title: Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data.
abstract: Low pathogenic avian influenza A viruses (IAVs) have a natural host reservoir in wild waterbirds and the potential to spread to other host species. Here, we investigated the evolutionary, spatial and temporal dynamics of avian IAVs in Eurasian wild birds. We used whole-genome sequences collected as part of an intensive long-term Eurasian wild bird surveillance study, and combined this genetic data with temporal and spatial information to explore the virus evolutionary dynamics. Frequent reassortment and co-circulating lineages were observed for all eight genomic RNA segments over time. There was no apparent species-specific effect on the diversity of the avian IAVs. There was a spatial and temporal relationship between the Eurasian sequences and significant viral migration of avian IAVs from West Eurasia towards Central Eurasia. The observed viral migration patterns differed between segments. Furthermore, we discuss the challenges faced when analysing these surveillance and sequence data, and the caveats to be borne in mind when drawing conclusions from the apparent results of such analyses.
authors.affiliation: Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
authors.forename: Nicola S
authors.initials: NS
authors.lastname: Lewis
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Josanne H
authors.initials: JH
authors.lastname: Verhagen
authors.affiliation: Institute of Ecology, Ilia State University, 3/5 Cholokashvili, Tbilisi, Georgia.
authors.forename: Zurab
authors.initials: Z
authors.lastname: Javakhishvili
authors.affiliation: Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK.
authors.forename: Colin A
authors.initials: CA
authors.lastname: Russell
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Pascal
authors.initials: P
authors.lastname: Lexmond
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Kim B
authors.initials: KB
authors.lastname: Westgeest
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Theo M
authors.initials: TM
authors.lastname: Bestebroer
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Halpin
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: Xudong
authors.initials: X
authors.lastname: Lin
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: Amy
authors.initials: A
authors.lastname: Ransier
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: Nadia B
authors.initials: NB
authors.lastname: Fedorova
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.|Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Neus
authors.initials: N
authors.lastname: Latorre-Margalef
authors.affiliation: Department of Medical Sciences, Zoonosis Science Center, Uppsala University, Uppsala, Sweden.
authors.forename: Björn
authors.initials: B
authors.lastname: Olsen
authors.affiliation: Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.
authors.forename: Gavin
authors.initials: G
authors.lastname: Smith
authors.affiliation: Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore.|Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX, 77030, USA.
authors.forename: Justin
authors.initials: J
authors.lastname: Bahl
authors.affiliation: J. Craig Venter Institute, Rockville, MD, 20850, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.affiliation: Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Waldenström
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Ron A M
authors.initials: RAM
authors.lastname: Fouchier
authors.affiliation: Department of Viroscience, Erasmus MC, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
authors.forename: Miranda
authors.initials: M
authors.lastname: de Graaf
mesh_terms: D025041:Animal Migration; D000818:Animals; D000835:Animals, Wild / Q000821:virology; D001717:Birds / Q000502:physiology / Q000821:virology; D019143:Evolution, Molecular; D016679:Genome, Viral; D009980:Influenza A virus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000503:physiopathology / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D012367:RNA, Viral / Q000235:genetics
chemical_list: D012367:RNA, Viral