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Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evol 2022; 8:veac074. [PMID: 36128050 PMCID: PMC9477075 DOI: 10.1093/ve/veac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/12/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
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Affiliation(s)
- Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | - Jayna Ragwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala SE751 85, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
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2
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Transatlantic spread of highly pathogenic avian influenza H5N1 by wild birds from Europe to North America in 2021. Sci Rep 2022; 12:11729. [PMID: 35821511 PMCID: PMC9276711 DOI: 10.1038/s41598-022-13447-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) viruses of the A/Goose/Guangdong/1/1996 lineage (GsGd), which threaten the health of poultry, wildlife and humans, are spreading across Asia, Europe, Africa and North America but are currently absent from South America and Oceania. In December 2021, H5N1 HPAI viruses were detected in poultry and a free-living gull in St. John's, Newfoundland and Labrador, Canada. Our phylogenetic analysis showed that these viruses were most closely related to HPAI GsGd viruses circulating in northwestern Europe in spring 2021. Our analysis of wild bird migration suggested that these viruses may have been carried across the Atlantic via Iceland, Greenland/Arctic or pelagic routes. The here documented incursion of HPAI GsGd viruses into North America raises concern for further virus spread across the Americas by wild bird migration.
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Wang D, Li M, Xiong C, Yan Y, Hu J, Hao M, Liang B, Chen J, Chen G, Yang G, Li Y, Zhang J, Gulyaeva M, Shestopalov A, Shi W, Bi Y, Liu H, Wang H, Liu D, Chen J. Ecology of avian influenza viruses in migratory birds wintering within the Yangtze River wetlands. Sci Bull (Beijing) 2021; 66:2014-2024. [PMID: 36654171 DOI: 10.1016/j.scib.2021.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/15/2021] [Accepted: 03/09/2021] [Indexed: 02/03/2023]
Abstract
Migratory birds are considered natural reservoirs of avian influenza A viruses (AIVs). To further our viral ecology knowledge and understand the subsequent risk posed by wild birds, we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River, China. We collected over 8000 samples and isolated 122 AIV strains. Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases. The results showed that the Yangtze River wintering wetlands functioned as a mixing ground, where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences; moreover, a portion of AIV gene segments were persistent inter-seasonally. Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes. In addition, we observed that viral gene segments in wintering wetlands were closely related to known North American isolates, indicating that intercontinental gene flow occurred. Notably, highly pathogenic H5 and low pathogenic H9 viruses, which usually circulate in poultry, were found to have crossed the poultry/wild bird interface, with the viruses introduced to wintering birds. Overall, this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands. Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.
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Affiliation(s)
- Decheng Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingxin Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaochao Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Yan
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juefu Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China
| | - Mengchan Hao
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China
| | - Bilin Liang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Chen
- Hubei Wildlife Rescue, Research and Development Center, Wuhan 430074, China
| | - Guang Chen
- Hubei Wildlife Rescue, Research and Development Center, Wuhan 430074, China
| | - Guoxiang Yang
- Hubei Wildlife Rescue, Research and Development Center, Wuhan 430074, China
| | - Yong Li
- Hubei Wildlife Rescue, Research and Development Center, Wuhan 430074, China
| | - Jun Zhang
- Hubei Wildlife Rescue, Research and Development Center, Wuhan 430074, China
| | - Marina Gulyaeva
- Novosibirsk State University, Novosibirsk 630090, Russia; Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexander Shestopalov
- Novosibirsk State University, Novosibirsk 630090, Russia; Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Center for Influenza Research and Early Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China
| | - Haizhou Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China
| | - Hanzhong Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
| | - Jianjun Chen
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China; National Virus Resource Center, Chinese Academy of Sciences, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Influenza Research and Early Warning (CASCIRE), Chinese Academy of Sciences, Beijing 100101, China.
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4
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Everest H, Hill SC, Daines R, Sealy JE, James J, Hansen R, Iqbal M. The Evolution, Spread and Global Threat of H6Nx Avian Influenza Viruses. Viruses 2020; 12:v12060673. [PMID: 32580412 PMCID: PMC7354632 DOI: 10.3390/v12060673] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022] Open
Abstract
Avian influenza viruses of the subtype H6Nx are being detected globally with increasing frequency. Some H6Nx lineages are becoming enzootic in Asian poultry and sporadic incursions into European poultry are occurring more frequently. H6Nx viruses that contain mammalian adaptation motifs pose a zoonotic threat and have caused human cases. Although currently understudied globally, H6Nx avian influenza viruses pose a substantial threat to both poultry and human health. In this review we examine the current state of knowledge of H6Nx viruses including their global distribution, tropism, transmission routes and human health risk.
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Affiliation(s)
- Holly Everest
- The Pirbright Institute, Woking GU24 0NF, UK
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Sarah C Hill
- Department of Zoology, University of Oxford, Oxford OX1 3SZ UK
- Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Rebecca Daines
- The Pirbright Institute, Woking GU24 0NF, UK
- Pathobiology and Population Sciences, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | | | - Joe James
- Department of Virology, Animal and Plant Health Agency, Addlestone KT15 3NB, UK
| | - Rowena Hansen
- Department of Virology, Animal and Plant Health Agency, Addlestone KT15 3NB, UK
| | - Munir Iqbal
- The Pirbright Institute, Woking GU24 0NF, UK
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5
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Okuya K, Kanazawa N, Kanda T, Kuwahara M, Matsuu A, Horie M, Masatani T, Toda S, Ozawa M. Genetic characterization of an avian H4N6 influenza virus isolated from the Izumi plain, Japan. Microbiol Immunol 2018; 61:513-518. [PMID: 29023947 DOI: 10.1111/1348-0421.12545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/18/2017] [Accepted: 09/27/2017] [Indexed: 12/31/2022]
Abstract
An influenza A virus of H4N6 subtype was isolated from the Izumi plain, Japan, in 2013. Genetic analyses revealed that two viral genes (M and NS gene segments) of this isolate were genetically distinct from those of the H4N6 virus isolated from the same place in 2012. Furthermore, three viral genes (PB2, PB1 and M gene segments) of this isolate share high similarity with those of the North American isolates of 2014. These results suggest a high frequency of genetic reassortment of avian influenza viruses in Asian waterfowl and intercontinental movements of avian influenza viruses via migratory waterfowl.
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Affiliation(s)
- Kosuke Okuya
- Joint Faculty of Veterinary Medicine, Laboratory of Animal Hygiene, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan
| | - Norihiro Kanazawa
- Joint Faculty of Veterinary Medicine, Laboratory of Animal Hygiene, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan
| | - Takehiro Kanda
- Joint Faculty of Veterinary Medicine, Laboratory of Animal Hygiene, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan
| | | | - Aya Matsuu
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Yamaguchi 753-8515, Japan
| | - Masayuki Horie
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Yamaguchi 753-8515, Japan
| | - Tatsunori Masatani
- Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Yamaguchi 753-8515, Japan
| | - Shigehisa Toda
- Kagoshima Crane Conservation Committee, Izumi, Kagoshima 899-0208, Japan
| | - Makoto Ozawa
- Joint Faculty of Veterinary Medicine, Laboratory of Animal Hygiene, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan.,Transboundary Animal Diseases Research Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Kagoshima 890-0065, Japan.,United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Yamaguchi 753-8515, Japan
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6
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Fourment M, Darling AE, Holmes EC. The impact of migratory flyways on the spread of avian influenza virus in North America. BMC Evol Biol 2017; 17:118. [PMID: 28545432 PMCID: PMC5445350 DOI: 10.1186/s12862-017-0965-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/11/2017] [Indexed: 11/16/2022] Open
Abstract
Background Wild birds are the major reservoir hosts for influenza A viruses (AIVs) and have been implicated in the emergence of pandemic events in livestock and human populations. Understanding how AIVs spread within and across continents is therefore critical to the development of successful strategies to manage and reduce the impact of influenza outbreaks. In North America many bird species undergo seasonal migratory movements along a North-South axis, thereby providing opportunities for viruses to spread over long distances. However, the role played by such avian flyways in shaping the genetic structure of AIV populations remains uncertain. Results To assess the relative contribution of bird migration along flyways to the genetic structure of AIV we performed a large-scale phylogeographic study of viruses sampled in the USA and Canada, involving the analysis of 3805 to 4505 sequences from 36 to 38 geographic localities depending on the gene segment data set. To assist in this we developed a maximum likelihood-based genetic algorithm to explore a wide range of complex spatial models, depicting a more complete picture of the migration network than determined previously. Conclusions Based on phylogenies estimated from nucleotide sequence data sets, our results show that AIV migration rates are significantly higher within than between flyways, indicating that the migratory patterns of birds play a key role in viral dispersal. These findings provide valuable insights into the evolution, maintenance and transmission of AIVs, in turn allowing the development of improved programs for surveillance and risk assessment.
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Affiliation(s)
- Mathieu Fourment
- ithree institute, University of Technology Sydney, Sydney, Australia. .,Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
| | - Aaron E Darling
- ithree institute, University of Technology Sydney, Sydney, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia
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7
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Huang Y, Yang S, Hu B, Xu C, Gao D, Zhu M, Huang Q, Zhang L, Wu J, Zhang X, Khan MI. Genetic, pathogenic and antigenic diversity of Newcastle disease viruses in Shandong Province, China. Vet Microbiol 2015; 180:237-44. [DOI: 10.1016/j.vetmic.2015.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/29/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022]
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8
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Fries AC, Nolting JM, Bowman AS, Lin X, Halpin RA, Wester E, Fedorova N, Stockwell TB, Das SR, Dugan VG, Wentworth DE, Gibbs HL, Slemons RD. Spread and persistence of influenza A viruses in waterfowl hosts in the North American Mississippi migratory flyway. J Virol 2015; 89:5371-81. [PMID: 25741003 PMCID: PMC4442537 DOI: 10.1128/jvi.03249-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED While geographic distance often restricts the spread of pathogens via hosts, this barrier may be compromised when host species are mobile. Migratory waterfowl in the order Anseriformes are important reservoir hosts for diverse populations of avian-origin influenza A viruses (AIVs) and are assumed to spread AIVs during their annual continental-scale migrations. However, support for this hypothesis is limited, and it is rarely tested using data from comprehensive surveillance efforts incorporating both the temporal and spatial aspects of host migratory patterns. We conducted intensive AIV surveillance of waterfowl using the North American Mississippi Migratory Flyway (MMF) over three autumn migratory seasons. Viral isolates (n = 297) from multiple host species were sequenced and analyzed for patterns of gene dispersal between northern staging and southern wintering locations. Using a phylogenetic and nucleotide identity framework, we observed a larger amount of gene dispersal within this flyway rather than between the other three longitudinally identified North American flyways. Across seasons, we observed patterns of regional persistence of diversity for each genomic segment, along with limited survival of dispersed AIV gene lineages. Reassortment increased with both time and distance, resulting in transient AIV constellations. This study shows that within the MMF, AIV gene flow favors spread along the migratory corridor within a season, and also that intensive surveillance during bird migration is important for identifying virus dispersal on time scales relevant to pandemic responsiveness. In addition, this study indicates that comprehensive monitoring programs to capture AIV diversity are critical for providing insight into AIV evolution and ecology in a major natural reservoir. IMPORTANCE Migratory birds are a reservoir for antigenic and genetic diversity of influenza A viruses (AIVs) and are implicated in the spread of virus diversity that has contributed to previous pandemic events. Evidence for dispersal of avian-origin AIVs by migratory birds is rarely examined on temporal scales relevant to pandemic or panzootic threats. Therefore, characterizing AIV movement by hosts within a migratory season is important for implementing effective surveillance strategies. We conducted surveillance following birds along a major North American migratory route and observed that within a migratory season, AIVs rapidly reassorted and gene lineages were dispersed primarily within the migratory corridor. Patterns of regional persistence were observed across seasons for each gene segment. We show that dispersal of AIV gene lineages by migratory birds occurs quickly along migratory routes and that surveillance for AIVs threatening human and animal health should focus attention on these routes.
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Affiliation(s)
- Anthony C Fries
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Xudong Lin
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Eric Wester
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Nadia Fedorova
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - Suman R Das
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | - Vivien G Dugan
- J. Craig Venter Institute, Virology, Rockville, Maryland, USA
| | | | - H Lisle Gibbs
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, USA Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - Richard D Slemons
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
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Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States. INFECTION GENETICS AND EVOLUTION 2014; 26:185-93. [PMID: 24910106 DOI: 10.1016/j.meegid.2014.05.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/14/2014] [Accepted: 05/27/2014] [Indexed: 11/21/2022]
Abstract
The Southwest United States, including Arizona and New Mexico, has a diverse climate and is home to many different avian species. We sequenced the hemagglutinin (HA) gene of twenty influenza specimens for the years 2007-2009. This included four from Arizona, and sixteen from New Mexico. We analyzed the sequences and determined the following HA subtypes: H3, H4, H6, H8, and H11. For each subtype, we combined our virus sequences with those from a public database, and inferred phylogeographic models of influenza diffusion. Statistical phylogeography indicated that overall evolutionary diffusion of avian influenza viruses is geographically structured (p<0.05). In addition, we found that diffusion to the Southwest was often from nearby states including California. For H3, H4 and H6, the intra-flyway gene flow rates were significantly (p<0.001) higher than those of inter-flyway. Such rate difference was also observed in H8 and H11, yet, without statistical significance (p=0.132, p=0.190, respectively). Excluding any one flyway from the calculation generated similar results, suggesting that such barrier effect on gene flow rates is not exclusively produced by any single flyway. We also calculated the Bayes factor test for the significant non-zero rates between states and identified significant routes both within and across flyways. Such inter-flyway spread of influenza was probably the result of birds from four flyways co-mingling on breeding grounds in northern regions or marshaling on staging areas post breeding in Canada or Alaska, before moving south each fall. This study provides an initial analysis of evolutionary diffusion of avian influenza virus to and from the Southwest United States. However, more sequences from this region need to be generated to determine the role of host migration and other factors on influenza diffusion.
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10
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Huang Y, Wille M, Benkaroun J, Munro H, Bond AL, Fifield DA, Robertson GJ, Ojkic D, Whitney H, Lang AS. Perpetuation and reassortment of gull influenza A viruses in Atlantic North America. Virology 2014; 456-457:353-63. [PMID: 24889254 DOI: 10.1016/j.virol.2014.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 03/24/2014] [Accepted: 04/04/2014] [Indexed: 12/09/2022]
Abstract
Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of sampled gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics.
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Affiliation(s)
- Yanyan Huang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Michelle Wille
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Jessica Benkaroun
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Hannah Munro
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Alexander L Bond
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - David A Fifield
- Newfoundland and Labrador Department of Natural Resources, P.O. Box 7400, St. John's, NL, Canada A1E 3Y5
| | - Gregory J Robertson
- Wildlife Research Division, Environment Canada, 6 Bruce St., Mount Pearl, NL, Canada A1N 4T3
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Box 3612, Guelph, ON, Canada N1H 6R8
| | - Hugh Whitney
- Newfoundland and Labrador Department of Natural Resources, P.O. Box 7400, St. John's, NL, Canada A1E 3Y5
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9.
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