Bayesian Inference Reveals Host-Specific Contributions to the Epidemic Expansion of Influenza A H5N1.
Since its first isolation in 1996 in Guangdong, China, the highly pathogenic avian influenza virus (HPAIV) H5N1 has circulated in avian hosts for almost two decades and spread to more than 60 countries worldwide. The role of different avian hosts and the domestic-wild bird interface has been critical in shaping the complex HPAIV H5N1 disease ecology, but remains difficult to ascertain. To shed light on the large-scale H5N1 transmission patterns and disentangle the contributions of different avian hosts on the tempo and mode of HPAIV H5N1 dispersal, we apply Bayesian evolutionary inference techniques to comprehensive sets of hemagglutinin and neuraminidase gene sequences sampled between 1996 and 2011 throughout Asia and Russia. Our analyses demonstrate that the large-scale H5N1 transmission dynamics are structured according to different avian flyways, and that the incursion of the Central Asian flyway specifically was driven by Anatidae hosts coinciding with rapid rate of spread and an epidemic wavefront acceleration. This also resulted in long-distance dispersal that is likely to be explained by wild bird migration. We identify a significant degree of asymmetry in the large-scale transmission dynamics between Anatidae and Phasianidae, with the latter largely representing poultry as an evolutionary sink. A joint analysis of host dynamics and continuous spatial diffusion demonstrates that the rate of viral dispersal and host diffusivity is significantly higher for Anatidae compared with Phasianidae. These findings complement risk modeling studies and satellite tracking of wild birds in demonstrating a continental-scale structuring into areas of H5N1 persistence that are connected through migratory waterfowl.
Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium nidia.sequeiratrovao@rega.kuleuven.be.
Nídia Sequeira
NS
Trovão
Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles.
Marc A
MA
Suchard
Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium.
Guy
G
Baele
Biological Control and Spatial Ecology, Université Libre de Bruxelles, Brussels, Belgium Fonds National de la Recherche Scientifique, Brussels, Belgium.
Marius
M
Gilbert
Department of Microbiology and Immunology, Rega Institute, KU Leuven-University of Leuven, Leuven, Belgium.
Philippe
P
Lemey
D025041:Animal Migration; D000818:Animals; D001208:Asia / Q000453:epidemiology; D001499:Bayes Theorem; D005075:Biological Evolution; D001717:Birds / Q000235:genetics / Q000821:virology*; D002681:China / Q000453:epidemiology; D004196:Disease Outbreaks; D054884:Host-Pathogen Interactions; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics / Q000472:pathogenicity / Q000502:physiology*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000473:pathology / Q000821:virology*; D058974:Phylogeography / Q000379:methods; D012426:Russia / Q000453:epidemiology; D017422:Sequence Analysis, DNA
Bayesian inference; H5N1; disease ecology; phylogeography; viral evolution