Virus Genes

, Volume 44, Issue 3, pp 415–428

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

  • Yvette A. Girard
  • Jonathan A. Runstadler
  • Florian Aldehoff
  • Walter Boyce

DOI: 10.1007/s11262-011-0706-5

Cite this article as:
Girard, Y.A., Runstadler, J.A., Aldehoff, F. et al. Virus Genes (2012) 44: 415. doi:10.1007/s11262-011-0706-5


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.


Avian influenza virus Pacific Flyway Bayesian Phylogeny Anseriformes Charadriiformes 

Supplementary material

11262_2011_706_MOESM1_ESM.pdf (183 kb)
Online Resource 1 (PDF 182 kb)
11262_2011_706_MOESM2_ESM.pdf (194 kb)
Online Resource 2 (PDF 193 kb)
11262_2011_706_MOESM3_ESM.pdf (189 kb)
Online Resource 3 (PDF 188 kb)
11262_2011_706_MOESM4_ESM.pdf (273 kb)
Online Resource 4 (PDF 272 kb)
11262_2011_706_MOESM5_ESM.pdf (293 kb)
Supplementary material 5 (PDF 292 kb)
11262_2011_706_MOESM6_ESM.pdf (288 kb)
Online Resource 6 (PDF 287 kb)
11262_2011_706_MOESM7_ESM.pdf (305 kb)
Online Resource 7 (PDF 304 kb)

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Yvette A. Girard
    • 1
  • Jonathan A. Runstadler
    • 2
  • Florian Aldehoff
    • 3
  • Walter Boyce
    • 1
  1. 1.School of Veterinary Medicine, Wildlife Health CenterUniversity of California DavisDavisUSA
  2. 2.Division of Comparative Medicine and Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  3. 3.Institute of Arctic Biology, Department of Biology and WildlifeUniversity of AlaskaFairbanksUSA

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