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Genetic structure of Pacific Flyway avian influenza viruses is shaped by geographic location, host species, and sampling period

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Abstract

The eight gene segments of avian influenza virus (AIV) reassort frequently and rapidly to generate novel genotypes and subtypes that are transmissible to a broad range of hosts. There is evidence that AIV can have a restricted host range and can segregate in space and time. Host–virus relationships at the species, geographic, and spatial scales have not been fully defined for AIV populations of the Pacific Flyway, particularly among the diverse waterfowl that occupy the Flyway in Alaska and California. Using the sequence analysis program Bayesian Tip-association Significance testing (BaTS) created for analysis of phylogeny–trait associations, we determined whether the genetic structure of Pacific Flyway AIVs sampled between 2006 and 2008 was influenced by the host species, geographic location of virus collection, and time of sampling. In posterior sets of trees, genetically similar viruses clustered by host species for thick-billed murres and glaucous gulls (order Charadriiformes), and for northern shovelers, northern pintails, and mallards (order Anseriformes). AIVs from Alaska and California were strongly spatially structured, clustering separately by region across all segments. The timing of sampling influenced the genetic structure of California AIV gene segments, possibly reflecting waves of host species movement into wintering areas. The strength of phylogeny–trait association varied by virus segment and by trait of interest, which we hypothesize is related to the frequent genetic reassortment and interspecies transmission in waterfowl.

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Acknowledgments

We thank the field and laboratory personnel at the University of Alaska Fairbanks and the University of California Davis who were involved in bird sampling and processing of virus isolates for analysis. Thanks to Tracey Goldstein (UC Davis) and Tasha Belfiore for helpful guidance on the data analysis and manuscript preparation. Funding for this research was provided by the National Institute of Allergy and Infectious Disease (contract HHSN266200700009C).

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Authors and Affiliations

  1. School of Veterinary Medicine, Wildlife Health Center, University of California Davis, One Shields Avenue, Davis, CA, 95616, USA

    Yvette A. Girard & Walter Boyce

  2. Division of Comparative Medicine and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

    Jonathan A. Runstadler

  3. Institute of Arctic Biology, Department of Biology and Wildlife, University of Alaska, Fairbanks, AK, 99775, USA

    Florian Aldehoff

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  1. Yvette A. Girard
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  2. Jonathan A. Runstadler
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Correspondence to Yvette A. Girard.

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Girard, Y.A., Runstadler, J.A., Aldehoff, F. et al. Genetic structure of Pacific Flyway avian influenza viruses is shaped by geographic location, host species, and sampling period. Virus Genes 44, 415–428 (2012). https://doi.org/10.1007/s11262-011-0706-5

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