 epidemic, using all available sequences of the hemagglutinin (HA) and neuraminidase (NA) gene regions that were collected in Europe and Russia during the outbreak. We use discrete-trait phylodynamic models within a Bayesian statistical framework to explore the evolution of HPAIV. Our results indicate that the genetic diversity and effective population size of HPAIV peaked between mid-2005 and early 2006, followed by drastic decline in 2007, which coincides with the end of the epidemic in Europe. Our results also suggest that domestic birds were the most likely source of the spread of the virus from Russia into Europe. Additionally, estimates of viral dispersal routes indicate that Russia, Romania, and Germany were key epicenters of these outbreaks. Our study quantifies the dynamics of a major European HPAIV pandemic and substantiates the ability of phylodynamic models to improve molecular surveillance of novel AIVs. View Full-Text
Keywords: H5N1; highly pathogenic avian influenza; phylodynamic models; Bayesian inference; phylogeography; Europe; Russia; surveillance H5N1; highly pathogenic avian influenza; phylodynamic models; Bayesian inference; phylogeography; Europe; Russia; surveillance
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Alkhamis, M.A.; Moore, B.R.; Perez, A.M. Phylodynamics of H5N1 Highly Pathogenic Avian Influenza in Europe, 2005–2010: Potential for Molecular Surveillance of New Outbreaks. Viruses 2015, 7, 3310-3328.

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