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Druzyaka AV, Druzyaka OR, Sharshov KA, Kasianov N, Dubovitskiy N, Derko AA, Frolov IG, Torniainen J, Wang W, Minina MA, Shestopalov AM. Stable Isotope Analysis Reveals Common Teal ( Anas crecca) Molting Sites in Western Siberia: Implications for Avian Influenza Virus Spread. Microorganisms 2024; 12:357. [PMID: 38399761 PMCID: PMC10891923 DOI: 10.3390/microorganisms12020357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The wetlands of southwestern Siberia (SWS) are a crossroads of bird migration routes, bringing avian influenza (AIV) strains that were previously isolated in different regions of the continent to Siberia. It is known that Anseriformes that breed in SWS migrate for the winter to central Hindustan or further west, while their migration routes to southeast Asia (SEA) remain unconfirmed. Here, we mapped the molting sites of the migrating Common Teals (Anas crecca) via analyzing stable hydrogen isotope content in feathers of hunters' prey and supplemented the analysis with the genetic structure of viruses isolated from teals in the same region. Post-breeding molt of autumn teals most likely occurred within the study region, whereas probable pre-breeding molting grounds of spring teals were in the south of Hindustan. This link was supported by viral phylogenetic analysis, which showed a close relationship between SWS isolates and viruses from south and southeast Asia. Most viral segments have the highest genetic similarity and the closest phylogenetic relationships with viruses from teal wintering areas in southeast Asian countries, including India and Korea. We assume that the winter molt of SWS breeding teals on the Hindustan coast suggests contacts with the local avifauna, including species migrating along the coast to SEA. Perhaps this is one of the vectors of AIV transmission within Eurasia.
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Affiliation(s)
- Alexey V. Druzyaka
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Olga R. Druzyaka
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Kirill A. Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Nikita Kasianov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Anastasiya A. Derko
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Ivan G. Frolov
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
- Institute of Zoology, Ministry of Science and Higher Education of the Republic of Kazakhstan, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Jyrki Torniainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
- Open Science Centre, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Mariya A. Minina
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
| | - Alexander M. Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
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Kent CM, Bevins SN, Mullinax JM, Sullivan JD, Prosser DJ. Waterfowl show spatiotemporal trends in influenza A H5 and H7 infections but limited taxonomic variation. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2906. [PMID: 37522765 DOI: 10.1002/eap.2906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023]
Abstract
Influenza A viruses in wild birds pose threats to the poultry industry, wild birds, and human health under certain conditions. Of particular importance are wild waterfowl, which are the primary reservoir of low-pathogenicity influenza viruses that ultimately cause high-pathogenicity outbreaks in poultry farms. Despite much work on the drivers of influenza A virus prevalence, the underlying viral subtype dynamics are still mostly unexplored. Nevertheless, understanding these dynamics, particularly for the agriculturally significant H5 and H7 subtypes, is important for mitigating the risk of outbreaks in domestic poultry farms. Here, using an expansive surveillance database, we take a large-scale look at the spatial, temporal, and taxonomic drivers in the prevalence of these two subtypes among influenza A-positive wild waterfowl. We document spatiotemporal trends that are consistent with past work, particularly an uptick in H5 viruses in late autumn and H7 viruses in spring. Interestingly, despite large species differences in temporal trends in overall influenza A virus prevalence, we document only modest differences in the relative abundance of these two subtypes and little, if any, temporal differences among species. As such, it appears that differences in species' phenology, physiology, and behaviors that influence overall susceptibility to influenza A viruses play a much lesser role in relative susceptibility to different subtypes. Instead, species are likely to freely pass viruses among each other regardless of subtype. Importantly, despite the similarities among species documented here, individual species still may play important roles in moving viruses across large geographic areas or sustaining local outbreaks through their different migratory behaviors.
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Affiliation(s)
- Cody M Kent
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
- Department of Biology, Frostburg State University, Frostburg, Maryland, USA
| | - Sarah N Bevins
- US Department of Agriculture, Wildlife Services, National Wildlife Disease Program, Fort Collins, Colorado, USA
| | - Jennifer M Mullinax
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Jeffery D Sullivan
- US Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, USA
| | - Diann J Prosser
- US Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, USA
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Kusack JW, Tozer DC, Harvey KM, Schummer ML, Hobson KA. Assigning harvested waterfowl to geographic origin using feather δ2H isoscapes: What is the best analytical approach? PLoS One 2023; 18:e0288262. [PMID: 37428774 DOI: 10.1371/journal.pone.0288262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/22/2023] [Indexed: 07/12/2023] Open
Abstract
Establishing links between breeding, stopover, and wintering sites for migratory species is important for their effective conservation and management. Isotopic assignment methods used to create these connections rely on the use of predictable, established relationships between the isotopic composition of environmental hydrogen and that of the non-exchangeable hydrogen in animal tissues, often in the form of a calibration equation relating feather (δ2Hf) values derived from known-origin individuals and amount-weighted long-term precipitation (δ2Hp) data. The efficacy of assigning waterfowl to moult origin using stable isotopes depends on the accuracy of these relationships and their statistical uncertainty. Most current calibrations for terrestrial species in North America are done using amount-weighted mean growing-season δ2Hp values, but the calibration relationship is less clear for aquatic and semi-aquatic species. Our objective was to critically evaluate current methods used to calibrate δ2Hp isoscapes to predicted δ2Hf values for waterfowl. Specifically, we evaluated the strength of the relationships between δ2Hp values from three commonly used isoscapes and known-origin δ2Hf values three published datasets and one collected as part of this study, also grouping these data into foraging guilds (dabbling vs diving ducks). We then evaluated the performance of assignments using these calibrations by applying a cross-validation procedure. It remains unclear if any of the tested δ2Hp isoscapes better predict surface water inputs into food webs for foraging waterfowl. We found only marginal differences in the performance of the tested known-origin datasets, where the combined foraging-guild-specific datasets showed lower assignment precision and model fit compared to data for individual species. We recommend the use of the more conservative combined foraging-guild-specific datasets to assign geographic origin for all dabbling duck species. Refining these relationships is important for improved waterfowl management and contributes to a better understanding of the limitations of assignment methods when using the isotope approach.
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Affiliation(s)
- Jackson W Kusack
- Department of Biology, Biological and Geological Sciences Building, Western University, London, Ontario, Canada
- Long Point Waterfowl and Wetlands Research Program, Birds Canada, Port Rowan, Ontario, Canada
| | - Douglas C Tozer
- Long Point Waterfowl and Wetlands Research Program, Birds Canada, Port Rowan, Ontario, Canada
| | - Kayla M Harvey
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
| | - Michael L Schummer
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, United States of America
| | - Keith A Hobson
- Department of Biology, Biological and Geological Sciences Building, Western University, London, Ontario, Canada
- Environment and Climate Change Canada, Saskatoon, Saskatchewan, Canada
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Treshchalina A, Postnikova Y, Gambaryan A, Ishmukhametov A, Prilipov A, Sadykova G, Lomakina N, Boravleva E. Monitoring of Avian Influenza Viruses and Paramyxoviruses in Ponds of Moscow and the Moscow Region. Viruses 2022; 14:v14122624. [PMID: 36560628 PMCID: PMC9781285 DOI: 10.3390/v14122624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022] Open
Abstract
The ponds of the Moscow region during the autumn migration of birds are a place with large concentrations of mallard ducks, which are the main hosts of avulaviruses (avian paramyxoviruses) and influenza A viruses (IAV). The purpose of this study was the determination of the biological diversity of IAV and avulaviruses isolated from mallards in Moscow's ponds. A phylogenetic analysis of IAV was performed based on complete genome sequencing, and virus genomic reassortment in nature was studied. Almost all IAV genome segments clustered with apathogenic duck viruses according to phylogenetic analysis. The origin of the genes of Moscow isolates were different; some of them belong to European evolutionary branches, some to Asian ones. The majority of closely related viruses have been isolated in the Western Eurasian region. Much less frequently, closely related viruses have been isolated in Siberia, China, and Korea. The quantity and diversity of isolated viruses varied considerably depending on the year and have decreased since 2014, perhaps due to the increasing proportion of nesting and wintering ducks in Moscow.
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Affiliation(s)
- Anastasia Treshchalina
- M. P. Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia
- Correspondence: ; Tel.: +7-(985)476-77-54
| | - Yulia Postnikova
- Department of Virology, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Alexandra Gambaryan
- M. P. Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia
| | - Aydar Ishmukhametov
- M. P. Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia
| | - Alexei Prilipov
- Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia
| | - Galina Sadykova
- Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia
| | - Natalia Lomakina
- Gamaleya National Center of Epidemiology and Microbiology of the Russian Ministry of Health, 123098 Moscow, Russia
| | - Elizaveta Boravleva
- M. P. Chumakov Federal Scientific Center for the Research and Development of Immune-and-Biological Products, Village of Institute of Poliomyelitis, Settlement “Moskovskiy”, 108819 Moscow, Russia
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Nam JH, Españo E, Song EJ, Shim SM, Na W, Jeong SH, Kim J, Jang J, Song D, Kim JK. Surveillance of avian influenza viruses from 2009 to 2013 in South Korea. Sci Rep 2021; 11:23991. [PMID: 34907256 PMCID: PMC8671502 DOI: 10.1038/s41598-021-03353-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2022] Open
Abstract
Avian influenza viruses (AIVs) are carried by wild migratory waterfowl across migratory flyways. To determine the strains of circulating AIVs that may pose a risk to poultry and humans, regular surveillance studies must be performed. Here, we report the surveillance of circulating AIVs in South Korea during the winter seasons of 2009–2013. A total of 126 AIVs were isolated from 7942 fecal samples from wild migratory birds, with a total isolation rate of 1.59%. H1‒H7 and H9‒H11 hemagglutinin (HA) subtypes, and N1‒N3, N5, and N7‒N9 neuraminidase (NA) subtypes were successfully isolated, with H6 and N2 as the most predominant HA and NA subtypes, respectively. Sequence identity search showed that the HA and NA genes of the isolates were highly similar to those of low-pathogenicity influenza strains from the East Asian-Australasian flyway. No match was found for the HA genes of high-pathogenicity influenza strains. Thus, the AIV strains circulating in wild migratory birds from 2009 to 2013 in South Korea likely had low pathogenicity. Continuous surveillance studies such as this one must be performed to identify potential precursors of influenza viruses that may threaten animal and human health.
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Affiliation(s)
- Jeong-Hyun Nam
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea.,Division of Acute Viral Diseases, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Erica Españo
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea
| | - Eun-Jung Song
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea.,Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Sang-Mu Shim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea.,Division of Acute Viral Diseases, Center for Emerging Virus Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, Chungbuk, 28159, Republic of Korea
| | - Woonsung Na
- Laboratory Animal Medicine, College of Veterinary Medicine, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Seo-Hee Jeong
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea
| | - Jiyeon Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea
| | - Jaebong Jang
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea
| | - Daesub Song
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea.
| | - Jeong-Ki Kim
- Department of Pharmacy, Korea University College of Pharmacy, Sejong, 30019, Republic of Korea.
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Wu G, Holan SH, Avril A, Waldenström J. A Bayesian semiparametric Jolly–Seber model with individual heterogeneity: An application to migratory mallards at stopover. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Alexis Avril
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University
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Reassortment and Persistence of Influenza A Viruses from Diverse Geographic Origins within Australian Wild Birds: Evidence from a Small, Isolated Population of Ruddy Turnstones. J Virol 2021; 95:JVI.02193-20. [PMID: 33627387 DOI: 10.1128/jvi.02193-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/10/2021] [Indexed: 12/28/2022] Open
Abstract
Australian lineages of avian influenza A viruses (AIVs) are thought to be phylogenetically distinct from those circulating in Eurasia and the Americas, suggesting the circulation of endemic viruses seeded by occasional introductions from other regions. However, processes underlying the introduction, evolution and maintenance of AIVs in Australia remain poorly understood. Waders (order Charadriiformes, family Scolopacidae) may play a unique role in the ecology and evolution of AIVs, particularly in Australia, where ducks, geese, and swans (order Anseriformes, family Anatidae) rarely undertake intercontinental migrations. Across a 5-year surveillance period (2011 to 2015), ruddy turnstones (Arenaria interpres) that "overwinter" during the Austral summer in southeastern Australia showed generally low levels of AIV prevalence (0 to 2%). However, in March 2014, we detected AIVs in 32% (95% confidence interval [CI], 25 to 39%) of individuals in a small, low-density, island population 90 km from the Australian mainland. This epizootic comprised three distinct AIV genotypes, each of which represent a unique reassortment of Australian-, recently introduced Eurasian-, and recently introduced American-lineage gene segments. Strikingly, the Australian-lineage gene segments showed high similarity to those of H10N7 viruses isolated in 2010 and 2012 from poultry outbreaks 900 to 1,500 km to the north. Together with the diverse geographic origins of the American and Eurasian gene segments, these findings suggest extensive circulation and reassortment of AIVs within Australian wild birds over vast geographic distances. Our findings indicate that long-term surveillance in waders may yield unique insights into AIV gene flow, especially in geographic regions like Oceania, where Anatidae species do not display regular inter- or intracontinental migration.IMPORTANCE High prevalence of avian influenza viruses (AIVs) was detected in a small, low-density, isolated population of ruddy turnstones in Australia. Analysis of these viruses revealed relatively recent introductions of viral gene segments from both Eurasia and North America, as well as long-term persistence of introduced gene segments in Australian wild birds. These data demonstrate that the flow of viruses into Australia may be more common than initially thought and that, once introduced, these AIVs have the potential to be maintained within the continent. These findings add to a growing body of evidence suggesting that Australian wild birds are unlikely to be ecologically isolated from the highly pathogenic H5Nx viruses circulating among wild birds throughout the Northern Hemisphere.
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Moriguchi S, Hosoda R, Ushine N, Kato T, Hayama SI. Surveillance system for avian influenza in wild birds and implications of its improvement with insights into the highly pathogenic avian influenza outbreaks in Japan. Prev Vet Med 2020; 187:105234. [PMID: 33360671 DOI: 10.1016/j.prevetmed.2020.105234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 11/03/2020] [Accepted: 12/09/2020] [Indexed: 12/09/2022]
Abstract
Since the re-emergence of a highly pathogenic avian influenza (HPAI) in 2004, outbreaks of the viral subtypes HPAI, H5N1, H5N8, and H5N6 in wild birds, poultry, and zoo birds have occurred in Japan. In 2008, a nation-wide avian influenza (AI) surveillance program was started for the early detection of the HPAI virus (HPAIV) and for the assessment of HPAIV infection among wild birds. In this study, we aimed to conduct an overview of the AI surveillance system of wild birds in Japan, including those in the regions and prefectures, to assess its overall performance and develop insights on its improvement. We analyzed past surveillance data in Japan and conducted questionnaire surveys for the officers in 11 regional branches of the Ministry of Environment and the nature conservation divisions of 47 prefectures to acquire details regarding those AI surveillance. We found that the early detection of HPAIV in wild birds was successfully achieved in only one of the five outbreak seasons during the 2008-2019 period in Japan, and the assessment of HPAIV infection had possibly not been adequate in the national surveillance system. In the winter season, AI surveillance in most prefectures were mainly conducted by means of passive surveillance through reported dead birds and active surveillance through collected waterbird feces. Conversely, less than half of the prefectures conducted bird monitoring, patrolling in migratory bird habitats, and AI antigen testing in rescued birds. In areas surrounding HPAI occurrence sites (<10 km), bird monitoring and patrolling efforts were enhanced. However, AI testing efforts in waterbird feces and rescued birds were decreased. The AI surveillance for endangered bird species and in national wildlife protection areas was conducted by the branches of the Ministry of Environment and by the prefectures. Based on our results, we concluded that for maximum efficiency, legislation which specialized in wildlife pathogens should be necessary to prepare adequate national budget and testing capacity for appropriate surveillance system with periodical assessment for surveillance results and the system.
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Affiliation(s)
- Sachiko Moriguchi
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan.
| | - Rin Hosoda
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Nana Ushine
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Takuya Kato
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
| | - Shin-Ichi Hayama
- Laboratory of Wildlife Medicine, School of Veterinary Medicine, Nippon Veterinary and Life Science University, Tokyo, Japan
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9
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Shivambu TC, Shivambu N, Downs CT. Impact assessment of seven alien invasive bird species already introduced to South Africa. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02221-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
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Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
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11
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López‐Calderón C, Van Wilgenburg SL, Roth AM, Flaspohler DJ, Hobson KA. An evaluation of isotopic (δ
2
H) methods to provide estimates of avian breeding and natal dispersal. Ecosphere 2019. [DOI: 10.1002/ecs2.2663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- C. López‐Calderón
- Department of Zoology Faculty of Biology University of Seville Green Building, Avenue Reina Mercedes Seville E‐41012 Spain
| | | | - Amber M. Roth
- Department of Wildlife, Fisheries and Conservation Biology School of Forest Resources University of Maine Orono Maine USA
| | - David J. Flaspohler
- School of Forest Resources and Environmental Science Michigan Technological University Houghton Michigan USA
| | - Keith A. Hobson
- Science and Technology Branch Environment and Climate Change Canada Saskatoon Saskatchewan S7N 3H5 Canada
- University of Western Ontario London Ontario N6A 5B7 Canada
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12
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Franklin AB, Bevins SN, Ellis JW, Miller RS, Shriner S, Root JJ, Walsh DP, Deliberto TJ. Predicting the initial spread of novel Asian origin influenza A viruses in the continental USA by wild waterfowl. Transbound Emerg Dis 2018; 66:705-714. [DOI: 10.1111/tbed.13070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/05/2018] [Accepted: 11/01/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Alan. B. Franklin
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Sarah N. Bevins
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Jeremy W. Ellis
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Ryan S. Miller
- U. S. Department of Agriculture APHIS‐VS Center for Epidemiology and Animal Health Fort Collins Colorado
| | - Susan A. Shriner
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - J. Jeffrey Root
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
| | - Daniel P. Walsh
- U. S. Geological Survey National Wildlife Health Center Madison Wisconsin
| | - Thomas J. Deliberto
- U. S. Department of Agriculture APHIS‐WS National Wildlife Research Center Fort Collins Colorado
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van Toor ML, Avril A, Wu G, Holan SH, Waldenström J. As the Duck Flies—Estimating the Dispersal of Low-Pathogenic Avian Influenza Viruses by Migrating Mallards. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00208] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Hird SM, Ganz H, Eisen JA, Boyce WM. The Cloacal Microbiome of Five Wild Duck Species Varies by Species and Influenza A Virus Infection Status. mSphere 2018; 3:e00382-18. [PMID: 30355662 PMCID: PMC6200988 DOI: 10.1128/msphere.00382-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/26/2018] [Indexed: 02/08/2023] Open
Abstract
Waterfowl, especially ducks of the genus Anas, are natural reservoir species for influenza A virus (IAV). Duck populations contain nearly all the known diversity of IAVs, and the birds are asymptomatic to infection. Previous work established that IAV infection status is correlated with changes in the cloacal microbiome in juvenile mallards. Here, we analyze five Anas species to determine whether these duck species have similar IAV+ and IAV- cloacal microbiomes, or if the relationships among a host, influenza virus, and the microbiome are species specific. We assessed taxonomic composition of the microbiome, alpha diversity, and beta diversity and found very few patterns related to microbiome and infection status across species, while detecting strong differences within species. A host species-specific signal was stronger in IAV- ducks than IAV+ ducks, and the effect size of host species on the microbiome was three times higher in IAV- birds than IAV+ birds. The mallards and the northern shovelers, the species with highest sample sizes but also with differing feeding ecology, showed especially contrasting patterns in microbiome composition, alpha diversity, and beta diversity. Our results indicate that the microbiome may have a unique relationship with influenza virus infection at the species level.IMPORTANCE Waterfowl are natural reservoir species for influenza A virus (IAV). Thus, they maintain high levels of pathogen diversity, are asymptomatic to the infection, and also contribute to the risk of a global influenza pandemic. An individual's microbiome is a critical part in how a vertebrate manages pathogens and illness. Here, we describe the cloacal microbiome of 300 wild ducks, from five species (four with previously undescribed microbiomes), including both IAV-negative and IAV-positive individuals. We demonstrate that there is not one consistent "flu-like" microbiome or response to flu across species. Individual duck species appear to have unique relationships between their microbiomes and IAV, and IAV-negative birds have a stronger tie to host species than the IAV-positive birds. In a broad context, understanding the role of the microbiome in IAV reservoir species may have future implications for avian disease management.
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Affiliation(s)
- Sarah M Hird
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Holly Ganz
- AnimalBiome, Oakland, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
| | - Jonathan A Eisen
- Genome Center, University of California, Davis, Davis, California, USA
| | - Walter M Boyce
- Pathology, Microbiology and Immunology, University of California, Davis, Davis, California, USA
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Wille M, Latorre-Margalef N, Tolf C, Halpin R, Wentworth D, Fouchier RAM, Raghwani J, Pybus OG, Olsen B, Waldenström J. Where do all the subtypes go? Temporal dynamics of H8-H12 influenza A viruses in waterfowl. Virus Evol 2018; 4:vey025. [PMID: 30151242 PMCID: PMC6101617 DOI: 10.1093/ve/vey025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Influenza A virus (IAV) is ubiquitous in waterfowl. In the northern hemisphere IAV prevalence is highest during the autumn and coincides with a peak in viral subtype diversity. Although haemagglutinin subtypes H1-H12 are associated with waterfowl hosts, subtypes H8-H12 are detected very infrequently. To better understand the role of waterfowl in the maintenance of these rare subtypes, we sequenced H8-H12 viruses isolated from Mallards (Anas platyrhynchos) from 2002 to 2009. These rare viruses exhibited varying ecological and phylodynamic features. The Eurasian clades of H8 and H12 phylogenies were dominated by waterfowl sequences; mostly viruses sequenced in this study. H11, once believed to be a subtype that infected charadriiformes (shorebirds), exhibited patterns more typical of common virus subtypes. Finally, subtypes H9 and H10, which have maintained lineages in poultry, showed markedly different patterns: H10 was associated with all possible NA subtypes and this drove HA lineage diversity within years. Rare viruses belonging to subtypes H8-H12 were highly reassorted, indicating that these rare subtypes are part of the broader IAV pool. Our results suggest that waterfowl play a role in the maintenance of these rare subtypes, but we recommend additional sampling of non-traditional hosts to better understand the reservoirs of these rare viruses.
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Affiliation(s)
- Michelle Wille
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Neus Latorre-Margalef
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.,Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Conny Tolf
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Rebecca Halpin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, MD, USA
| | - David Wentworth
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, MD, USA
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Björn Olsen
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
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Söderquist P, Elmberg J, Gunnarsson G, Thulin CG, Champagnon J, Guillemain M, Kreisinger J, Prins HHT, Crooijmans RPMA, Kraus RHS. Admixture between released and wild game birds: a changing genetic landscape in European mallards (Anas platyrhynchos). EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1156-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Unraveling migratory connectivity of two European diving ducks: a stable isotope approach. EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-1048-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hill NJ, Runstadler JA. A Bird's Eye View of Influenza A Virus Transmission: Challenges with Characterizing Both Sides of a Co-Evolutionary Dynamic. Integr Comp Biol 2016; 56:304-16. [PMID: 27252222 PMCID: PMC5964799 DOI: 10.1093/icb/icw055] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In nature, wild birds and influenza A viruses (IAV) are continually co-evolving, locked into a back-and-forth of resistance and conquest that has approached a stable equilibrium over time. This co-evolutionary relationship between bird host and IAV may appear stable at the organismal level, but is highly dynamic at the molecular level manifesting in a constant trade-off between transmissibility and virulence of the virus. Characterizing both sides of the host-virus dynamic has presented a challenge for ecologists and virologists alike, despite the potential for this approach to provide insights into which conditions destabilize the equilibrium state resulting in outbreaks or mortality of hosts in extreme cases. The use of different methods that are either host-centric or virus-centric has made it difficult to reconcile the disparate fields of host ecology and virology for investigating and ultimately predicting wild bird-mediated transmission of IAV. This review distills some of the key lessons learned from virological and ecological studies and explores the promises and pitfalls of both approaches. Ultimately, reconciling ecological and virological approaches hinges on integrating scales for measuring host-virus interactions. We argue that prospects for finding common scales for measuring wild bird-influenza dynamics are improving due to advances in genomic sequencing, host-tracking technology and remote sensing data, with the unit of time (months, year, or seasons) providing a starting point for crossover.
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Affiliation(s)
- Nichola J Hill
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
| | - Jonathan A Runstadler
- Massachusetts Institute of Technology, Division of Comparative Medicine & Department of Biological Engineering, 77 Massachusetts Ave, Cambridge 02139
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Avril A, Grosbois V, Latorre-Margalef N, Gaidet N, Tolf C, Olsen B, Waldenström J. Capturing individual-level parameters of influenza A virus dynamics in wild ducks using multistate models. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12699] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Alexis Avril
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS); Linnaeus University; SE-39182 Kalmar Sweden
| | - Vladimir Grosbois
- CIRAD; Campus International de Baillarguet; 34398 Montpellier France
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS); Linnaeus University; SE-39182 Kalmar Sweden
- Department of Population Health; College of Veterinary Medicine; Southeastern Cooperative Wildlife Disease Study; University of Georgia; Athens GA 30602 USA
| | - Nicolas Gaidet
- CIRAD; Campus International de Baillarguet; 34398 Montpellier France
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS); Linnaeus University; SE-39182 Kalmar Sweden
| | - Björn Olsen
- Zoonosis Science Centre; Department of Medical Biochemistry and Microbiology; Uppsala University; SE-751 85 Uppsala Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS); Linnaeus University; SE-39182 Kalmar Sweden
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Guo X, Flores C, Munoz-Aguayo J, Halvorson DA, Lauer D, Cardona CJ. Historical and Recent Cases of H3 Influenza A Virus in Turkeys in Minnesota. Avian Dis 2016; 59:512-7. [PMID: 26629625 DOI: 10.1637/11166-051815-reg] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Subtype H3 influenza A viruses (IAVs) are abundant in wild waterfowl and also infect humans, pigs, horses, dogs, and seals. In Minnesota, turkeys are important and frequent hosts of IAV from wild waterfowl and from pigs. Over 48 yr of surveillance history, 11 hemagglutinin (HA) subtypes of IAV from waterfowl, as well as two HA subtypes from swine, H1 and H3, have infected turkeys in Minnesota. However, there have only been two cases of avian-origin H3 IAV infections in turkeys during this 48-yr period. The first avian-origin IAV infection was detected in seven breeder and commercial flocks in 1982 and was caused by a mixed H3H4/N2 infection. In 2013, an avian-origin H3H9/N2 outbreak occurred in five flocks of turkeys between 15 and 56 wk of age. Phylogenetic analysis of the HA gene segment from the 2013 isolate indicated that the virus was related to a wild bird lineage H3 IAV. A meta-analysis of historical H3 infections in domesticated poultry demonstrated that avian-origin H3 infections have occurred in chickens and ducks but were rare in turkeys. H9N2 virus was subsequently selected during the egg cultivation of the 2013 H3H9/N2 mixed virus. A growth curve analysis suggested that passage 3 of A/Turkey/Minnesota/13-20710-2/2013(mixed) had a slightly lower replication rate than a similar avian-origin H3N2. The challenge studies indicated that the infectious dose of avian-origin H3N2 for turkey poults was greater than 10(6) 50% egg infective dose. Considered together, these data suggest that avian-origin H3 introductions to turkeys are rare events.
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Affiliation(s)
- Xi Guo
- A College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108
| | - Cristian Flores
- B Mid-Central Research and Outreach Center, Willmar, MN 56201
| | | | - David A Halvorson
- A College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108
| | - Dale Lauer
- C Minnesota Poultry Testing Laboratory, Minnesota Board of Animal Health, Willmar, MN 56201
| | - Carol J Cardona
- A College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108
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Ferreira HL, Vangeluwe D, Van Borm S, Poncin O, Dumont N, Ozhelvaci O, Munir M, van den Berg T, Lambrecht B. Differential Viral Fitness Between H1N1 and H3N8 Avian Influenza Viruses Isolated from Mallards (Anas platyrhynchos). Avian Dis 2016; 59:498-507. [PMID: 26629623 DOI: 10.1637/11074-033015-reg] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Homosubtypic and heterosubtypic immunity in mallards (Anas platyrhynchos) play an important role in the avian influenza virus (AIV) diversity. The mechanisms of AIV replication among wild birds and the role of immunity in AIV diversity have thus not been completely clarified. During the monitoring of AI circulation among wild waterfowl in 2007-2008, two viruses (H3N8 and H1N1) were isolated from ducks caught in a funnel trap located in La Hulpe wetland in Belgium. H3N8 viruses were revealed to be more prevalent in the mallard population than was H1N1, which might suggest a better adaptation to this species. In order to investigate this hypothesis, we characterized both isolated viruses biologically by experimental inoculation. Virus excretion and humoral response induced by both isolated viruses were evaluated in mallards after a first infection followed by a homo- or heterosubtypic reinfection under controlled experimental conditions. The H1N1 virus had a delayed peak of excretion of 4 days compared to the H3N8, but the virus shedding was more limited, earlier, and shorter after each reinfection. Moreover, the H3N8 virus could spread to all ducks after homo- or heterosubtypic reinfections and during a longer period. Although the humoral response induced by both viruses after infection and reinfection could be detected efficiently by competitive ELISA, only a minimal H1 antibody response and almost no H3-specific antibodies could be detected by the HI test. Our results suggest that the H3N8 isolate replicates better in mallards under experimental controlled conditions.
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Affiliation(s)
- Helena Lage Ferreira
- A FZEA-USP, Av. Duque de Caxias Norte, 225, Pirassununga - Sao Paulo 13635-900, Brazil
| | - Didier Vangeluwe
- B Royal Belgian Institute of Natural Sciences Belgian Ringing Centre, Vautier Street 29, 1000 Brussels, Belgium
| | - Steven Van Borm
- C CODA-CERVA-VAR, Groeselenberg 99, B-1180 Brussels, Belgium
| | - Olivier Poncin
- B Royal Belgian Institute of Natural Sciences Belgian Ringing Centre, Vautier Street 29, 1000 Brussels, Belgium
| | - Nathalie Dumont
- C CODA-CERVA-VAR, Groeselenberg 99, B-1180 Brussels, Belgium
| | - Orkun Ozhelvaci
- C CODA-CERVA-VAR, Groeselenberg 99, B-1180 Brussels, Belgium
| | - Muhammad Munir
- D The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, United Kingdom
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22
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Altizer S, Hobson KA, Davis AK, De Roode JC, Wassenaar LI. Do Healthy Monarchs Migrate Farther? Tracking Natal Origins of Parasitized vs. Uninfected Monarch Butterflies Overwintering in Mexico. PLoS One 2015; 10:e0141371. [PMID: 26606389 PMCID: PMC4659535 DOI: 10.1371/journal.pone.0141371] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 10/06/2015] [Indexed: 11/19/2022] Open
Abstract
Long-distance migration can lower parasite prevalence if strenuous journeys remove infected animals from wild populations. We examined wild monarch butterflies (Danaus plexippus) to investigate the potential costs of the protozoan Ophryocystis elektroscirrha on migratory success. We collected monarchs from two wintering sites in central Mexico to compare infection status with hydrogen isotope (δ2H) measurements as an indicator of latitude of origin at the start of fall migration. On average, uninfected monarchs had lower δ2H values than parasitized butterflies, indicating that uninfected butterflies originated from more northerly latitudes and travelled farther distances to reach Mexico. Within the infected class, monarchs with higher quantitative spore loads originated from more southerly latitudes, indicating that heavily infected monarchs originating from farther north are less likely to reach Mexico. We ruled out the alternative explanation that lower latitudes give rise to more infected monarchs prior to the onset of migration using citizen science data to examine regional differences in parasite prevalence during the summer breeding season. We also found a positive association between monarch wing area and estimated distance flown. Collectively, these results emphasize that seasonal migrations can help lower infection levels in wild animal populations. Our findings, combined with recent declines in the numbers of migratory monarchs wintering in Mexico and observations of sedentary (winter breeding) monarch populations in the southern U.S., suggest that shifts from migratory to sedentary behavior will likely lead to greater infection prevalence for North American monarchs.
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Affiliation(s)
- Sonia Altizer
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Keith A. Hobson
- Environment Canada, 11 Innovation Blvd., Saskatoon, Saskatchewan, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Andrew K. Davis
- Odum School of Ecology, University of Georgia, Athens, Georgia, United States of America
| | - Jacobus C. De Roode
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
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Gutiérrez-Expósito C, Ramírez F, Afán I, Forero MG, Hobson KA. Toward a Deuterium Feather Isoscape for Sub-Saharan Africa: Progress, Challenges and the Path Ahead. PLoS One 2015; 10:e0135938. [PMID: 26356677 PMCID: PMC4565548 DOI: 10.1371/journal.pone.0135938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/29/2015] [Indexed: 11/18/2022] Open
Abstract
A key challenge to the application of continent-wide feather isoscapes for geographic assignment of migrant birds is the lack of ground-truthed samples. This is especially true for long-distance Palearctic-Afrotropical migrants. We used spatially-explicit information on the δ2H composition of archived feathers from Green-backed/Grey-backed Camaroptera, to create a feather δ2H isoscape for sub-Saharan Africa. We sampled from 34 out of 41 sub-Saharan countries, totaling 205 sampling localities. Feather samples were obtained from museum collections (n = 224, from 1950 to 2014) for δ2H assay. Region, altitude, annual rainfall and seasonal patterns in precipitation were revealed as relevant explanatory variables for spatial patterns in feather δ2H. Predicted feather δ2H values ranged from -4.0 ‰ to -63.3 ‰, with higher values observed in the Great Rift Valley and South Africa, and lower values in central Africa. Our feather isoscape differed from that modelled previously using a precipitation δ2H isoscape and an assumed feather-to-precipitation calibration, but the relatively low model goodness fit (F10,213 = 5.98, p<0.001, R2 = 0.18) suggests that other, non-controlled variables might be driving observed geographic patterns in feather δ2H values. Additional ground-truthing studies are therefore recommended to improve the accuracy of the African feather δ2H isoscape.
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Affiliation(s)
- Carlos Gutiérrez-Expósito
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (CSIC), Sevilla, Spain
- * E-mail:
| | - Francisco Ramírez
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Isabel Afán
- Laboratorio de SIG y Teledetección (LAST-EBD), Estación Biológica de Doñana (CSIC), Sevilla, Spain
| | - Manuela G. Forero
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (CSIC), Sevilla, Spain
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Evolutionary Dynamics and Global Diversity of Influenza A Virus. J Virol 2015; 89:10993-1001. [PMID: 26311890 DOI: 10.1128/jvi.01573-15] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/17/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The increasing number of zoonotic infections caused by influenza A virus (IAV) subtypes of avian origin (e.g., H5N1 and H7N9) in recent years underscores the need to better understand the factors driving IAV evolution and diversity. To evaluate the current feasibility of global analyses to contribute to this aim, we evaluated information in the public domain to explore IAV evolutionary dynamics, including nucleotide substitution rates and selection pressures, using 14 IAV subtypes in 32 different countries over a 12-year period (2000 to 2011). Using geospatial information from 39,785 IAV strains, we examined associations between subtype diversity and socioeconomic, biodiversity, and agricultural indices. Our analyses showed that nucleotide substitution rates for 11 of the 14 evaluated subtypes tended to be higher in Asian countries, particularly in East Asia, than in Canada and the United States. Similarly, at a regional level, subtypes H5N1, H5N2, and H6N2 exhibited significantly higher substitution rates in East Asia than in North America. In contrast, the selection pressures (measured as ratios of nonsynonymous to synonymous evolutionary changes [dN/dS ratios]) acting on individual subtypes showed little geographic variation. We found that the strongest predictors for the detected subtype diversity at the country level were reporting effort (i.e., total number of strains reported) and health care spending (an indicator of economic development). Our analyses also identified major global gaps in IAV reporting (including a lack of sequences submitted from large portions of Africa and South America and a lack of geolocation information) and in broad subtype testing which, until addressed, will continue to hinder efforts to track the evolution and diversity of IAV around the world. IMPORTANCE In recent years, an increasing number of influenza A virus (IAV) subtypes, including H5N1, H7N9, and H10N8, have been detected in humans. High fatality rates have led to an increased urgency to better understand where and how novel pathogenic influenza virus strains emerge. Our findings showed that mutational rates of 11 commonly encountered subtypes were higher in East Asian countries than in North America, suggesting that there may be a greater risk for the emergence of novel pathogenic strains in East Asia. In assessing the potential drivers of IAV subtype diversity, our analyses confirmed that reporting effort and health care spending were the best predictors of the observed subtype diversity at the country level. These findings underscore the need to increase sampling and reporting efforts for all subtypes in many undersampled countries throughout the world.
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Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico. PLoS One 2014; 9:e107330. [PMID: 25226523 PMCID: PMC4165766 DOI: 10.1371/journal.pone.0107330] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/16/2014] [Indexed: 01/03/2023] Open
Abstract
Highly pathogenic (HP) avian influenza virus (AIV) H7N3 outbreaks occurred 3 times in the Americas in the past 10 years and caused severe economic loss in the affected regions. In June/July 2012, new HP H7N3 outbreaks occurred at commercial farms in Jalisco, Mexico. Outbreaks continued to be identified in neighbouring states in Mexico till August 2013. To explore the origin of this outbreak, time resolved phylogenetic trees were generated from the eight segments of full-length AIV sequences in North America using BEAST. Location, subtype, avian host species and pathogenicity were modelled as discrete traits upon the trees using continuous time Markov chains. A further joint analysis among segments was performed using a hierarchical phylogenetic model (HPM) which allowed trait rates (location, subtype, host species) to be jointly inferred across different segments. The complete spatial diffusion process was visualised through virtual globe software. Our result indicated the Mexico HP H7N3 originated from the large North America low pathogenicity AIV pool through complicated reassortment events. Different segments were contributed by wild waterfowl from different N. American flyways. Five of the eight segments (HA, NA, NP, M, NS) were introduced from wild birds migrating along the central North American flyway, and PB2, PB1 and PA were introduced via the western North American flyway. These results highlight a potential role for Mexico as a hotspot of virus reassortment as it is where wild birds from different migration routes mix during the winter.
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De Marco MA, Valentini A, Foni E, Savarese MC, Cotti C, Chiapponi C, Raffini E, Donatelli I, Delogu M. Is there a relation between genetic or social groups of mallard ducks and the circulation of low pathogenic avian influenza viruses? Vet Microbiol 2014; 170:418-24. [PMID: 24690373 DOI: 10.1016/j.vetmic.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 02/21/2014] [Accepted: 03/03/2014] [Indexed: 11/19/2022]
Abstract
We investigated the circulation dynamics of low pathogenic avian influenza viruses (LPAIVs) in the mallard (Anas platyrhynchos) reservoir in Italy. In particular, we evaluated the temporal distribution of virologic findings by combining virus isolation data with a new population genetic-based study approach. Thus, during 11 consecutive sampling periods (wintering periods between 1993/94 and 2003/04), categorised into 40 sampling sub-periods, cloacal swab samples were collected from 996 wild and 16 captive-reared mallards, to be screened by RT-PCR before attempting influenza A virus isolation in embryonated eggs. Forty-eight LPAIVs were isolated from wild mallards and antigenically characterised by haemagglutination-inhibition and neuraminidase-inhibition assays. When considering LPAIV antigenic subtypes in which more than one mallard tested virus isolation positive (H1N1, n. 22; H2N3, n. 2; H5N3, n. 2; H6N5, n. 3; H6N8, n. 2; H7N3, n. 3; H11N6, n. 5), at least two birds infected with a specific HN subtype clustered within one same sampling sub-period. In the context of the novel population genetic approach, total DNA was extracted from a subset of 16 captive-reared and 65 wild ducks (2000/01 and 2001/02 sampling periods) to assess genetic diversity by amplified fragment length polymorphisms (AFLP) markers. Analyses of AFLP results showed that captive-reared mallards clustered together, whereas two main independent clusters characterised the distribution pattern of most wild mallards. Within this subset of samples, nearly identical H7N3 LPAIV strains were isolated from two wild mallards belonging to the same genetic cluster. Blood sera were also collected from the above subset of mallards and examined for antibodies to the homologous H7N3 virus strain. Four out of six wild mallards testing H7N3-seropositive by haemagglutination-inhibition assay (2001/02 period) belonged to the genetic cluster including H7N3 virus shedding ducks. Overall, our data raise the possibility of an enhanced transmission and circulation of LPAIVs in genetic or social groups of wild mallards, gathered in flocks possibly related by parentage and/or geographic origin.
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Affiliation(s)
- Maria A De Marco
- Laboratory of Genetics, Institute for Environmental Protection and Research, Via Ca' Fornacetta, 40064 Ozzano Emilia, BO, Italy.
| | - Alessio Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Emanuela Foni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via dei Mercati, 43126 Parma, Italy
| | - Maria C Savarese
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Claudia Cotti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 40064 Ozzano Emilia, BO, Italy
| | - Chiara Chiapponi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via dei Mercati, 43126 Parma, Italy
| | - Elisabetta Raffini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Via del Limite, 48022 Lugo, RA, Italy
| | - Isabella Donatelli
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena, 00161 Rome, Italy
| | - Mauro Delogu
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra, 40064 Ozzano Emilia, BO, Italy
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Jiang L, Deng X, Gao Y, Li K, Chai H, Fan Z, Ren X, Wang Q, Zhang L, Yun B, Yin C, Chen Y, Qin L, Gao H, Wang Y, Hua Y, Wang X. First isolation of reticuloendotheliosis virus from mallards in China. Arch Virol 2014; 159:2051-7. [PMID: 24643331 DOI: 10.1007/s00705-013-1821-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 07/04/2013] [Indexed: 11/26/2022]
Abstract
Reticuloendotheliosis virus (REV) causes an oncogenic, immunosuppressive and runting syndrome in many avian hosts worldwide. REV infection has never been reported in mallard ducks, however. To identify REV infection in mallards, we collected 40 mallard duck samples from Jilin Province of China. In this study, the REV strain, DBYR1102, was first isolated from a mallard in China and identified by PCR, indirect immunofluorescence assay and electron microscopy. The gp90 gene and complete LTR of DBYR1102 were amplified and sequenced. Phylogenetic analysis based on gp90 genes of REV indicated that the REV strain DBYR1102 is closely related to strain HLJR0901 from northeastern China, the prairie chicken isolate APC-566, and REV subtype III, represented by chick syncytial virus. This new strain is distantly related to two other subtypes of REV, 170A and SNV. Phylogenetic analysis based on the LTR yielded information similar to that obtained with the gp90 genes. The results of this study not only expand our epidemiological understanding of REV in the wild birds of China but also demonstrate the potential role of wild waterfowl in REV transmission.
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Affiliation(s)
- Lili Jiang
- College of Wildlife Resources, Northeast Forestry University, Harbin, 150040, China
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Olson SH, Parmley J, Soos C, Gilbert M, Latorre-Margalef N, Hall JS, Hansbro PM, Leighton F, Munster V, Joly D. Sampling strategies and biodiversity of influenza A subtypes in wild birds. PLoS One 2014; 9:e90826. [PMID: 24599502 PMCID: PMC3944928 DOI: 10.1371/journal.pone.0090826] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 02/04/2014] [Indexed: 02/07/2023] Open
Abstract
Wild aquatic birds are recognized as the natural reservoir of avian influenza A viruses (AIV), but across high and low pathogenic AIV strains, scientists have yet to rigorously identify most competent hosts for the various subtypes. We examined 11,870 GenBank records to provide a baseline inventory and insight into patterns of global AIV subtype diversity and richness. Further, we conducted an extensive literature review and communicated directly with scientists to accumulate data from 50 non-overlapping studies and over 250,000 birds to assess the status of historic sampling effort. We then built virus subtype sample-based accumulation curves to better estimate sample size targets that capture a specific percentage of virus subtype richness at seven sampling locations. Our study identifies a sampling methodology that will detect an estimated 75% of circulating virus subtypes from a targeted bird population and outlines future surveillance and research priorities that are needed to explore the influence of host and virus biodiversity on emergence and transmission.
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Affiliation(s)
- Sarah H. Olson
- Wildlife Conservation Society, Bronx, New York, United States of America
| | - Jane Parmley
- Canadian Cooperative Wildlife Health Centre – Department of Pathobiology, University of Guelph, Guelph, Ontario, Canada
| | - Catherine Soos
- Environment Canada, Science & Technology Branch, Saskatoon, Saskatchewan, Canada
| | - Martin Gilbert
- Wildlife Conservation Society, Bronx, New York, United States of America
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
- Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, Athens, Georgia, United States of America
| | - Jeffrey S. Hall
- United States Geological Survey (USGS) National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Phillip M. Hansbro
- Priority Research Centre for Asthma and Respiratory Disease, University of Newcastle and Hunter Medical Research Institute, Newcastle, New South Wales, Australia
| | - Frederick Leighton
- Canadian Cooperative Wildlife Health Centre, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Vincent Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Damien Joly
- Metabiota, Nanaimo, British Columbia, Canada
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Latorre-Margalef N, Tolf C, Grosbois V, Avril A, Bengtsson D, Wille M, Osterhaus ADME, Fouchier RAM, Olsen B, Waldenström J. Long-term variation in influenza A virus prevalence and subtype diversity in migratory mallards in northern Europe. Proc Biol Sci 2014; 281:20140098. [PMID: 24573857 DOI: 10.1098/rspb.2014.0098] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Data on long-term circulation of pathogens in wildlife populations are seldom collected, and hence understanding of spatial-temporal variation in prevalence and genotypes is limited. Here, we analysed a long-term surveillance series on influenza A virus (IAV) in mallards collected at an important migratory stopover site from 2002 to 2010, and characterized seasonal dynamics in virus prevalence and subtype diversity. Prevalence dynamics were influenced by year, but retained a common pattern for all years whereby prevalence was low in spring and summer, but increased in early autumn with a first peak in August, and a second more pronounced peak during October-November. A total of 74 haemagglutinin (HA)/neuraminidase (NA) combinations were isolated, including all NA and most HA (H1-H12) subtypes. The most common subtype combinations were H4N6, H1N1, H2N3, H5N2, H6N2 and H11N9, and showed a clear linkage between specific HA and NA subtypes. Furthermore, there was a temporal structuring of subtypes within seasons based on HA phylogenetic relatedness. Dissimilar HA subtypes tended to have different temporal occurrence within seasons, where the subtypes that dominated in early autumn were rare in late autumn, and vice versa. This suggests that build-up of herd immunity affected IAV dynamics in this system.
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Affiliation(s)
- Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS ), Linnaeus University, , Kalmar 391 82, Sweden, Department of Population Health, College of Veterinary Medicine, Southeastern Cooperative Wildlife Disease Study, University of Georgia, , Athens, GA 30602, USA, International Research Center in Agriculture for Development (CIRAD)-UPR AGIRs, Animal and Integrate Risk Management, , Campus international de Baillarguet, Montpellier 34398, France, Department of Virology, Erasmus Medical Center, , Rotterdam, The Netherlands, Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, , Uppsala 751 85, Sweden
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Tolf C, Wille M, Haidar AK, Avril A, Zohari S, Waldenström J. Prevalence of avian paramyxovirus type 1 in Mallards during autumn migration in the western Baltic Sea region. Virol J 2013; 10:285. [PMID: 24028398 PMCID: PMC3847450 DOI: 10.1186/1743-422x-10-285] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 08/13/2013] [Indexed: 11/30/2022] Open
Abstract
Background Newcastle disease virus (NDV) is the causative agent of the Newcastle disease, a severe disease in birds associated with substantial economic losses to the poultry industry worldwide. Sweden is situated along the Western European waterfowl flyway and applies a non-vaccination policy combined with directives of immediate euthanisation of NDV infected flocks. During the last decades there have been several outbreaks with NDV in poultry in Sweden. However, less is known about the virus prevalence in the wild bird population including waterfowl, a well-established reservoir of avian paramyxovirus type 1 (APMV-1), the paramyxovirus serotype that include pathogenic NDV. Methods The survey constituted of 2332 samples from Mallards (Anas platyrhynchos), trapped in the southern part of Sweden during autumn migration in 2010. These samples were screened for APMV-1 by real-time reverse transcription PCR, and viral strains from positive samples were isolated and characterized by sequence analysis of the fusion gene and by phylogenetic analysis. Conclusions Twenty of these samples were positive for APMV-1, hence a virus prevalence of 0.9% (95% Confidence Interval [95% CI]=0.54%, 1.35%). The highest APMV-1 prevalence was detected in juvenile Mallards sampled in November (n=887, prevalence 1.24% ([95% CI])=0.67%, 2.24%). Sequence analysis and evaluation of phylogenetic relatedness indicated that isolated APMV-1 strains were lentogenic, and phylogenetically most closely related to genotype Ib strains within the clade of class II viruses. The sampling system employed enabled us to follow APMV-1 infections and the shedding of one particular viral strain in one individual bird over several days. Furthermore, combining previous screening results with the APMV-1 detections in this study showed that more than 50% of Mallards that tested positive for APMV-1 RNA were co-infected with influenza A virus.
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Affiliation(s)
- Conny Tolf
- Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University, Kalmar SE-391 82, Sweden.
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31
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Huang Y, Wille M, Dobbin A, Robertson GJ, Ryan P, Ojkic D, Whitney H, Lang AS. A 4-year study of avian influenza virus prevalence and subtype diversity in ducks of Newfoundland, Canada. Can J Microbiol 2013; 59:701-8. [PMID: 24102224 DOI: 10.1139/cjm-2013-0507] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The island of Newfoundland, Canada, is at the eastern edge of North America and has migratory bird connections with the continental mainland as well as across the North Atlantic Ocean. Here, we report a 4-year avian influenza virus (AIV) epidemiological study in ducks in the St. John's region of Newfoundland. The overall prevalence of AIV detection in ducks during this study was 7.2%, with American Black Ducks contributing the vast majority of the collected samples and the AIV positives. The juvenile ducks showed a significantly higher AIV detection rate (10.6%) compared with adults (3.4%). Seasonally, AIV prevalence rates were higher in the autumn (8.4%), but positives were still detected in the winter (4.6%). Preliminary serology tests showed a high incidence of previous AIV infection (20/38, 52.6%). A total of 43 viruses were characterized for their HA-NA or HA subtypes, which revealed a large diversity of AIV subtypes and little recurrence of subtypes from year to year. Investigation of the movement patterns of ducks in this region showed that it is a largely non-migratory duck population, which may contribute to the observed pattern of high AIV subtype turnover. Phylogenetic analysis of 4 H1N1 and one H5N4 AIVs showed these viruses were highly similar to other low pathogenic AIV sequences from waterfowl in North America and assigned all gene segments into American-avian clades. Notably, the H1N1 viruses, which were identified in consecutive years, possessed homologous genomes. Such detection of homologous AIV genomes across years is rare, but indicates the role of the environmental reservoir in viral perpetuation.
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Affiliation(s)
- Yanyan Huang
- a Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada
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van Toor ML, Hedenström A, Waldenström J, Fiedler W, Holland RA, Thorup K, Wikelski M. Flexibility of continental navigation and migration in European mallards. PLoS One 2013; 8:e72629. [PMID: 24023629 PMCID: PMC3758317 DOI: 10.1371/journal.pone.0072629] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 07/17/2013] [Indexed: 11/18/2022] Open
Abstract
The ontogeny of continent-wide navigation mechanisms of the individual organism, despite being crucial for the understanding of animal movement and migration, is still poorly understood. Several previous studies, mainly conducted on passerines, indicate that inexperienced, juvenile birds may not generally correct for displacement during fall migration. Waterbirds such as the mallard (Anas platyrhynchos, Linnaeus 1758) are more flexible in their migration behavior than most migratory songbirds, but previous experiments with waterbirds have not yet allowed clear conclusions about their navigation abilities. Here we tested whether immature mallard ducks correct for latitudinal displacement during fall migration within Europe. During two consecutive fall migration periods, we caught immature females on a stopover site in southeast Sweden, and translocated a group of them ca. 1,000 km to southern Germany. We followed the movements of the ducks via satellite GPS-tracking and observed their migration decisions during the fall and consecutive spring migration. The control animals released in Ottenby behaved as expected from banding recoveries: they continued migration during the winter and in spring returned to the population’s breeding grounds in the Baltics and Northwest Russia. Contrary to the control animals, the translocated mallards did not continue migration and stayed at Lake Constance. In spring, three types of movement tactics could be observed: 61.5% of the ducks (16 of 26) stayed around Lake Constance, 27% (7 of 26) migrated in a northerly direction towards Sweden and 11.5% of the individuals (3 of 26) headed east for ca. 1,000 km and then north. We suggest that young female mallards flexibly adjust their migration tactics and develop a navigational map that allows them to return to their natal breeding area.
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Affiliation(s)
- Mariëlle L. van Toor
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology,Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
- * E-mail:
| | | | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Wolfgang Fiedler
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology,Radolfzell, Germany
| | - Richard A. Holland
- School of Biological Sciences, Queen’s University Belfast, United Kingdom
| | - Kasper Thorup
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Wikelski
- Department of Migration and Immuno-Ecology, Max Planck Institute for Ornithology,Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
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Bahl J, Krauss S, Kühnert D, Fourment M, Raven G, Pryor SP, Niles LJ, Danner A, Walker D, Mendenhall IH, Su YCF, Dugan VG, Halpin RA, Stockwell TB, Webby RJ, Wentworth DE, Drummond AJ, Smith GJD, Webster RG. Influenza a virus migration and persistence in North American wild birds. PLoS Pathog 2013; 9:e1003570. [PMID: 24009503 PMCID: PMC3757048 DOI: 10.1371/journal.ppat.1003570] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 06/18/2013] [Indexed: 12/15/2022] Open
Abstract
Wild birds have been implicated in the emergence of human and livestock influenza. The successful prediction of viral spread and disease emergence, as well as formulation of preparedness plans have been hampered by a critical lack of knowledge of viral movements between different host populations. The patterns of viral spread and subsequent risk posed by wild bird viruses therefore remain unpredictable. Here we analyze genomic data, including 287 newly sequenced avian influenza A virus (AIV) samples isolated over a 34-year period of continuous systematic surveillance of North American migratory birds. We use a Bayesian statistical framework to test hypotheses of viral migration, population structure and patterns of genetic reassortment. Our results reveal that despite the high prevalence of Charadriiformes infected in Delaware Bay this host population does not appear to significantly contribute to the North American AIV diversity sampled in Anseriformes. In contrast, influenza viruses sampled from Anseriformes in Alberta are representative of the AIV diversity circulating in North American Anseriformes. While AIV may be restricted to specific migratory flyways over short time frames, our large-scale analysis showed that the long-term persistence of AIV was independent of bird flyways with migration between populations throughout North America. Analysis of long-term surveillance data provides vital insights to develop appropriately informed predictive models critical for pandemic preparedness and livestock protection.
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Affiliation(s)
- Justin Bahl
- 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, Texas, United States of America
| | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Denise Kühnert
- Department of Computer Science, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Mathieu Fourment
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Garnet Raven
- Environment Canada, Canadian Wildlife Service, Edmonton, Alberta, Canada
| | - S. Paul Pryor
- Environment Canada, Canadian Wildlife Service, Edmonton, Alberta, Canada
| | - Lawrence J. Niles
- Conserve Wildlife Foundation of New Jersey, Bordentown, New Jersey, United States of America
| | - Angela Danner
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - David Walker
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - Ian H. Mendenhall
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Yvonne C. F. Su
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
| | - Vivien G. Dugan
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- Division of Microbiology and Infectious Diseases/National Institute of Allergy and Infectious Diseases/National Institutes of Health/Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Rebecca A. Halpin
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | | | - Richard J. Webby
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
| | - David E. Wentworth
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Alexei J. Drummond
- Department of Computer Science, University of Auckland, Auckland, New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
| | - Gavin J. D. Smith
- Laboratory of Virus Evolution, Program in Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, United States of America
- * E-mail: (GJDS); (RGW)
| | - Robert G. Webster
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, United States of America
- * E-mail: (GJDS); (RGW)
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Green AJ, Elmberg J. Ecosystem services provided by waterbirds. Biol Rev Camb Philos Soc 2013; 89:105-22. [PMID: 23786594 DOI: 10.1111/brv.12045] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 05/16/2013] [Accepted: 05/23/2013] [Indexed: 11/29/2022]
Abstract
Ecosystem services are ecosystem processes that directly or indirectly benefit human well-being. There has been much recent literature identifying different services and the communities and species that provide them. This is a vital first step towards management and maintenance of these services. In this review, we specifically address the waterbirds, which play key functional roles in many aquatic ecosystems, including as predators, herbivores and vectors of seeds, invertebrates and nutrients, although these roles have often been overlooked. Waterbirds can maintain the diversity of other organisms, control pests, be effective bioindicators of ecological conditions, and act as sentinels of potential disease outbreaks. They also provide important provisioning (meat, feathers, eggs, etc.) and cultural services to both indigenous and westernized societies. We identify key gaps in the understanding of ecosystem services provided by waterbirds and areas for future research required to clarify their functional role in ecosystems and the services they provide. We consider how the economic value of these services could be calculated, giving some examples. Such valuation will provide powerful arguments for waterbird conservation.
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Affiliation(s)
- Andy J Green
- Department of Wetland Ecology, Estación Biológica de Doñana, CSIC, E-41092, Sevilla, Spain
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35
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A stable isotope (δ 2H) approach to deriving origins of harvested woodcock (Scolopax rusticola) taken in France. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0742-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Runstadler J, Hill N, Hussein ITM, Puryear W, Keogh M. Connecting the study of wild influenza with the potential for pandemic disease. INFECTION GENETICS AND EVOLUTION 2013; 17:162-87. [PMID: 23541413 DOI: 10.1016/j.meegid.2013.02.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 02/25/2013] [Accepted: 02/28/2013] [Indexed: 01/08/2023]
Abstract
Continuing outbreaks of pathogenic (H5N1) and pandemic (SOIVH1N1) influenza have underscored the need to understand the origin, characteristics, and evolution of novel influenza A virus (IAV) variants that pose a threat to human health. In the last 4-5years, focus has been placed on the organization of large-scale surveillance programs to examine the phylogenetics of avian influenza virus (AIV) and host-virus relationships in domestic and wild animals. Here we review the current gaps in wild animal and environmental surveillance and the current understanding of genetic signatures in potentially pandemic strains.
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Kraus RHS, van Hooft P, Megens HJ, Tsvey A, Fokin SY, Ydenberg RC, Prins HHT. Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms. Mol Ecol 2012; 22:41-55. [PMID: 23110616 DOI: 10.1111/mec.12098] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 01/13/2023]
Abstract
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.
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Affiliation(s)
- Robert H S Kraus
- Resource Ecology Group, Wageningen University, PO Box 47, 6700 AA, Wageningen, The Netherlands.
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Hill NJ, Takekawa JY, Ackerman JT, Hobson KA, Herring G, Cardona CJ, Runstadler JA, Boyce WM. Migration strategy affects avian influenza dynamics in mallards (Anas platyrhynchos). Mol Ecol 2012; 21:5986-99. [PMID: 22971007 DOI: 10.1111/j.1365-294x.2012.05735.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 06/02/2012] [Accepted: 06/18/2012] [Indexed: 11/30/2022]
Abstract
Studies of pathogen transmission typically overlook that wildlife hosts can include both migrant and resident populations when attempting to model circulation. Through the application of stable isotopes in flight feathers, we estimated the migration strategy of mallards (Anas platyrhynchos) occurring on California wintering grounds. Our study demonstrates that mallards- a principal host of avian influenza virus (AIV) in nature, contribute differently to virus gene flow depending on migration strategy. No difference in AIV prevalence was detected between resident (9.6%), intermediate-distance (9.6%) and long-distance migrants (7.4%). Viral diversity among the three groups was also comparable, possibly owing to viral pool mixing when birds converge at wetlands during winter. However, migrants and residents contributed differently to the virus gene pool at wintering wetlands. Migrants introduced virus from northern breeding grounds (Alaska and the NW Pacific Rim) into the wintering population, facilitating gene flow at continental scales, but circulation of imported virus appeared to be limited. In contrast, resident mallards acted as AIV reservoirs facilitating year-round circulation of limited subtypes (i.e. H5N2) at lower latitudes. This study supports a model of virus exchange in temperate regions driven by the convergence of wild birds with separate geographic origins and exposure histories.
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Affiliation(s)
- Nichola J Hill
- US Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592, USA
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Molecular epidemiology of outbreak-associated and wild-waterfowl-derived newcastle disease virus strains in Finland, including a novel class I genotype. J Clin Microbiol 2012; 50:3664-73. [PMID: 22972821 DOI: 10.1128/jcm.01427-12] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Newcastle disease (ND) is a highly contagious, severe disease of poultry caused by pathogenic strains of Newcastle disease virus (NDV; or avian paramyxovirus-1). NDV is endemic in wild birds worldwide and one of the economically most important poultry pathogens. Most of the published strains are outbreak-associated strains, while the apathogenic NDV strains that occur in wild birds, posing a constant threat to poultry with their capability to convert into more virulent forms, have remained less studied. We screened for NDV RNA in cloacal and oropharyngeal samples from wild waterfowl in Finland during the years 2006 to 2010: 39 of 715 birds were positive (prevalence, 5.5%). The partial or full-length F genes of 37 strains were sequenced for phylogenetic purposes. We also characterized viruses derived from three NDV outbreaks in Finland and discuss the relationships between these outbreak-associated and the wild-bird-associated strains. We found that all waterfowl NDV isolates were lentogenic strains of class I or class II genotype I. We also isolated a genetically distinct class I strain (teal/Finland/13111/2008) grouping phylogenetically together with only strain HIECK87191, isolated in Northern Ireland in 1987. Together they seem to form a novel class I genotype genetically differing from other known NDVs by at least 12%.
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