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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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2
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Gass JD, Kellogg HK, Hill NJ, Puryear WB, Nutter FB, Runstadler JA. Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic. Viruses 2022; 14:1531. [PMID: 35891510 PMCID: PMC9315492 DOI: 10.3390/v14071531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host-pathogen-environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Hunter K. Kellogg
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA;
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
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Prosser DJ, Chen J, Ahlstrom CA, Reeves AB, Poulson RL, Sullivan JD, McAuley D, Callahan CR, McGowan PC, Bahl J, Stallknecht DE, Ramey AM. Maintenance and dissemination of avian-origin influenza A virus within the northern Atlantic Flyway of North America. PLoS Pathog 2022; 18:e1010605. [PMID: 35666770 PMCID: PMC9203021 DOI: 10.1371/journal.ppat.1010605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/16/2022] [Accepted: 05/19/2022] [Indexed: 11/25/2022] Open
Abstract
Wild waterbirds, the natural reservoirs for avian influenza viruses, undergo migratory movements each year, connecting breeding and wintering grounds within broad corridors known as flyways. In a continental or global view, the study of virus movements within and across flyways is important to understanding virus diversity, evolution, and movement. From 2015 to 2017, we sampled waterfowl from breeding (Maine) and wintering (Maryland) areas within the Atlantic Flyway (AF) along the east coast of North America to investigate the spatio-temporal trends in persistence and spread of influenza A viruses (IAV). We isolated 109 IAVs from 1,821 cloacal / oropharyngeal samples targeting mallards (Anas platyrhynchos) and American black ducks (Anas rubripes), two species having ecological and conservation importance in the flyway that are also host reservoirs of IAV. Isolates with >99% nucleotide similarity at all gene segments were found between eight pairs of birds in the northern site across years, indicating some degree of stability among genome constellations and the possibility of environmental persistence. No movement of whole genome constellations were identified between the two parts of the flyway, however, virus gene flow between the northern and southern study locations was evident. Examination of banding records indicate direct migratory waterfowl movements between the two locations within an annual season, providing a mechanism for the inferred viral gene flow. Bayesian phylogenetic analyses provided evidence for virus dissemination from other North American wild birds to AF dabbling ducks (Anatinae), shorebirds (Charidriformes), and poultry (Galliformes). Evidence was found for virus dissemination from shorebirds to gulls (Laridae), and dabbling ducks to shorebirds and poultry. The findings from this study contribute to the understanding of IAV ecology in waterfowl within the AF.
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Affiliation(s)
- Diann J. Prosser
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Jiani Chen
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Christina A. Ahlstrom
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Andrew B. Reeves
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
- U.S. Geological Survey, National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Jeffery D. Sullivan
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Daniel McAuley
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, United States of America
| | - Carl R. Callahan
- U.S. Fish and Wildlife Service, Chesapeake Bay Field Office, Annapolis, Maryland, United States of America
| | - Peter C. McGowan
- U.S. Fish and Wildlife Service, Chesapeake Bay Field Office, Annapolis, Maryland, United States of America
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrew M. Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
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Hubálek Z. Pathogenic microorganisms associated with gulls and terns (Laridae). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zdeněk Hubálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail:
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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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Will A, Thiebot JB, Ip HS, Shoogukwruk P, Annogiyuk M, Takahashi A, Shearn-Bochsler V, Killian ML, Torchetti M, Kitaysky A. Investigation of the 2018 thick-billed murre ( Uria lomvia) die-off on St. Lawrence Island rules out food shortage as the cause. DEEP-SEA RESEARCH. PART II, TOPICAL STUDIES IN OCEANOGRAPHY 2020; 181-182:104879. [PMID: 33716412 PMCID: PMC7949294 DOI: 10.1016/j.dsr2.2020.104879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Die-offs of seabirds in Alaska have occurred with increased frequency since 2015. In 2018, on St. Lawrence Island, seabirds were reported washing up dead on beaches starting in late May, peaking in June, and continuing until early August. The cause of death was documented to be starvation, leading to the conclusion that a severe food shortage was to blame. We use physiology and colony-based observations to examine whether food shortage is a sufficient explanation for the die-off, or if evidence indicates an alternative cause of starvation such as disease. Specifically, we address what species were most affected, the timing of possible food shortages, and food shortage severity in a historical context. We found that thick-billed murres (Uria lomvia) were most affected by the die-off, making up 61% of all bird carcasses encountered during beach surveys. Thick-billed murre carcasses were proportionately more numerous (26:1) than would be expected based on ratios of thick-billed murres to co-occurring common murres (U. aalge) observed on breeding study plots (7:1). Concentrations of the stress hormone corticosterone, a reliable physiological indicator of nutritional stress, in thick-billed murre feathers grown in the fall indicate that foraging conditions in the northern Bering Sea were poor in the fall of 2017 and comparable in severity to those experienced by murres during the 1976-1977 Bering Sea regime shift. Concentrations of corticosterone in feathers grown during the pre-breeding molt indicate that foraging conditions in late winter 2018 were similar to previous years. The 2018 murre egg harvest in the village of Savoonga (on St. Lawrence Is.) was one-fifth the 1993-2012 average, and residents observed that fewer birds laid eggs in 2018. Exposure of thick-billed murres to nutritional stress in August, however, was no different in 2018 compared to 2016, 2017, and 2019, and was comparable to levels observed on St. George Island in 2003-2017. Prey abundance, measured by the National Oceanic and Atmospheric Administration in bottom-trawl surveys, was also similar in 2018 to 2017 and 2019, supporting the evidence that food was not scarce in the summer of 2018 in the vicinity of St. Lawrence Island. Of two moribund thick-billed murres collected at the end of the mortality event, one tested positive for a novel re-assortment H10 strain of avian influenza with Eurasian components, likely contracted during the non-breeding season. It is not currently known how widely spread infection of murres with the novel virus was, thus insufficient evidence exists to attribute the die-off to an outbreak of avian influenza. We conclude that food shortage alone is not an adequate explanation for the mortality of thick-billed murres in 2018, and highlight the importance of rapid response to mortality events in order to document alternative or confounding causes of mortality.
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Affiliation(s)
- Alexis Will
- National Institute of Polar Research, Tokyo, Japan
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska
- Corresponding author: (A. Will)
| | | | - Hon S. Ip
- U.S. Geological Survey, National Wildlife Health Center., Madison, Wisconsin
| | | | | | | | | | - Mary Lea Killian
- National Veterinary Services Laboratories, United States Department of Agriculture, Ames, Iowa
| | - Mia Torchetti
- National Veterinary Services Laboratories, United States Department of Agriculture, Ames, Iowa
| | - Alexander Kitaysky
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska
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Ramey AM, Reeves AB. Ecology of Influenza A Viruses in Wild Birds and Wetlands of Alaska. Avian Dis 2020; 64:109-122. [PMID: 32550610 DOI: 10.1637/0005-2086-64.2.109] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 03/05/2020] [Indexed: 11/05/2022]
Abstract
Alaska represents a globally important region for the ecology of avian-origin influenza A viruses (IAVs) given the expansive wetlands in this region, which serve as habitat for numerous hosts of IAVs that disperse among four continents during the annual cycle. Extensive sampling of wild birds for IAVs in Alaska since 1991 has greatly extended inference regarding intercontinental viral exchange between North America and East Asia and the importance of Beringian endemic species to IAV ecology within this region. Data on IAVs in aquatic birds inhabiting Alaska have also been useful for helping to establish global patterns of prevalence in wild birds and viral dispersal across the landscape. In this review, we summarize the main findings from investigations of IAVs in wild birds and wetlands of Alaska with the aim of providing readers with an understanding of viral ecology within this region. More specifically, we review viral detections, evidence of IAV exposure, and genetic characterization of isolates derived from wild bird samples collected in Alaska by host taxonomy. Additionally, we provide a short overview of wetland complexes within Alaska that may be important to IAV ecology at the continental scale.
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Affiliation(s)
- Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508,
| | - Andrew B Reeves
- U.S. Geological Survey, Alaska Science Center, Anchorage, AK 99508
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8
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Lee MM, Jaspers VLB, Gabrielsen GW, Jenssen BM, Ciesielski TM, Mortensen ÅK, Lundgren SS, Waugh CA. Evidence of avian influenza virus in seabirds breeding on a Norwegian high-Arctic archipelago. BMC Vet Res 2020; 16:48. [PMID: 32028933 PMCID: PMC7006154 DOI: 10.1186/s12917-020-2265-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Background Wild aquatic birds serve as the natural reservoir for avian influenza virus (AIV), a disease with significant implications for avian and mammalian health. Climate change is predicted to impact the dynamics of AIV, particularly in areas such as the Arctic, but the baseline data needed to detect these shifts is often unavailable. In this study, plasma from two species of gulls breeding on the high-Arctic Svalbard archipelago were screened for antibodies to AIV. Results AIV antibodies were found in black-legged kittiwake (Rissa tridactyla) samples from multiple years, as well as in glaucous gulls (Larus hyperboreous) samples. Conclusions Despite small sample sizes, evidence of exposure to AIV was found among Svalbard gulls. A wider survey of Svalbard avian species is warranted to establish knowledge on the extent of AIV exposure on Svalbard and to determine whether active infections are present.
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Affiliation(s)
- Megan Marie Lee
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway.,Biological Sciences Program, Goucher College, 1021 Dulaney Valley Road, Baltimore, MD, 21204, USA
| | - Veerle L B Jaspers
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Geir Wing Gabrielsen
- Norwegian Polar Institute, Fram Centre, Postbox 6606 Langnes, NO-9296, Tromsø, Norway
| | - Bjørn Munro Jenssen
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Tomasz Maciej Ciesielski
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Åse-Karen Mortensen
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Silje Strand Lundgren
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway
| | - Courtney A Waugh
- Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, NO-7491, Trondheim, Norway. .,Faculty of Biosciences and Aquaculture, Nord University, Steinkjer, Trøndelag, Norway.
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Yeo SJ, Than DD, Park HS, Sung HW, Park H. Molecular Characterization of a Novel Avian Influenza A (H2N9) Strain Isolated from Wild Duck in Korea in 2018. Viruses 2019; 11:v11111046. [PMID: 31717636 PMCID: PMC6893532 DOI: 10.3390/v11111046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/02/2019] [Accepted: 11/06/2019] [Indexed: 01/03/2023] Open
Abstract
A novel avian influenza virus (A/wild duck/Korea/K102/2018) (H2N9) was isolated from wild birds in South Korea in 2018, and phylogenetic and molecular analyses were conducted on complete gene sequences obtained by next-generation sequencing. Phylogenetic analysis indicated that the hemagglutinin (HA) and neuraminidase (NA) genes of the A/wild duck/Korea/K102/2018 (H2N9) virus belonged to the Eurasian countries, whereas other internal genes (polymerase basic protein 1 (PB1), PB2, nucleoprotein (NP), polymerase acidic protein (PA), matrix protein (M), and non-structural protein (NS)) belonged to the East Asian countries. A monobasic amino acid (PQIEPR/GLF) at the HA cleavage site, E627 in the PB2 gene, and no deletion of the stalk region in the NA gene indicated that the A/wild duck/Korea/K102/2018 (H2N9) isolate was a typical low pathogenicity avian influenza (LPAI). Nucleotide sequence similarity analysis of HA revealed that the highest homology (98.34%) is to that of A/duck/Mongolia/482/2015 (H2N3), and amino acid sequence of NA was closely related to that of A/duck/Bangladesh/8987/2010 (H10N9) (96.45%). In contrast, internal genes showed homology higher than 98% compared to those of other isolates derived from duck and wild birds of China or Japan in 2016–2018. The newly isolated A/wild duck/Korea/K102/2018 (H2N9) strain is the first reported avian influenza virus in Korea, and may have evolved from multiple genotypes in wild birds and ducks in Mongolia, China, and Japan.
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Affiliation(s)
- Seon-Ju Yeo
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
| | - Duc-Duong Than
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
| | - Hong-Seog Park
- GnCBio Inc, 4F, Yegan Plaza, 36, Banseok-ro, Yuseong-gu, Daejeon 34069, Korea;
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (H.W.S.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
- Correspondence: (H.W.S.); (H.P.)
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Kayed AS, Kandeil A, Gomaa MR, El-Shesheny R, Mahmoud S, Hegazi N, Fayez M, Sheta B, McKenzie PP, Webby RJ, Kayali G, Ali MA. Surveillance for avian influenza viruses in wild birds at live bird markets, Egypt, 2014-2016. Influenza Other Respir Viruses 2019; 13:407-414. [PMID: 30714323 PMCID: PMC6586179 DOI: 10.1111/irv.12634] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/18/2018] [Accepted: 12/31/2018] [Indexed: 01/16/2023] Open
Abstract
AIM Egypt is the habitat for a large number of bird species and serves as a vital stopover for millions of migratory birds during their annual migration between the Palearctic and Afrotropical ecozones. Surveillance for avian influenza viruses (AIVs) is critical to assessing risks for potential spreading of these viruses among domestic poultry. Surveillance for AIV among hunted and captured wild birds in Egypt was conducted in order to understand the characteristics of circulating viruses. METHODS Sampling of wild bird species occurred in two locations along the Mediterranean Coast of Egypt in the period from 2014 to 2016. A total of 1316 samples (cloacal and oropharyngeal swabs) were collected from 20 different species of hunted or captured resident and migratory birds sold at live bird markets. Viruses were propagated then sequenced. Phylogenetic analysis and receptor binding affinities were studied. RESULTS Eighteen AIVs (1.37%) were isolated from migratory Anseriformes at live bird markets. Further characterization of the viral isolates identified five hemagglutinin (H3, H5, H7, H9, and H10) and five neuraminidase (N1, N2, N3, N6, and N9) subtypes, which were related to isolates reported in the Eurasian region. Two of the 18 isolates were highly pathogenic H5N1 viruses related to clade 2.2.1, while three isolates were G1-like H9N2 viruses. CONCLUSIONS Our data show significant diversity of AIVs in Anserifromes sold at live bird markets in Egypt. This allows for genetic exchanges between imported and enzootic viruses and put the exposed humans at a higher risk of infection.
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Affiliation(s)
- Ahmed S Kayed
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt
| | - Ahmed Kandeil
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt
| | - Mokhtar R Gomaa
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt
| | - Rabeh El-Shesheny
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt.,Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Sara Mahmoud
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt
| | - Nabil Hegazi
- Faculty of Agriculture, Department of Microbiology, Cairo University, Giza, Egypt
| | - Mohamed Fayez
- Faculty of Agriculture, Department of Microbiology, Cairo University, Giza, Egypt
| | - Basma Sheta
- Faculty of Science, Zoology Department, Damietta University, New Damietta, Egypt
| | - Pamela P McKenzie
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Ghazi Kayali
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, Texas.,Human Link, Baabda, Lebanon
| | - Mohamed A Ali
- Environmental Research Division, Water Pollution Research Department, Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Giza, Egypt
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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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12
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Genetic evidence for the intercontinental movement of avian influenza viruses possessing North American-origin nonstructural gene allele B into South Korea. INFECTION GENETICS AND EVOLUTION 2018; 66:18-25. [PMID: 30196122 DOI: 10.1016/j.meegid.2018.09.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 01/23/2023]
Abstract
Avian influenza viruses (AIVs) are genetically separated by geographical barriers, resulting in the independent evolution of North American and Eurasian lineages. In the present study, to determine whether AIVs possessing the North American-origin nonstructural (NS) gene were previously introduced into South Korea, we performed a genetic analysis of AIVs isolated from fecal samples of migratory birds. We detected seven viruses possessing the North American-origin NS allele B among 413 AIV-positive samples obtained during AI surveillance between 2012 and 2017. We found evidence for the intercontinental transmission of at least three genetically distinct clusters of the B allele of the North American-origin NS gene into Eurasia at a low frequency. The host species of three viruses were identified as the greater white-fronted goose (Anser albifrons) using a DNA barcoding technique. Moreover, we used GPS-CDMA-based telemetry to determine the migration route of the greater white-fronted goose between the Far East of Russia and South Korea and found that this species may play an important role as an intermediate vector in the intercontinental transmission of AIVs. To improve our understanding of the role of wild birds in the ecology of AIVs, advanced AIV surveillance is required in the Far East of Russia as well as in Alaska region of Beringia accompanied by host identification and wild bird tracking.
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13
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H13 influenza viruses in wild birds have undergone genetic and antigenic diversification in nature. Virus Genes 2018; 54:543-549. [PMID: 29796944 DOI: 10.1007/s11262-018-1573-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 05/19/2018] [Indexed: 10/16/2022]
Abstract
Among 16 haemagglutinin (HA) subtypes of avian influenza viruses (AIVs), H13 AIVs have rarely been isolated in wild waterfowl. H13 AIVs cause asymptomatic infection and are maintained mainly in gull and tern populations; however, the recorded antigenic information relating to the viruses has been limited. In this study, 2 H13 AIVs, A/duck/Hokkaido/W345/2012 (H13N2) and A/duck/Hokkaido/WZ68/2012 (H13N2), isolated from the same area in the same year in our surveillance, were genetically and antigenically analyzed with 10 representative H13 strains including a prototype strain, A/gull/Maryland/704/1977 (H13N6). The HA genes of H13 AIVs were phylogenetically divided into 3 groups (I, II, and III). A/duck/Hokkaido/W345/2012 (H13N2) was genetically classified into Group III. This virus was distinct from a prototype strain, A/gull/Maryland/704/1977 (H13N6), and the virus, A/duck/Hokkaido/WZ68/2012 (H13N2), both belonging to Group I. Antigenic analysis indicated that the viruses of Group I were antigenically closely related to those of Group II, but distinct from those of Group III, including A/duck/Hokkaido/W345/2012 (H13N2). In summary, our study indicates that H13 AIVs have undergone antigenic diversification in nature.
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14
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Emergence and multiple reassortments of French 2015-2016 highly pathogenic H5 avian influenza viruses. INFECTION GENETICS AND EVOLUTION 2018; 61:208-214. [PMID: 29649578 DOI: 10.1016/j.meegid.2018.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 11/23/2022]
Abstract
From November 2015 to August 2016, 81 outbreaks of highly pathogenic (HP) H5 avian influenza virus were detected in poultry farms from South-Western France. These viruses were mainly detected in farms raising waterfowl, but also in chicken or guinea fowl flocks, and did not induce severe signs in waterfowl although they did meet the HP criteria. Three different types of neuraminidases (N1, N2 and N9) were associated with the HP H5 gene. Full genomes sequences of 24 H5HP and 6 LP viruses that circulated in the same period were obtained by next generation sequencing, from direct field samples or after virus isolation in SPF embryonated eggs. Phylogenetic analyses of the eight viral segments confirmed that they were all related to the avian Eurasian lineage. In addition, analyses of the "Time of the Most Recent Common Ancestor" showed that the common ancestor of the H5HP sequences from South-Western France could date back to early 2014 (±1 year). This pre-dated the first detection of H5 HP in poultry farms and was consistent with a silent circulation of these viruses for several months. Finally, the phylogenetic study of the different segments showed that several phylogenetic groups could be established. Twelve genotypes of H5HP were detected implying that at least eleven reassortment events did occur after the H5HP cleavage site emerged. This indicates that a large number of co-infections with both highly pathogenic H5 and other avian influenza viruses must have occurred, a finding that lends further support to prolonged silent circulation.
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15
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Reeves AB, Hall JS, Poulson RL, Donnelly T, Stallknecht DE, Ramey AM. Influenza A virus recovery, diversity, and intercontinental exchange: A multi-year assessment of wild bird sampling at Izembek National Wildlife Refuge, Alaska. PLoS One 2018; 13:e0195327. [PMID: 29621333 PMCID: PMC5950690 DOI: 10.1371/journal.pone.0195327] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/20/2018] [Indexed: 11/18/2022] Open
Abstract
Western Alaska is a potential point-of-entry for foreign-origin influenza A viruses (IAVs) into North America via migratory birds. We sampled waterfowl and gulls for IAVs at Izembek National Wildlife Refuge (NWR) in western Alaska, USA, during late summer and autumn months of 2011-2015, to evaluate the abundance and diversity of viruses at this site. We collected 4842 samples across five years from 25 species of wild birds resulting in the recovery, isolation, and sequencing of 172 IAVs. With the intent of optimizing sampling efficiencies, we used information derived from this multi-year effort to: 1) evaluate from which species we consistently recover viruses, 2) describe viral subtypes of isolates by host species and year, 3) characterize viral gene segment sequence diversity with respect to host species, and assess potential differences in the viral lineages among the host groups, and 4) examine how evidence of intercontinental exchange of IAVs relates to host species. We consistently recovered viruses from dabbling ducks (Anas spp.), emperor geese (Chen canagica) and glaucous-winged gulls (Larus glaucescens). There was little evidence for differences in viral subtypes and diversity from different waterfowl hosts, however subtypes and viral diversity varied between waterfowl host groups and glaucous-winged gulls. Furthermore, higher proportions of viral sequences from northern pintails (Anas acuta), emperor geese and glaucous-winged gulls were grouped in phylogenetic clades that included IAV sequences originating from wild birds sampled in Asia as compared to non-pintail dabbling ducks, a difference that may be related to intercontinental migratory tendencies of host species. Our summary of research and surveillance efforts at Izembek NWR will assist in future prioritization of which hosts to sample and swab types to collect in Alaska and elsewhere in order to maximize isolate recovery, subtype and sequence diversity for resultant viruses, and detection of evidence for intercontinental viral exchange.
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Affiliation(s)
- Andrew B. Reeves
- United States Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail: (ABR); (AMR)
| | - Jeffrey S. Hall
- United States Geological Survey National Wildlife Health Center, Madison, Wisconsin, United States of America
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Tyrone Donnelly
- United States Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Andrew M. Ramey
- United States Geological Survey Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail: (ABR); (AMR)
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16
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Ramey AM, DeLiberto TJ, Berhane Y, Swayne DE, Stallknecht DE. Lessons learned from research and surveillance directed at highly pathogenic influenza A viruses in wild birds inhabiting North America. Virology 2018; 518:55-63. [PMID: 29453059 DOI: 10.1016/j.virol.2018.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/29/2018] [Accepted: 02/02/2018] [Indexed: 11/19/2022]
Abstract
Following detections of highly pathogenic (HP) influenza A viruses (IAVs) in wild birds inhabiting East Asia after the turn of the millennium, the intensity of sampling of wild birds for IAVs increased throughout much of North America. The objectives for many research and surveillance efforts were directed towards detecting Eurasian origin HP IAVs and understanding the potential of such viruses to be maintained and dispersed by wild birds. In this review, we highlight five important lessons learned from research and surveillance directed at HP IAVs in wild birds inhabiting North America: (1) Wild birds may disperse IAVs between North America and adjacent regions via migration, (2) HP IAVs can be introduced to wild birds in North America, (3) HP IAVs may cross the wild bird-poultry interface in North America, (4) The probability of encountering and detecting a specific virus may be low, and (5) Population immunity of wild birds may influence HP IAV outbreaks in North America. We review empirical support derived from research and surveillance efforts for each lesson learned and, furthermore, identify implications for future surveillance efforts, biosecurity, and population health. We conclude our review by identifying five additional areas in which we think future mechanistic research relative to IAVs in wild birds in North America are likely to lead to other important lessons learned in the years ahead.
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Affiliation(s)
- Andrew M Ramey
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Thomas J DeLiberto
- National Wildlife Disease Program, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, Fort Collins, CO 80521, USA
| | - Yohannes Berhane
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, Manitoba, Canada R3E 3M4; Department of Animal Science, University of Manitoba, Winnipeg, Canada
| | - David E Swayne
- Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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17
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Hill NJ, Hussein ITM, Davis KR, Ma EJ, Spivey TJ, Ramey AM, Puryear WB, Das SR, Halpin RA, Lin X, Fedorova NB, Suarez DL, Boyce WM, Runstadler JA. Reassortment of Influenza A Viruses in Wild Birds in Alaska before H5 Clade 2.3.4.4 Outbreaks. Emerg Infect Dis 2018; 23:654-657. [PMID: 28322698 PMCID: PMC5367406 DOI: 10.3201/eid2304.161668] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Sampling of mallards in Alaska during September 2014-April 2015 identified low pathogenic avian influenza A virus (subtypes H5N2 and H1N1) that shared ancestry with highly pathogenic reassortant H5N2 and H5N1 viruses. Molecular dating indicated reassortment soon after interhemispheric movement of H5N8 clade 2.3.4.4, suggesting genetic exchange in Alaska or surrounds before outbreaks.
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18
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Multiple introductions of reassorted highly pathogenic avian influenza viruses (H5N8) clade 2.3.4.4b causing outbreaks in wild birds and poultry in Egypt. INFECTION GENETICS AND EVOLUTION 2017; 58:56-65. [PMID: 29248796 DOI: 10.1016/j.meegid.2017.12.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/10/2017] [Accepted: 12/13/2017] [Indexed: 01/16/2023]
Abstract
Recently, an increased incidence of outbreaks of highly pathogenic avian influenza (HPAI) H5N8 in poultry linked to infected migratory birds has been reported from different European, Asian and African countries. In Egypt, incursion of HPAI H5N8 virus of clade 2.3.4.4b has been recently registered. Full genomic characterization of 3 virus isolates from wild birds and poultry (backyard and commercial farm sectors) showed high nucleotide similarity among the HA, NA, M, and NS gene segments of the three Egyptian HPAI H5N8 viruses, indicating that they are descendants of a common ancestral virus. However, the analyzed Egyptian H5N8 viruses revealed distinct genotypes involving different origins of the PB2, PB1, PA and/or NP segments. In genotype-1 represented by strain A/common-coot/Egypt/CA285/2016 the PB2 and NP segments showed closest relationship to H5N6 and H6N2 viruses, recently detected in Italy. The second is replacement of PB1 and NP genes A novel reassortant, represented by strain A/duck/Egypt/SS19/2017, showed an exchange of PB1 and NP genes which might have originated from H6N8 or H1N1 and H6N2 viruses. Finally, replacement of PA and NP genes characterized strain A/duck/Egypt/F446/2017. Bayesian phylogeographic analyses revealed that Egyptian H5N8 viruses are highly likely derived from Russian 2016 HPAI H5N8 virus (A/great_crested_grebe/Uvs-Nuur_Lake/341/2016 (H5N8)) and the reassortment likely occurred before incursion to Egypt.
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19
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Hartby CM, Krog JS, Merkel F, Holm E, Larsen LE, Hjulsager CK. First Characterization of Avian Influenza Viruses from Greenland 2014. Avian Dis 2017; 60:302-10. [PMID: 27309071 DOI: 10.1637/11119-050515-regr] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In late February 2014, unusually high numbers of wild thick-billed murres (Uria lomvia) were found dead on the coast of South Greenland. To investigate the cause of death, 45 birds were submitted for laboratory examination in Denmark. Avian influenza viruses (AIVs) with subtypes H11N2 and low pathogenic H5N1 were detected in some of the birds. Characterization of the viruses by full genome sequencing revealed that all the gene segments belonged to the North American lineage of AIVs. The seemingly sparse and mixed subtype occurrence of low pathogenic AIVs in these birds, in addition to the emaciated appearance of the birds, suggests that the murre die-off was due to malnutrition as a result of sparse food availability or inclement weather. Here we present the first characterization of AIVs isolated in Greenland, and our results support the idea that wild birds in Greenland may be involved in the movement of AIV between North America and Europe.
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Affiliation(s)
- Christina Marie Hartby
- National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg, Denmark
| | - Jesper Schak Krog
- National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg, Denmark
| | - Flemming Merkel
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland.,Arctic Environment, Department of Bioscience, Aarhus University, 4000 Roskilde, Denmark
| | - Elisabeth Holm
- National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg, Denmark
| | - Lars Erik Larsen
- National Veterinary Institute, Technical University of Denmark, 1870 Frederiksberg, Denmark
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20
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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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21
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Ramey AM, Walther P, Link P, Poulson RL, Wilcox BR, Newsome G, Spackman E, Brown JD, Stallknecht DE. Optimizing Surveillance for South American Origin Influenza A Viruses Along the United States Gulf Coast Through Genomic Characterization of Isolates from Blue-winged Teal (Anas discors). Transbound Emerg Dis 2016; 63:194-202. [PMID: 25056712 PMCID: PMC4305350 DOI: 10.1111/tbed.12244] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Indexed: 11/27/2022]
Abstract
Relative to research focused on inter-continental viral exchange between Eurasia and North America, less attention has been directed towards understanding the redistribution of influenza A viruses (IAVs) by wild birds between North America and South America. In this study, we genomically characterized 45 viruses isolated from blue-winged teal (Anas discors) along the Texas and Louisiana Gulf Coast during March of 2012 and 2013, coincident with northward migration of this species from Neotropical wintering areas to breeding grounds in the United States and Canada. No evidence of South American lineage genes was detected in IAVs isolated from blue-winged teal supporting restricted viral gene flow between the United States and southern South America. However, it is plausible that blue-winged teal redistribute IAVs between North American breeding grounds and wintering areas throughout the Neotropics, including northern South America, and that viral gene flow is limited by geographical barriers further south (e.g., the Amazon Basin). Surveillance for the introduction of IAVs from Central America and northern South America into the United States may be further optimized through genomic characterization of viruses resulting from coordinated, concurrent sampling efforts targeting blue-winged teal and sympatric species throughout the Neotropics and along the United States Gulf Coast.
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Affiliation(s)
- Andrew M. Ramey
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Patrick Walther
- US Fish and Wildlife Service, Texas Chenier Plain Refuge Complex, P.O. Box 278 4017 FM 563, Anahuac, Texas 77514, USA
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, 2000 Quail Drive, Room 436, Baton Rouge, Louisiana 70808, USA
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Benjamin R. Wilcox
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - George Newsome
- City of Beaumont Wastewater Treatment Plant, 4900 Lafin Road, Beaumont, Texas 77705, USA
| | - Erica Spackman
- US Department of Agriculture, Agriculture Research Service, Southeast Poultry Research Laboratory, 934 College Station Road, Athens, GA 30605, USA
| | - Justin D. Brown
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
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22
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Lang AS, Lebarbenchon C, Ramey AM, Robertson GJ, Waldenström J, Wille M. Assessing the Role of Seabirds in the Ecology of Influenza A Viruses. Avian Dis 2016; 60:378-86. [DOI: 10.1637/11135-050815-regr] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University, St. John’s, NL, A1B 3X9, Canada
| | - Camille Lebarbenchon
- Université de La Réunion, UMR PIMIT (Processus Infectieux en Milieu Insulaire Tropical), INSERM 1187, CNRS 9192, IRD 249, Saint Denis, Reunion Island
| | - Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center, 4210 University Drive, Anchorage, AK 99508
| | - Gregory J. Robertson
- Wildlife Research Division, Environment Canada, 6 Bruce St., Mount Pearl, NL, A1N 4T3, Canada
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
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23
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Bozick BA, Real LA. INTEGRATING PARASITES AND PATHOGENS INTO THE STUDY OF GEOGRAPHIC RANGE LIMITS. QUARTERLY REVIEW OF BIOLOGY 2016; 90:361-80. [PMID: 26714350 DOI: 10.1086/683698] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The geographic distributions of all species are limited, and the determining factors that set these limits are of fundamental importance to the fields of ecology and evolutionary biology. Plant and animal ranges have been of primary concern, while those of parasites, which represent much of the Earth's biodiversity, have been neglected. Here, we review the determinants of the geographic ranges of parasites and pathogens, and explore how parasites provide novel systems with which to investigate the ecological and evolutionary processes governing host/parasite spatial distributions. Although there is significant overlap in the causative factors that determine range borders of parasites and free-living species, parasite distributions are additionally constrained by the geographic range and ecology of the host species' population, as well as by evolutionary factors that promote host-parasite coevolution. Recently, parasites have been used to infer population demographic and ecological information about their host organisms and we conclude that this strategy can be further exploited to understand geographic range limitations of both host and parasite populations.
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24
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Arnal A, Vittecoq M, Pearce-Duvet J, Gauthier-Clerc M, Boulinier T, Jourdain E. Laridae: A neglected reservoir that could play a major role in avian influenza virus epidemiological dynamics. Crit Rev Microbiol 2015; 41:508-19. [DOI: 10.3109/1040841x.2013.870967] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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25
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Saito T, Tanikawa T, Uchida Y, Takemae N, Kanehira K, Tsunekuni R. Intracontinental and intercontinental dissemination of Asian H5 highly pathogenic avian influenza virus (clade 2.3.4.4) in the winter of 2014-2015. Rev Med Virol 2015; 25:388-405. [DOI: 10.1002/rmv.1857] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/02/2015] [Accepted: 08/13/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Takehiko Saito
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
- United Graduate School of Veterinary Sciences; Gifu University; Gifu City Japan
| | - Taichiro Tanikawa
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Yuko Uchida
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Nobuhiro Takemae
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Katsushi Kanehira
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - Ryota Tsunekuni
- Influenza and Prion Disease Research Center; National Institute of Animal Health National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
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26
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Ramey AM, Reeves AB, Poulson RL, Wasley J, Esler D, Stallknecht DE. Sampling of Sea Ducks for Influenza A Viruses in Alaska during Winter Provides Lack of Evidence for Epidemiologic Peak of Infection. J Wildl Dis 2015; 51:938-41. [PMID: 26267465 PMCID: PMC11368530 DOI: 10.7589/2015-03-057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Sampling of sea ducks for influenza A viruses in Alaska during winter provided no evidence for an epidemiologic peak of infection. Isolates were recovered, however, that provide information on viral diversity and dispersal that may not be realized through sampling efforts focused on other avian taxa.
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Affiliation(s)
- Andrew M. Ramey
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Andrew B. Reeves
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
| | - Jeff Wasley
- Four Flyways Outfitters, 413 5th Avenue North, Onalaska, Wisconsin 54650, USA
| | - Daniel Esler
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, Alaska 99508, USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, The University of Georgia, 589 D. W. Brooks Drive, Athens, Georgia 30602, USA
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Pappas C, Yang H, Carney PJ, Pearce MB, Katz JM, Stevens J, Tumpey TM. Assessment of transmission, pathogenesis and adaptation of H2 subtype influenza viruses in ferrets. Virology 2015; 477:61-71. [PMID: 25659818 DOI: 10.1016/j.virol.2015.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/02/2014] [Accepted: 01/04/2015] [Indexed: 12/12/2022]
Abstract
After their disappearance from the human population in 1968, influenza H2 viruses have continued to circulate in the natural avian reservoir. The isolation of this virus subtype from multiple bird species as well as swine highlights the need to better understand the potential of these viruses to spread and cause disease in humans. Here we analyzed the virulence, transmissibility and receptor-binding preference of two avian influenza H2 viruses (H2N2 and H2N3) and compared them to a swine H2N3 (A/swine/Missouri/2124514/2006 [swMO]), and a human H2N2 (A/England/10/1967 [Eng/67]) virus using the ferret model as a mammalian host. Both avian H2 viruses possessed the capacity to spread efficiently between cohoused ferrets, and the swine (swMO) and human (Eng/67) viruses transmitted to naïve ferrets by respiratory droplets. Further characterization of the swMO hemagglutinin (HA) by x-ray crystallography and glycan microarray array identified receptor-specific adaptive mutations. As influenza virus quasispecies dynamics during transmission have not been well characterized, we sequenced nasal washes collected during transmission studies to better understand experimental adaptation of H2 HA. The avian H2 viruses isolated from ferret nasal washes contained mutations in the HA1, including a Gln226Leu substitution, which is a mutation associated with α2,6 sialic acid (human-like) binding preference. These results suggest that the molecular structure of HA in viruses of the H2 subtype continue to have the potential to adapt to a mammalian host and become transmissible, after acquiring additional genetic markers.
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Affiliation(s)
- Claudia Pappas
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Hua Yang
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Paul J Carney
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Melissa B Pearce
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Jacqueline M Katz
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - James Stevens
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA
| | - Terrence M Tumpey
- Influenza Division, NCIRD, Centers for Disease Control and Prevention, 1600 Clifton Road NE, Atlanta, GA 30333, USA.
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Savory FR, Varma V, Ramakrishnan U. Identifying geographic hot spots of reassortment in a multipartite plant virus. Evol Appl 2014; 7:569-79. [PMID: 24944570 PMCID: PMC4055178 DOI: 10.1111/eva.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 03/05/2014] [Indexed: 11/26/2022] Open
Abstract
Reassortment between different species or strains plays a key role in the evolution of multipartite plant viruses and can have important epidemiological implications. Identifying geographic locations where reassortant lineages are most likely to emerge could be a valuable strategy for informing disease management and surveillance efforts. We developed a predictive framework to identify potential geographic hot spots of reassortment based upon spatially explicit analyses of genome constellation diversity. To demonstrate the utility of this approach, we examined spatial variation in the potential for reassortment among Cardamom bushy dwarf virus (CBDV; Nanoviridae, Babuvirus) isolates in Northeast India. Using sequence data corresponding to six discrete genome components for 163 CBDV isolates, a quantitative measure of genome constellation diversity was obtained for locations across the sampling region. Two key areas were identified where viruses with highly distinct genome constellations cocirculate, and these locations were designated as possible geographic hot spots of reassortment, where novel reassortant lineages could emerge. Our study demonstrates that the potential for reassortment can be spatially dependent in multipartite plant viruses and highlights the use of evolutionary analyses to identify locations which could be actively managed to facilitate the prevention of outbreaks involving novel reassortant strains.
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Affiliation(s)
- Fiona R Savory
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
| | - Varun Varma
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
| | - Uma Ramakrishnan
- National Centre for Biological Sciences, TATA Institute of Fundamental Research Bangalore, India
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Huang Y, Wille M, Benkaroun J, Munro H, Bond AL, Fifield DA, Robertson GJ, Ojkic D, Whitney H, Lang AS. Perpetuation and reassortment of gull influenza A viruses in Atlantic North America. Virology 2014; 456-457:353-63. [PMID: 24889254 DOI: 10.1016/j.virol.2014.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 03/24/2014] [Accepted: 04/04/2014] [Indexed: 12/09/2022]
Abstract
Gulls are important hosts of avian influenza A viruses (AIVs) and gull AIVs often contain gene segments of mixed geographic and host lineage origins. In this study, the prevalence of AIV in gulls of Newfoundland, Canada from 2008 to 2011 was analyzed. Overall prevalence was low (30/1645, 1.8%) but there was a distinct peak of infection in the fall. AIV seroprevalence was high in Newfoundland gulls, with 50% of sampled gulls showing evidence of previous infection. Sequences of 16 gull AIVs were determined and analyzed to shed light on the transmission, reassortment and persistence dynamics of gull AIVs in Atlantic North America. Intercontinental and waterfowl lineage reassortment was prevalent. Of particular note were a wholly Eurasian AIV and another with an intercontinental reassortant waterfowl lineage virus. These patterns of geographic and inter-host group transmission highlight the importance of characterization of gull AIVs as part of attempts to understand global AIV dynamics.
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Affiliation(s)
- Yanyan Huang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Michelle Wille
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Jessica Benkaroun
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Hannah Munro
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - Alexander L Bond
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9
| | - David A Fifield
- Newfoundland and Labrador Department of Natural Resources, P.O. Box 7400, St. John's, NL, Canada A1E 3Y5
| | - Gregory J Robertson
- Wildlife Research Division, Environment Canada, 6 Bruce St., Mount Pearl, NL, Canada A1N 4T3
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Box 3612, Guelph, ON, Canada N1H 6R8
| | - Hugh Whitney
- Newfoundland and Labrador Department of Natural Resources, P.O. Box 7400, St. John's, NL, Canada A1E 3Y5
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, NL, Canada A1B 3X9.
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Huang Y, Wille M, Dobbin A, Walzthöni NM, Robertson GJ, Ojkic D, Whitney H, Lang AS. Genetic structure of avian influenza viruses from ducks of the Atlantic flyway of North America. PLoS One 2014; 9:e86999. [PMID: 24498009 PMCID: PMC3907406 DOI: 10.1371/journal.pone.0086999] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
Wild birds, including waterfowl such as ducks, are reservoir hosts of influenza A viruses. Despite the increased number of avian influenza virus (AIV) genome sequences available, our understanding of AIV genetic structure and transmission through space and time in waterfowl in North America is still limited. In particular, AIVs in ducks of the Atlantic flyway of North America have not been thoroughly investigated. To begin to address this gap, we analyzed 109 AIV genome sequences from ducks in the Atlantic flyway to determine their genetic structure and to document the extent of gene flow in the context of sequences from other locations and other avian and mammalian host groups. The analyses included 25 AIVs from ducks from Newfoundland, Canada, from 2008–2011 and 84 available reference duck AIVs from the Atlantic flyway from 2006–2011. A vast diversity of viral genes and genomes was identified in the 109 viruses. The genetic structure differed amongst the 8 viral segments with predominant single lineages found for the PB2, PB1 and M segments, increased diversity found for the PA, NP and NS segments (2, 3 and 3 lineages, respectively), and the highest diversity found for the HA and NA segments (12 and 9 lineages, respectively). Identification of inter-hemispheric transmissions was rare with only 2% of the genes of Eurasian origin. Virus transmission between ducks and other bird groups was investigated, with 57.3% of the genes having highly similar (≥99% nucleotide identity) genes detected in birds other than ducks. Transmission between North American flyways has been frequent and 75.8% of the genes were highly similar to genes found in other North American flyways. However, the duck AIV genes did display spatial distribution bias, which was demonstrated by the different population sizes of specific viral genes in one or two neighbouring flyways compared to more distant flyways.
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Affiliation(s)
- Yanyan Huang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Michelle Wille
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Ashley Dobbin
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Natasha M. Walzthöni
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Environment Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada
| | - Hugh Whitney
- Newfoundland and Labrador Department of Natural Resources, St. John's, Newfoundland and Labrador, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
- * E-mail:
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Huang Y, Robertson GJ, Ojkic D, Whitney H, Lang AS. Diverse inter-continental and host lineage reassortant avian influenza A viruses in pelagic seabirds. INFECTION GENETICS AND EVOLUTION 2014; 22:103-11. [PMID: 24462905 DOI: 10.1016/j.meegid.2014.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/18/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022]
Abstract
Avian influenza A viruses (AIVs) often infect waterfowl, gulls and shorebirds, but other bird groups including pelagic seabirds also serve as hosts. In this study, we analyzed 21 AIVs found in two distant breeding colonies of Common Murre (Uria aalge) in Newfoundland and Labrador, Canada, during 2011. Phylogenetic analyses and genotype assignments were performed for the 21 Common Murre viruses together with all Common and Thick-billed Murre (Uria lomvia) AIV sequences available in public sequence databases. All fully characterized viruses from the Common Murres in 2011 were H1N2 subtype, but the genome sequences revealed greater diversity and the viruses belonged to four distinct genotypes. The four genotypes shared most segments in common, but reassortment was observed for PB2 and M segments. This provided direct genetic data of AIV diversification through segment reassortment during an outbreak of AIV infection in high-density breeding colonies. Analysis of the total collection of available murre viruses revealed a diverse collection of subtypes and gene lineages with high similarity to those found in viruses from waterfowl and gulls, and there was no indication of murre-specific AIV gene lineages. Overall, the virus gene pool in murres was predominantly made up of AIV lineages associated with waterfowl, but also featured considerable gull lineage genes and inter-continental reassortments. In particular, all but one of the 21 Common Murre viruses from 2011 in Newfoundland contained 1 or 2 Eurasian segments and 16 contained 1 gull lineage segment. This mosaic nature of characterized murre AIV genomes might reflect an under-recognized role of these pelagic seabirds in virus transmission across space and between bird host taxa.
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Affiliation(s)
- Yanyan Huang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Gregory J Robertson
- Wildlife Research Division, Environment Canada, Mount Pearl, NL A1N 4T3, Canada.
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Hugh Whitney
- Newfoundland and Labrador Department of Natural Resources, St. John's, NL A1E 3Y5, Canada.
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Evaluation of Seabirds in Newfoundland and Labrador, Canada, as Hosts of Influenza A Viruses. J Wildl Dis 2014; 50:98-103. [DOI: 10.7589/2012-10-247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Tønnessen R, Hauge AG, Hansen EF, Rimstad E, Jonassen CM. Host restrictions of avian influenza viruses: in silico analysis of H13 and H16 specific signatures in the internal proteins. PLoS One 2013; 8:e63270. [PMID: 23646204 PMCID: PMC3639990 DOI: 10.1371/journal.pone.0063270] [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: 11/24/2012] [Accepted: 04/02/2013] [Indexed: 12/01/2022] Open
Abstract
Gulls are the primary hosts of H13 and H16 avian influenza viruses (AIVs). The molecular basis for this host restriction is only partially understood. In this study, amino acid sequences from Eurasian gull H13 and H16 AIVs and Eurasian AIVs (non H13 and H16) were compared to determine if specific signatures are present only in the internal proteins of H13 and H16 AIVs, using a bioinformatics approach. Amino acids identified in an initial analysis performed on 15 selected sequences were checked against a comprehensive set of AIV sequences retrieved from Genbank to verify them as H13 and H16 specific signatures. Analysis of protein similarities and prediction of subcellular localization signals were performed to search for possible functions associated with the confirmed signatures. H13 and H16 AIV specific signatures were found in all the internal proteins examined, but most were found in the non-structural protein 1 (NS1) and in the nucleoprotein. A putative functional signature was predicted to be present in the nuclear export protein. Moreover, it was predicted that the NS1 of H13 and H16 AIVs lack one of the nuclear localization signals present in NS1 of other AIV subtypes. These findings suggest that the signatures found in the internal proteins of H13 and H16 viruses are possibly related to host restriction.
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Affiliation(s)
- Ragnhild Tønnessen
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, Oslo, Norway.
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Tønnessen R, Kristoffersen AB, Jonassen CM, Hjortaas MJ, Hansen EF, Rimstad E, Hauge AG. Molecular and epidemiological characterization of avian influenza viruses from gulls and dabbling ducks in Norway. Virol J 2013; 10:112. [PMID: 23575317 PMCID: PMC3639200 DOI: 10.1186/1743-422x-10-112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 04/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background Wild aquatic birds constitute the natural reservoir for avian influenza viruses (AIVs). Separate Eurasian and American AIV gene pools exist. Here, the prevalence and diversity of AIVs in gulls and dabbling ducks in Norway were described. The influence of host species and temporal changes on AIV prevalence was examined. Five AIVs from Norway, including three from common gull (Larus canus), were analyzed along with 10 available AIV genomes from gulls in Eurasia to search for evidence of intracontinental and intercontinental reassortment of gene segments encoding the internal viral proteins. Methods Swabs collected from 2417 dabbling ducks and gulls in the south-west of Norway during five ordinary hunting seasons (August-December) in the period 2005–2010 were analyzed for presence of AIV. Multivariate linear regression was used to identify associations between AIV prevalence, host species and sampling time. Five AIVs from mallard (Anas platyrhynchos) (H3N8, H9N2) and common gull (H6N8, H13N2, H16N3) were full-length characterized and phylogenetically analyzed together with GenBank reference sequences. Results Low pathogenic AIVs were detected in 15.5% (CI: 14.1–17.0) of the samples. The overall AIV prevalence was lower in December compared to that found in August to November (p = 0.003). AIV was detected in 18.7% (CI: 16.8–20.6) of the dabbling ducks. A high AIV prevalence of 7.8% (CI; 5.9–10.0) was found in gulls. A similar temporal pattern in AIV prevalence was found in both bird groups. Thirteen hemagglutinin and eight neuraminidase subtypes were detected. No evidence of intercontinental reassortment was found. Eurasian avian (non H13 and H16) PB2 or PA genes were identified in five reference Eurasian gull (H13 and H16) AIV genomes from GenBank. The NA gene from the Norwegian H13N2 gull isolate was of Eurasian avian origin. Conclusions The similar temporal pattern in AIV prevalence found in dabbling ducks and gulls, the relatively high virus prevalence detected in gulls and the evidence of intracontinental reassortment in AIVs from gulls indicate that gulls that interact with dabbling ducks are likely to be mixing vessels for AIVs from waterfowl and gulls. Our results support that intercontinental reassortment is rare in AIVs from gulls in Eurasia.
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Affiliation(s)
- Ragnhild Tønnessen
- Department of Food Safety & Infection Biology, Norwegian School of Veterinary Science, P.O. Box 8146 Dep N-0033, Oslo, Norway.
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Fries AC, Nolting JM, Danner A, Webster RG, Bowman AS, Krauss S, Slemons RD. Evidence for the circulation and inter-hemispheric movement of the H14 subtype influenza A virus. PLoS One 2013; 8:e59216. [PMID: 23555632 PMCID: PMC3610705 DOI: 10.1371/journal.pone.0059216] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/12/2013] [Indexed: 11/18/2022] Open
Abstract
Three H14 influenza A virus (IAV) isolates recovered in 2010 during routine virus surveillance along the Mississippi Migratory Bird Flyway in Wisconsin, U.S.A. raised questions about the natural history of these rare viruses. These were the first H14 IAV isolates recovered in the Western Hemisphere and the only H14 IAV isolates recovered since the original four isolates in 1982 in Asia. Full length genomic sequencing of the 2010 H14 isolates demonstrated the hemagglutinin (HA) gene from the 1982 and 2010 H14 isolates showed 89.6% nucleotide and 95.6% amino acid similarity and phylogenetic analysis of these viruses placed them with strong support within the H14 subtype lineage. The level of genomic divergence observed between the 1982 and 2010 viruses provides evidence that the H14 HA segment was circulating undetected in hosts and was not maintained in environmental stasis. Further, the evolutionary relationship observed between 1982 H14 and the closely related H4 subtype HA segments were similar to contemporary comparisons suggesting limited adaptive divergence between these sister subtypes. The nonstructural (NS) segment of one 2010 isolate was placed in a NS clade isolated infrequently over the last several decades that includes the NS segment from a previously reported 1982 H14 isolate indicating the existence of an unidentified pool of genomic diversity. An additional neuraminidase reassortment event indicated a recent inter-hemispheric gene flow from Asia into the center of North America. These results demonstrate temporal and spatial gaps in the understanding of IAV natural history. Additionally, the reassortment history of these viruses raises concern for the inter-continental spread of IAVs and the efficacy of current IAV surveillance efforts in detecting genomic diversity of viruses circulating in wild birds.
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Affiliation(s)
- Anthony C Fries
- The Ohio State University, Department of Veterinary Preventive Medicine, Columbus, OH, USA.
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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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Evidence that life history characteristics of wild birds influence infection and exposure to influenza A viruses. PLoS One 2013; 8:e57614. [PMID: 23469210 PMCID: PMC3587647 DOI: 10.1371/journal.pone.0057614] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 01/23/2013] [Indexed: 11/19/2022] Open
Abstract
We report on life history characteristics, temporal, and age-related effects influencing the frequency of occurrence of avian influenza (AI) viruses in four species of migratory geese breeding on the Yukon-Kuskokwim Delta, Alaska. Emperor geese (Chen canagica), cackling geese (Branta hutchinsii), greater white-fronted geese (Anser albifrons), and black brant (Branta bernicla), were all tested for active infection of AI viruses upon arrival in early May, during nesting in June, and while molting in July and August, 2006–2010 (n = 14,323). Additionally, prior exposure to AI viruses was assessed via prevalence of antibodies from sera samples collected during late summer in 2009 and 2010. Results suggest that geese are uncommonly infected by low pathogenic AI viruses while in Alaska. The percent of birds actively shedding AI viruses varied annually, and was highest in 2006 and 2010 (1–3%) and lowest in 2007, 2008, and 2009 (<0.70%). Contrary to findings in ducks, the highest incidence of infected birds was in late spring when birds first arrived from staging and wintering areas. Despite low prevalence, most geese were previously exposed to AI viruses, as indicated by high levels of seroprevalence during late summer (47%–96% across species; n = 541). Seroprevalence was >95% for emperor geese, a species that spends part of its life cycle in Asia and is endemic to Alaska and the Bering Sea region, compared to 40–60% for the other three species, whose entire life cycles are within the western hemisphere. Birds <45 days of age showed little past exposure to AI viruses, although antibodies were detected in samples from 5-week old birds in 2009. Seroprevalence of known age black brant revealed that no birds <4 years old had seroconverted, compared to 49% of birds ≥4 years of age.
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Jiang W, Liu S, Hou G, Li J, Zhuang Q, Wang S, Zhang P, Chen J. Chinese and global distribution of H9 subtype avian influenza viruses. PLoS One 2012; 7:e52671. [PMID: 23285143 PMCID: PMC3528714 DOI: 10.1371/journal.pone.0052671] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/19/2012] [Indexed: 11/29/2022] Open
Abstract
H9 subtype avian influenza viruses (AIVs) are of significance in poultry and public health, but epidemiological studies about the viruses are scarce. In this study, phylogenetic relationships of the viruses were analyzed based on 1233 previously reported sequences and 745 novel sequences of the viral hemagglutinin gene. The novel sequences were obtained through large-scale surveys conducted in 2008-2011 in China. The results revealed distinct distributions of H9 subtype AIVs in different hosts, sites and regions in China and in the world: (1) the dominant lineage of H9 subtype AIVs in China in recent years is lineage h9.4.2.5 represented by A/chicken/Guangxi/55/2005; (2) the newly emerging lineage h9.4.2.6, represented by A/chicken/Guangdong/FZH/2011, has also become prevalent in China; (3) lineages h9.3.3, h9.4.1 and h9.4.2, represented by A/duck/Hokkaido/26/99, A/quail/Hong Kong/G1/97 and A/chicken/Hong Kong/G9/97, respectively, have become globally dominant in recent years; (4) lineages h9.4.1 and h9.4.2 are likely of more risk to public health than others; (5) different lineages have different transmission features and host tropisms. This study also provided novel experimental data which indicated that the Leu-234 (H9 numbering) motif in the viral hemagglutinin gene is an important but not unique determinant in receptor-binding preference. This report provides a detailed and updated panoramic view of the epidemiological distributions of H9 subtype AIVs globally and in China, and sheds new insights for the prevention of infection in poultry and preparedness for a potential pandemic caused by the viruses.
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Affiliation(s)
- Wenming Jiang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
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Kang HM, Choi JG, Kim MC, Kim HR, Oem JK, Bae YC, Paek MR, Kwon JH, Lee YJ. Isolation of a reassortant H13N2 virus from a mallard fecal sample in South Korea. Virol J 2012; 9:133. [PMID: 22824586 PMCID: PMC3423068 DOI: 10.1186/1743-422x-9-133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 06/27/2012] [Indexed: 11/29/2022] Open
Abstract
Background Virus subtype H13N2, A/mallard/Kr/SH38-45/2010 (H13N2), was first isolated from a mallard fecal sample in South Korea. Results Phylogenetic analysis of all eight viral genes revealed that this virus emerged by genetic mixing between Eurasian and North American gene pools, and possibly between wild ducks and gulls. The H13 and N2 surface genes clustered together in a group with Eurasian isolates from gulls and wild birds, respectively. The PB2, PA, NP, M and NS segments belonged to the Eurasian lineage, whereas the PB1 gene clustered in the North American lineage. Furthermore, they showed a bird-dependent pattern in phylogenetic analysis: the M gene was similar to subtype H13 viruses within gulls, whereas other segments were similar to avian influenza viruses of other subtypes from wild ducks. Conclusions The data suggests that the novel reassortant H13N2 virus isolated in South Korea might have emerged by genetic reassortment between intercontinental and interspecies transmission in wild birds.
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Affiliation(s)
- Hyun-Mi Kang
- Avian Disease Division, Animal, Plant and Fisheries Quarantine and Inspection Agency, Anyangsi, Gyeonggido, Republic of Korea
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Van Borm S, Rosseel T, Vangeluwe D, Vandenbussche F, van den Berg T, Lambrecht B. Phylogeographic analysis of avian influenza viruses isolated from Charadriiformes in Belgium confirms intercontinental reassortment in gulls. Arch Virol 2012; 157:1509-22. [PMID: 22580556 DOI: 10.1007/s00705-012-1323-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/22/2012] [Indexed: 11/28/2022]
Abstract
Nine influenza viruses isolated from gulls and shorebirds in Belgium (2008-2010), including H3N8, H5N2, H6N1, H11N9, H13N6, H13N8, and H16N3 subtypes, were targeted using random amplification and next-generation sequencing. The gene segments of these viruses segregated into three phylogeographic lineage types: (1) segments circulating in waterfowl in Eurasia with sporadic introduction in other species and in the Americas ("Eurasian avian"), (2) segments circulating in American waterfowl with sporadic introduction to other species and regions ("American avian"), and (3) segments circulating exclusively in gulls and shorebirds and having increased connectivity between the two hemispheres ("Charadriiformes specific"). Notably, an H6N1 and an H5N2 isolated from L. argentatus had mainly Eurasian avian genes but shared a matrix segment of American avian origin (first documentation in European gulls of transhemispheric reassortment). These data support the growing evidence of an important role of Charadriiformes birds in the dynamic nature of avian influenza ecology.
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Affiliation(s)
- Steven Van Borm
- Department of Virology, Veterinary and Agrochemical Research Center, Groeselenbergstraat 99, 1180 Uccle, Belgium.
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Tønnessen R, Valheim M, Rimstad E, Jonassen CM, Germundssond A. Experimental inoculation of chickens with gull-derived low pathogenic avian influenza virus subtype H16N3 causes limited infection. Avian Dis 2012; 55:680-5. [PMID: 22312991 DOI: 10.1637/9701-030411-resnote.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The infectivity, transmission, and pathogenicity potential of avian influenza virus (AIV) subtype H16N3, isolated from the European herring gull (Larus argentatus), was examined in chickens. Nineteen 6-wk-old commercial Lohmann white chickens were inoculated intranasally with 1 x 10(6) 50% egg infectious dose and clinical signs, humoral immune response, virus shedding, virus transmission, and pathologic changes in the respiratory tract were studied. Oropharyngeal and cloacal swabs were collected for viral RNA detection by real-time reverse transcriptase-PCR (rRT-PCR). Sera were collected and examined for H16-specific antibodies using a hemagglutination inhibition test. Tissue samples from the nasal cavity, trachea, and lung were collected at postmortem examination for histopathology and viral RNA detection by rRT-PCR. In one bird, bilateral serous nasal discharge was observed at 2 days postinoculation (DPI) and viral RNA was detected in oropharyngeal swabs at 2 and 4 DPI. Viral RNA was also detected from the oropharynx of an additional bird at 5 DPI. Moreover, H16-specific antibodies were detected in sera from these two birds at 14 and 21 DPI. No viral RNA was detected from cloacal swabs, and no virus transmission between virus-inoculated chickens and noninoculated contact chickens was observed. Tissue samples from the nasal cavity, trachea and lung were negative for viral RNA and no gross or histopathologic lesions were observed in the virus-inoculated birds. These results indicate that gull-derived AIV subtype H16N3 causes only limited infection in chickens under experimental conditions.
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Affiliation(s)
- Ragnhild Tønnessen
- Department of Food Safety and Infection Biology, Norwegian School of Veterinary Science, P.O. Box 8146 Dep, N-0033 Oslo, Norway.
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Genetic structure of Pacific Flyway avian influenza viruses is shaped by geographic location, host species, and sampling period. Virus Genes 2012; 44:415-28. [PMID: 22222690 DOI: 10.1007/s11262-011-0706-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
The eight gene segments of avian influenza virus (AIV) reassort frequently and rapidly to generate novel genotypes and subtypes that are transmissible to a broad range of hosts. There is evidence that AIV can have a restricted host range and can segregate in space and time. Host-virus relationships at the species, geographic, and spatial scales have not been fully defined for AIV populations of the Pacific Flyway, particularly among the diverse waterfowl that occupy the Flyway in Alaska and California. Using the sequence analysis program Bayesian Tip-association Significance testing (BaTS) created for analysis of phylogeny-trait associations, we determined whether the genetic structure of Pacific Flyway AIVs sampled between 2006 and 2008 was influenced by the host species, geographic location of virus collection, and time of sampling. In posterior sets of trees, genetically similar viruses clustered by host species for thick-billed murres and glaucous gulls (order Charadriiformes), and for northern shovelers, northern pintails, and mallards (order Anseriformes). AIVs from Alaska and California were strongly spatially structured, clustering separately by region across all segments. The timing of sampling influenced the genetic structure of California AIV gene segments, possibly reflecting waves of host species movement into wintering areas. The strength of phylogeny-trait association varied by virus segment and by trait of interest, which we hypothesize is related to the frequent genetic reassortment and interspecies transmission in waterfowl.
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Kraus RHS, Zeddeman A, van Hooft P, Sartakov D, Soloviev SA, Ydenberg RC, Prins HHT. Evolution and connectivity in the world-wide migration system of the mallard: inferences from mitochondrial DNA. BMC Genet 2011; 12:99. [PMID: 22093799 PMCID: PMC3258206 DOI: 10.1186/1471-2156-12-99] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 11/17/2011] [Indexed: 12/20/2022] Open
Abstract
Background Main waterfowl migration systems are well understood through ringing activities. However, in mallards (Anas platyrhynchos) ringing studies suggest deviations from general migratory trends and traditions in waterfowl. Furthermore, surprisingly little is known about the population genetic structure of mallards, and studying it may yield insight into the spread of diseases such as Avian Influenza, and in management and conservation of wetlands. The study of evolution of genetic diversity and subsequent partitioning thereof during the last glaciation adds to ongoing discussions on the general evolution of waterfowl populations and flyway evolution. Hypothesised mallard flyways are tested explicitly by analysing mitochondrial mallard DNA from the whole northern hemisphere. Results Phylogenetic analyses confirm two mitochondrial mallard clades. Genetic differentiation within Eurasia and North-America is low, on a continental scale, but large differences occur between these two land masses (FST = 0.51). Half the genetic variance lies within sampling locations, and a negligible portion between currently recognised waterfowl flyways, within Eurasia and North-America. Analysis of molecular variance (AMOVA) at continent scale, incorporating sampling localities as smallest units, also shows the absence of population structure on the flyway level. Finally, demographic modelling by coalescence simulation proposes a split between Eurasia and North-America 43,000 to 74,000 years ago and strong population growth (~100fold) since then and little migration (not statistically different from zero). Conclusions Based on this first complete assessment of the mallard's world-wide population genetic structure we confirm that no more than two mtDNA clades exist. Clade A is characteristic for Eurasia, and clade B for North-America although some representatives of clade A are also found in North-America. We explain this pattern by evaluating competing hypotheses and conclude that a complex mix of historical, recent and anthropogenic factors shaped the current mallard populations. We refute population classification based on flyways proposed by ornithologists and managers, because they seem to have little biological meaning. Our results have implications for wetland management and conservation, with special regard to the release of farmed mallards for hunting, as well as for the possible transmission of Avian Influenza by mallards due to migration.
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Affiliation(s)
- Robert H S Kraus
- Resource Ecology Group, Wageningen University, 6700 AA, Wageningen, The Netherlands.
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SYBR green-based real-time reverse transcription-PCR for typing and subtyping of all hemagglutinin and neuraminidase genes of avian influenza viruses and comparison to standard serological subtyping tests. J Clin Microbiol 2011; 50:37-45. [PMID: 22031706 DOI: 10.1128/jcm.01195-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Continuing outbreaks of H5N1 highly pathogenic (HP) avian influenza virus (AIV) infections of wild birds and poultry worldwide emphasize the need for global surveillance of wild birds. To support the future surveillance activities, we developed a SYBR green-based, real-time reverse transcriptase PCR (rRT-PCR) for detecting nucleoprotein (NP) genes and subtyping 16 hemagglutinin (HA) and 9 neuraminidase (NA) genes simultaneously. Primers were improved by focusing on Eurasian or North American lineage genes; the number of mixed-base positions per primer was set to five or fewer, and the concentration of each primer set was optimized empirically. Also, 30 cycles of amplification of 1:10 dilutions of cDNAs from cultured viruses effectively reduced minor cross- or nonspecific reactions. Under these conditions, 346 HA and 345 NA genes of 349 AIVs were detected, with average sensitivities of NP, HA, and NA genes of 10(1.5), 10(2.3), and 10(3.1) 50% egg infective doses, respectively. Utility of rRT-PCR for subtyping AIVs was compared with that of current standard serological tests by using 104 recent migratory duck virus isolates. As a result, all HA genes and 99% of the NA genes were genetically subtyped, while only 45% of HA genes and 74% of NA genes were serologically subtyped. Additionally, direct subtyping of AIVs in fecal samples was possible by 40 cycles of amplification: approximately 70% of HA and NA genes of NP gene-positive samples were successfully subtyped. This validation study indicates that rRT-PCR with optimized primers and reaction conditions is a powerful tool for subtyping varied AIVs in clinical and cultured samples.
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Reeves AB, Pearce JM, Ramey AM, Meixell BW, Runstadler JA. Interspecies transmission and limited persistence of low pathogenic avian influenza genomes among Alaska dabbling ducks. INFECTION GENETICS AND EVOLUTION 2011; 11:2004-10. [PMID: 21964597 DOI: 10.1016/j.meegid.2011.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 08/24/2011] [Accepted: 09/06/2011] [Indexed: 12/09/2022]
Abstract
The reassortment and geographic distribution of low pathogenic avian influenza (LPAI) virus genes are well documented, but little is known about the persistence of intact LPAI genomes among species and locations. To examine persistence of entire LPAI genome constellations in Alaska, we calculated the genetic identities among 161 full-genome LPAI viruses isolated across 4 years from five species of duck: northern pintail (Anas acuta), mallard (Anas platyrhynchos), American green-winged teal (Anas crecca), northern shoveler (Anas clypeata) and American wigeon (Anas americana). Based on pairwise genetic distance, highly similar LPAI genomes (>99% identity) were observed within and between species and across a range of geographic distances (up to and >1000 km), but most often between isolates collected 0-10 km apart. Highly similar viruses were detected between years, suggesting inter-annual persistence, but these were rare in our data set with the majority occurring within 0-9 days of sampling. These results identify LPAI transmission pathways in the context of species, space and time, an initial perspective into the extent of regional virus distribution and persistence, and insight into why no completely Eurasian genomes have ever been detected in Alaska. Such information will be useful in forecasting the movement of foreign-origin avian influenza strains should they be introduced to North America.
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Affiliation(s)
- Andrew B Reeves
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
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Evidence for limited exchange of avian influenza viruses between seaducks and dabbling ducks at Alaska Peninsula coastal lagoons. Arch Virol 2011; 156:1813-21. [PMID: 21766196 DOI: 10.1007/s00705-011-1059-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 06/23/2011] [Indexed: 10/18/2022]
Abstract
Avian influenza virus (AIV) prevalence and sequence data were analyzed for Steller's eiders (Polysticta stelleri) to assess the role of this species in transporting virus genes between continents and maintaining a regional viral reservoir with sympatric northern pintails (Anas acuta). AIV prevalence was 0.2% at Izembek Lagoon and 3.9% at Nelson Lagoon for Steller's eiders and 11.2% for northern pintails at Izembek Lagoon. Phylogenetic analysis of 13 AIVs from Steller's eiders revealed that 4.9% of genes were of Eurasian origin. Seven subtypes were detected, including two also observed in northern pintails. No AIV strains were highly similar (> 99%) at all gene segments between species; however, highly similar individual genes were detected. The proportion of highly similar genes was greater within rather than between species. Steller's eiders likely transport AIV genes between continents through long-distance migratory movements. Differences in AIV prevalence, subtype distribution, and the proportion of highly similar genes suggest limited AIV exchange between Steller's eiders and northern pintails at Alaska Peninsula coastal lagoons during autumn.
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Wille M, Robertson GJ, Whitney H, Bishop MA, Runstadler JA, Lang AS. Extensive geographic mosaicism in avian influenza viruses from gulls in the northern hemisphere. PLoS One 2011; 6:e20664. [PMID: 21697989 PMCID: PMC3115932 DOI: 10.1371/journal.pone.0020664] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 05/08/2011] [Indexed: 12/27/2022] Open
Abstract
Due to limited interaction of migratory birds between Eurasia and America, two independent avian influenza virus (AIV) gene pools have evolved. There is evidence of low frequency reassortment between these regions, which has major implications in global AIV dynamics. Indeed, all currently circulating lineages of the PB1 and PA segments in North America are of Eurasian origin. Large-scale analyses of intercontinental reassortment have shown that viruses isolated from Charadriiformes (gulls, terns, and shorebirds) are the major contributor of these outsider events. To clarify the role of gulls in AIV dynamics, specifically in movement of genes between geographic regions, we have sequenced six gull AIV isolated in Alaska and analyzed these along with 142 other available gull virus sequences. Basic investigations of host species and the locations and times of isolation reveal biases in the available sequence information. Despite these biases, our analyses reveal a high frequency of geographic reassortment in gull viruses isolated in America. This intercontinental gene mixing is not found in the viruses isolated from gulls in Eurasia. This study demonstrates that gulls are important as vectors for geographically reassorted viruses, particularly in America, and that more surveillance effort should be placed on this group of birds.
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Affiliation(s)
- Michelle Wille
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Environment Canada, Mount Pearl, Newfoundland, Canada
| | - Hugh Whitney
- Animal Health Division, Department of Natural Resources, St. John's, Newfoundland, Canada
| | - Mary Anne Bishop
- Prince William Sound Science Centre, Cordova, Alaska, United States of America
| | - Jonathan A. Runstadler
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Pearce JM, Reeves AB, Ramey AM, Hupp JW, Ip HS, Bertram M, Petrula MJ, Scotton BD, Trust KA, Meixell BW, Runstadler JA. Interspecific exchange of avian influenza virus genes in Alaska: the influence of trans-hemispheric migratory tendency and breeding ground sympatry. Mol Ecol 2011; 20:1015-25. [PMID: 21073586 PMCID: PMC3041836 DOI: 10.1111/j.1365-294x.2010.04908.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The movement and transmission of avian influenza viral strains via wild migratory birds may vary by host species as a result of migratory tendency and sympatry with other infected individuals. To examine the roles of host migratory tendency and species sympatry on the movement of Eurasian low-pathogenic avian influenza (LPAI) genes into North America, we characterized migratory patterns and LPAI viral genomic variation in mallards (Anas platyrhynchos) of Alaska in comparison with LPAI diversity of northern pintails (Anas acuta). A 50-year band-recovery data set suggests that unlike northern pintails, mallards rarely make trans-hemispheric migrations between Alaska and Eurasia. Concordantly, fewer (14.5%) of 62 LPAI isolates from mallards contained Eurasian gene segments compared to those from 97 northern pintails (35%), a species with greater inter-continental migratory tendency. Aerial survey and banding data suggest that mallards and northern pintails are largely sympatric throughout Alaska during the breeding season, promoting opportunities for interspecific transmission. Comparisons of full-genome isolates confirmed near-complete genetic homology (>99.5%) of seven viruses between mallards and northern pintails. This study found viral segments of Eurasian lineage at a higher frequency in mallards than previous studies, suggesting transmission from other avian species migrating inter-hemispherically or the common occurrence of endemic Alaskan viruses containing segments of Eurasian origin. We conclude that mallards are unlikely to transfer Asian-origin viruses directly to North America via Alaska but that they are likely infected with Asian-origin viruses via interspecific transfer from species with regular migrations to the Eastern Hemisphere.
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Affiliation(s)
- John M Pearce
- US Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
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Toennessen R, Germundsson A, Jonassen CM, Haugen I, Berg K, Barrett RT, Rimstad E. Virological and serological surveillance for type A influenza in the black-legged kittiwake (Rissa tridactyla). Virol J 2011; 8:21. [PMID: 21241499 PMCID: PMC3032712 DOI: 10.1186/1743-422x-8-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 01/17/2011] [Indexed: 12/02/2022] Open
Abstract
Background The epidemiology of avian influenza viruses (AIVs) in gulls is only partially known. The role of the world's most numerous gull species, the black-legged kittiwake (Rissa tridactyla), as a potential AIV reservoir species has been unclear. The prevalence of AIV and humoral response against AIV were therefore studied in a colony of apparently healthy black-legged kittiwakes breeding in a nesting cliff in the South West Barents Region of Norway (70°22' N, 31°10' E), in 2008 and 2009. Results AIVs were detected from the oropharynx and cloaca in low amounts, with prevalences of 15% and 5%, in 2008 and 2009, respectively. Direct, partial sequencing of the hemagglutinin (HA) gene revealed that the H4 subtype was present. In 2009, antibodies to influenza A virus were detected in sera from 57 of 80 adult birds. In contrast, none of the three-week-old chicks (n = 18) tested seropositive. Hemagglutination inhibition (HI) assays demonstrated that the adult kittiwakes primarily had antibodies specific to the gull-associated H13 and H16 subtypes, with antibodies to H16 being most common. Conclusions These results support that the highly pelagic black-legged kittiwake is a reservoir of AIV. The serological findings suggest that H16 might be the main AIV subtype in the black-legged kittiwake. Further studies are needed to understand the ecology of AIV in the black-legged kittiwake and in gulls in general.
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Affiliation(s)
- Ragnhild Toennessen
- Department of Food Safety & Infection Biology, Norwegian School of Veterinary Science, PO Box 8146 Dep, N-0033 Oslo, Norway.
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