title: Fluid Spatial Dynamics of West Nile Virus in the United States: Rapid Spread in a Permissive Host Environment.
abstract: The introduction of West Nile virus (WNV) into North America in 1999 is a classic example of viral emergence in a new environment, with its subsequent dispersion across the continent having a major impact on local bird populations. Despite the importance of this epizootic, the pattern, dynamics, and determinants of WNV spread in its natural hosts remain uncertain. In particular, it is unclear whether the virus encountered major barriers to transmission, or spread in an unconstrained manner, and if specific viral lineages were favored over others indicative of intrinsic differences in fitness. To address these key questions in WNV evolution and ecology, we sequenced the complete genomes of approximately 300 avian isolates sampled across the United States between 2001 and 2012. Phylogenetic analysis revealed a relatively star-like tree structure, indicative of explosive viral spread in the United States, although with some replacement of viral genotypes through time. These data are striking in that viral sequences exhibit relatively limited clustering according to geographic region, particularly for those viruses sampled from birds, and no strong phylogenetic association with well-sampled avian species. The genome sequence data analyzed here also contain relatively little evidence for adaptive evolution, particularly of structural proteins, suggesting that most viral lineages are of similar fitness and that WNV is well adapted to the ecology of mosquito vectors and diverse avian hosts in the United States. In sum, the molecular evolution of WNV in North America depicts a largely unfettered expansion within a permissive host and geographic population with little evidence of major adaptive barriers.
  
  
  OBJECTIVE
  How viruses spread in new host and geographic environments is central to understanding the emergence and evolution of novel infectious diseases and for predicting their likely impact. The emergence of the vector-borne West Nile virus (WNV) in North America in 1999 represents a classic example of this process. Using approximately 300 new viral genomes sampled from wild birds, we show that WNV experienced an explosive spread with little geographical or host constraints within birds and relatively low levels of adaptive evolution. From its introduction into the state of New York, WNV spread across the United States, reaching California and Florida within 4 years, a migration that is clearly reflected in our genomic sequence data, and with a general absence of distinct geographical clusters of bird viruses. However, some geographically distinct viral lineages were found to circulate in mosquitoes, likely reflecting their limited long-distance movement compared to avian species.
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Francesca
authors.initials: F
authors.lastname: Di Giallonardo
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors.forename: Jemma L
authors.initials: JL
authors.lastname: Geoghegan
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, USA.
authors.forename: Douglas E
authors.initials: DE
authors.lastname: Docherty
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, USA.
authors.forename: Robert G
authors.initials: RG
authors.lastname: McLean
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Zody
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: James
authors.initials: J
authors.lastname: Qu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Bruce W
authors.initials: BW
authors.lastname: Birren
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Christine M
authors.initials: CM
authors.lastname: Malboeuf
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
authors.forename: Ruchi M
authors.initials: RM
authors.lastname: Newman
authors.affiliation: U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, USA.
authors.forename: Hon S
authors.identifier: http://orcid.org/0000-0003-4844-7533
authors.initials: HS
authors.lastname: Ip
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia edward.holmes@sydney.edu.au.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
mesh_terms: D000818:Animals; D001715:Bird Diseases / Q000453:epidemiology* / Q000635:transmission* / Q000821:virology; D016000:Cluster Analysis; D018562:Disease Transmission, Infectious; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D058974:Phylogeography; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D014481:United States / Q000453:epidemiology; D014901:West Nile Fever / Q000453:epidemiology / Q000635:transmission / Q000662:veterinary*; D014902:West Nile virus / Q000145:classification / Q000235:genetics / Q000302:isolation & purification