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Gadzhiev A, Petherbridge G, Sharshov K, Sobolev I, Alekseev A, Gulyaeva M, Litvinov K, Boltunov I, Teymurov A, Zhigalin A, Daudova M, Shestopalov A. Pinnipeds and avian influenza: a global timeline and review of research on the impact of highly pathogenic avian influenza on pinniped populations with particular reference to the endangered Caspian seal ( Pusa caspica). Front Cell Infect Microbiol 2024; 14:1325977. [PMID: 39071164 PMCID: PMC11273096 DOI: 10.3389/fcimb.2024.1325977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 05/21/2024] [Indexed: 07/30/2024] Open
Abstract
This study reviews chronologically the international scientific and health management literature and resources relating to impacts of highly pathogenic avian influenza (HPAI) viruses on pinnipeds in order to reinforce strategies for the conservation of the endangered Caspian seal (Pusa caspica), currently under threat from the HPAI H5N1 subtype transmitted from infected avifauna which share its haul-out habitats. Many cases of mass pinniped deaths globally have occurred from HPAI spill-overs, and are attributed to infected sympatric aquatic avifauna. As the seasonal migrations of Caspian seals provide occasions for contact with viruses from infected migratory aquatic birds in many locations around the Caspian Sea, this poses a great challenge to seal conservation. These are thus critical locations for the surveillance of highly pathogenic influenza A viruses, whose future reassortments may present a pandemic threat to humans.
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Affiliation(s)
- Alimurad Gadzhiev
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
| | - Guy Petherbridge
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
- Caspian Centre for Nature Conservation, International Institute of Ecology and Sustainable Development, Association of Universities and Research Centers of Caspian Region States, Makhachkala, Russia
| | - Kirill Sharshov
- Research Institute of Virology, Federal Research Centre for Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Ivan Sobolev
- Research Institute of Virology, Federal Research Centre for Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Alekseev
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
- Research Institute of Virology, Federal Research Centre for Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina Gulyaeva
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Kirill Litvinov
- Laboratory of Ecological and Biological Research, Astrakhan State Nature Biosphere Reserve, Astrakhan, Russia
| | - Ivan Boltunov
- Department of Vertebrate Zoology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Abdulgamid Teymurov
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
| | - Alexander Zhigalin
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
| | - Madina Daudova
- Institute of Ecology and Sustainable Development, Dagestan State University, Makhachkala, Russia
| | - Alexander Shestopalov
- Research Institute of Virology, Federal Research Centre for Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Lean FZX, Falchieri M, Furman N, Tyler G, Robinson C, Holmes P, Reid SM, Banyard AC, Brown IH, Man C, Núñez A. Highly pathogenic avian influenza virus H5N1 infection in skua and gulls in the United Kingdom, 2022. Vet Pathol 2024; 61:421-431. [PMID: 38140946 DOI: 10.1177/03009858231217224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The reemergence of the highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in the United Kingdom in 2021-2022 has caused unprecedented epizootic events in wild birds and poultry. During the summer of 2022, there was a shift in virus transmission dynamics resulting in increased HPAIV infection in seabirds, and consequently, a profound impact on seabird populations. To understand the pathological impact of HPAIV in seabirds, we evaluated the virus antigen distribution and associated pathological changes in the tissues of great skua (Stercorarius skua, n = 8), long-tailed skua (Stercorarius longicaudus, n = 1), European herring gull (Larus argentatus, n = 5), and black-headed gull (Chroicocephalus ridibundus, n = 4), which succumbed to natural infection of HPAIV during the summer of 2022. Cases were collected from Shetland, including Scatness (mainland), No Ness (mainland), Clumlie (mainland), Hermaness (island), Fair Isle (island), Noss (island), and the West Midlands, South East, and South West of England. Grossly, gizzard ulceration was observed in one great skua and pancreatic necrosis was observed in 4 herring gulls, with intralesional viral antigen detected subsequently. Microscopical analysis revealed neuro-, pneumo-, lymphoid-, and cardiomyotropism of HPAIV H5N1, with the most common virus-associated pathological changes being pancreatic and splenic necrosis. Examination of the reproductive tract of the great skua revealed HPAIV-associated oophoritis and salpingitis, and virus replication within the oviductal epithelium. The emergence of HPAIV in seabirds Stercorariidae and Laridae, particularly during summer 2022, has challenged the dogma of HPAIV dynamics, posing a significant threat to wild bird life with potential implications for the reproductive performance of seabirds of conservation importance.
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Affiliation(s)
- Fabian Z X Lean
- Animal and Plant Health Agency, Weybridge, UK
- Royal Veterinary College, Hertfordshire, UK
| | | | | | | | | | - Paul Holmes
- APHA Shrewsbury Veterinary Investigation Centre, UK
| | | | | | - Ian H Brown
- Animal and Plant Health Agency, Weybridge, UK
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Flores RA, Cammayo-Fletcher PLT, Nguyen BT, Villavicencio AGM, Lee SY, Son Y, Kim JH, Park KI, Yoo WG, Jin YB, Min W, Kim WH. Genetic Characterization and Phylogeographic Analysis of the First H13N6 Avian Influenza Virus Isolated from Vega Gull in South Korea. Viruses 2024; 16:285. [PMID: 38400060 PMCID: PMC10891532 DOI: 10.3390/v16020285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Avian influenza virus (AIV) is a pathogen with zoonotic and pandemic potential. Migratory birds are natural reservoirs of all known subtypes of AIVs, except for H17N10 and H18N11, and they have been implicated in previous highly pathogenic avian influenza outbreaks worldwide. This study identified and characterized the first isolate of the H13N6 subtype from a Vega gull (Larus vegae mongolicus) in South Korea. The amino acid sequence of hemagglutinin gene showed a low pathogenic AIV subtype and various amino acid substitutions were found in the sequence compared to the reference sequence and known H13 isolates. High sequence homology with other H13N6 isolates was found in HA, NA, PB1, and PA genes, but not for PB2, NP, M, and NS genes. Interestingly, various point amino acid mutations were found on all gene segments, and some are linked to an increased binding to human-type receptors, resistance to antivirals, and virulence. Evolutionary and phylogenetic analyses showed that all gene segments are gull-adapted, with a phylogeographic origin of mostly Eurasian, except for PB2, PA, and M. Findings from this study support the evidence that reassortment of AIVs continuously occurs in nature, and migratory birds are vital in the intercontinental spread of avian influenza viruses.
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Affiliation(s)
- Rochelle A. Flores
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Paula Leona T. Cammayo-Fletcher
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Binh T. Nguyen
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Andrea Gail M. Villavicencio
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Seung Yun Lee
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Yongwoo Son
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Jae-Hoon Kim
- National Park Research Institute, Korean National Park Service, Wonju 26441, Gangwon, Republic of Korea;
| | - Kwang Il Park
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Won Gi Yoo
- Department of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju 52727, Gyeongnam, Republic of Korea;
| | - Yeung Bae Jin
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Wongi Min
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Woo H. Kim
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
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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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5
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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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Criado MF, Moresco KA, Stallknecht DE, Swayne DE. Low-pathogenicity influenza viruses replicate differently in laughing gulls and mallards. Influenza Other Respir Viruses 2021; 15:701-706. [PMID: 34109758 PMCID: PMC8542958 DOI: 10.1111/irv.12878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/16/2021] [Indexed: 11/26/2022] Open
Abstract
Wild aquatic birds are natural reservoirs of low-pathogenicity avian influenza viruses (LPAIVs). Laughing gulls inoculated with four gull-origin LPAIVs (H7N3, H6N4, H3N8, and H2N3) had a predominate respiratory infection. By contrast, mallards inoculated with two mallard-origin LPAIVs (H5N6 and H4N8) became infected and had similar virus titers in oropharyngeal (OP) and cloacal (CL) swabs. The trend toward predominate OP shedding in gulls suggest a greater role of direct bird transmission in maintenance, whereas mallards shedding suggests importance of fecal-oral transmission through water contamination. Additional infectivity and pathogenesis studies are needed to confirm this replication difference for LPAI viruses in gulls.
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Affiliation(s)
- Miria F Criado
- Southeast Poultry Research laboratory, United States National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
| | - Kira A Moresco
- Southeast Poultry Research laboratory, United States 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, USA
| | - David E Swayne
- Southeast Poultry Research laboratory, United States National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA, USA
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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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Verhagen JH, Poen M, Stallknecht DE, van der Vliet S, Lexmond P, Sreevatsan S, Poulson RL, Fouchier RAM, Lebarbenchon C. Phylogeography and Antigenic Diversity of Low-Pathogenic Avian Influenza H13 and H16 Viruses. J Virol 2020; 94:e00537-20. [PMID: 32321814 PMCID: PMC7307148 DOI: 10.1128/jvi.00537-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/13/2020] [Indexed: 11/20/2022] Open
Abstract
Low-pathogenic avian influenza viruses (LPAIVs) are genetically highly variable and have diversified into multiple evolutionary lineages that are primarily associated with wild-bird reservoirs. Antigenic variation has been described for mammalian influenza viruses and for highly pathogenic avian influenza viruses that circulate in poultry, but much less is known about antigenic variation of LPAIVs. In this study, we focused on H13 and H16 LPAIVs that circulate globally in gulls. We investigated the evolutionary history and intercontinental gene flow based on the hemagglutinin (HA) gene and used representative viruses from genetically distinct lineages to determine their antigenic properties by hemagglutination inhibition assays. For H13, at least three distinct genetic clades were evident, while for H16, at least two distinct genetic clades were evident. Twenty and ten events of intercontinental gene flow were identified for H13 and H16 viruses, respectively. At least two antigenic variants of H13 and at least one antigenic variant of H16 were identified. Amino acid positions in the HA protein that may be involved in the antigenic variation were inferred, and some of the positions were located near the receptor binding site of the HA protein, as they are in the HA protein of mammalian influenza A viruses. These findings suggest independent circulation of H13 and H16 subtypes in gull populations, as antigenic patterns do not overlap, and they contribute to the understanding of the genetic and antigenic variation of LPAIVs naturally circulating in wild birds.IMPORTANCE Wild birds play a major role in the epidemiology of low-pathogenic avian influenza viruses (LPAIVs), which are occasionally transmitted-directly or indirectly-from them to other species, including domestic animals, wild mammals, and humans, where they can cause subclinical to fatal disease. Despite a multitude of genetic studies, the antigenic variation of LPAIVs in wild birds is poorly understood. Here, we investigated the evolutionary history, intercontinental gene flow, and antigenic variation among H13 and H16 LPAIVs. The circulation of subtypes H13 and H16 seems to be maintained by a narrower host range, in particular gulls, than the majority of LPAIV subtypes and may therefore serve as a model for evolution and epidemiology of H1 to H12 LPAIVs in wild birds. The findings suggest that H13 and H16 LPAIVs circulate independently of each other and emphasize the need to investigate within-clade antigenic variation of LPAIVs in wild birds.
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Affiliation(s)
- Josanne H Verhagen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
- Linnaeus University, Department of Biology and Environmental Science, Kalmar, Sweden
| | - Marjolein Poen
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | | | - Pascal Lexmond
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Srinand Sreevatsan
- Michigan State University, College of Veterinary Medicine, Department of Pathobiology and Diagnostic Investigation, East Lansing, Michigan, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
| | - Ron A M Fouchier
- Erasmus Medical Center, Department of Viroscience, Rotterdam, The Netherlands
| | - Camille Lebarbenchon
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, USA
- Université de La Réunion, UMR Processus Infectieux en Milieu Insulaire Tropical, INSERM 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La Réunion, France
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Genetic Characterization of Avian Influenza A (H11N9) Virus Isolated from Mandarin Ducks in South Korea in 2018. Viruses 2020; 12:v12020203. [PMID: 32059510 PMCID: PMC7077279 DOI: 10.3390/v12020203] [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: 12/09/2019] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
In July 2018, a novel avian influenza virus (A/Mandarin duck/South Korea/KNU18-12/2018(H11N9)) was isolated from Mandarin ducks in South Korea. Phylogenetic and molecular analyses were conducted to characterize the genetic origins of the H11N9 strain. Phylogenetic analysis indicated that eight gene segments of strain H11N9 belonged to the Eurasian lineages. Analysis of nucleotide sequence similarity of both the hemagglutinin (HA) and neuraminidase (NA) genes revealed the highest homology with A/duck/Kagoshima/KU57/2014 (H11N9), showing 97.70% and 98.00% nucleotide identities, respectively. Additionally, internal genes showed homology higher than 98% compared to those of other isolates derived from duck and wild birds. Both the polymerase acidic (PA) and polymerase basic 1 (PB1) genes were close to the H5N3 strain isolated in China; whereas, other internal genes were closely related to that of avian influenza virus in Japan. A single basic amino acid at the HA cleavage site (PAIASR↓GLF), the lack of a five-amino acid deletion (residue 69–73) in the stalk region of the NA gene, and E627 in the polymerase basic 2 (PB2) gene indicated that the A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) isolate was a typical low-pathogenicity avian influenza. In vitro viral replication of H11N9 showed a lower titer than H1N1 and higher than H9N2. In mice, H11N9 showed lower adaptation than H1N1. The novel A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) isolate may have resulted from an unknown reassortment through the import of multiple wild birds in Japan and Korea in approximately 2016–2017, evolving to produce a different H11N9 compared to the previous H11N9 in Korea (2016). Further reassortment events of this virus occurred in PB1 and PA in China-derived strains. These results indicate that Japanese- and Chinese-derived avian influenza contributes to the genetic diversity of A/Mandarin duck/South Korea/KNU18-12/2018(H11N9) in Korea.
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Gambaryan AS, Matrosovich TY, Boravleva EY, Lomakina NF, Yamnikova SS, Tuzikov AB, Pazynina GV, Bovin NV, Fouchier RA, Klenk HD, Matrosovich MN. Receptor-binding properties of influenza viruses isolated from gulls. Virology 2018; 522:37-45. [DOI: 10.1016/j.virol.2018.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/03/2018] [Accepted: 07/05/2018] [Indexed: 01/21/2023]
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11
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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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Ali R, Blackburn RM, Kozlakidis Z. Next-Generation Sequencing and Influenza Virus: A Short Review of the Published Implementation Attempts. HAYATI JOURNAL OF BIOSCIENCES 2016. [DOI: 10.1016/j.hjb.2016.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
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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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Gulyaeva MA, Sharshov KA, Zaykovskaia AV, Shestopalova LV, Shestopalov AM. Experimental infection and pathology of clade 2.2 H5N1 virus in gulls. J Vet Sci 2016; 17:179-88. [PMID: 26243601 PMCID: PMC4921666 DOI: 10.4142/jvs.2016.17.2.179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/30/2015] [Accepted: 07/31/2015] [Indexed: 11/20/2022] Open
Abstract
During 2006, H5N1 HPAI caused an epizootic in wild birds, resulting in a die-off of Laridae in the Novosibirsk region at Chany Lake. In the present study, we infected common gulls (Larus canus) with a high dose of the H5N1 HPAI virus isolated from a common gull to determine if severe disease could be induced over the 28 day experimental period. Moderate clinical signs including diarrhea, conjunctivitis, respiratory distress and neurological signs were observed in virus-inoculated birds, and 50% died. The most common microscopic lesions observed were necrosis of the pancreas, mild encephalitis, mild myocarditis, liver parenchymal hemorrhages, lymphocytic hepatitis, parabronchi lumen hemorrhages and interstitial pneumonia. High viral titers were shed from the oropharyngeal route and virus was still detected in one bird at 25 days after infection. In the cloaca, the virus was detected sporadically in lower titers. The virus was transmitted to direct contact gulls. Thus, infected gulls can pose a significant risk of H5N1 HPAIV transmission to other wild migratory waterfowl and pose a risk to more susceptible poultry species. These findings have important implications regarding the mode of transmission and potential risks of H5N1 HPAI spread by gulls.
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Affiliation(s)
- Marina A Gulyaeva
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Kirill A Sharshov
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Experimental and Clinical Medicine, Russian Academy of Sciences, Novosibirsk 630117, Russia
| | - Anna V Zaykovskaia
- State Research Center of Virology and Biotechnology "Vector", Novosibirsk 630559, Russia
| | - Lidia V Shestopalova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Aleksander M Shestopalov
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.,Institute of Experimental and Clinical Medicine, Russian Academy of Sciences, Novosibirsk 630117, Russia
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Zhang Y, Zou SM, Li XD, Dong LB, Bo H, Gao RB, Wang DY, Shu YL. Detection of reassortant avian influenza A (H11N9) virus in environmental samples from live poultry markets in China. Infect Dis Poverty 2016; 5:59. [PMID: 27268229 PMCID: PMC4897819 DOI: 10.1186/s40249-016-0149-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Avian influenza viruses have caused human infection and posed the pandemic potential. Live poultry markets are considered as a source of human infection with avian influenza viruses. Avian influenza routine surveillance of live poultry markets is taken annually in China. We isolated the 2 H11N9 influenza virus from the surveillance program. To better understand the risk caused by these new viruses, we characterize the genetic and pathogenicity of the two viruses. METHODS Viral isolation was conducted with specific pathogen-free (SPF) embryonated chicken eggs. Whole genome was sequenced, and phylogenetic analysis was conducted. RESULTS Two H11N9 viruses were identified, with all 8 segments belonging to the Eurasian lineage. The HA, NA, M, NS and PA genes were similar to virus isolates from ducks, and the NP, PB2 and PB1 gene segments were most similar to those viruses from wild birds, indicating that the H11N9 viruses might represent reassortant viruses from poultry and wild birds. The HA receptor binding preference was avian-like, and the cleavage site sequence of HA showed low pathogenic. The NA gene showed 94.6 % identity with the novel H7N9 virus that emerged in 2013. There was no drug resistance mutation in the M2 protein. The Asn30Asp and Thr215Ala substitutions in the M1 protein implied a potentially increased pathogenicity in mice. Both viruses were low-pathogenic strains, as assessed by the standards of intravenous pathogenicity index (IVPI) tests. CONCLUSION Two reassortant H11N9 avian influenza viruses were detected. These viruses showed low pathogenicity to chickens in the IVPI test. Public health concern caused by the reassortant H11N9 viruses should be emphasized during the future surveillance.
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Affiliation(s)
- Ye Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Shu-Mei Zou
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xiao-Dan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Li-Bo Dong
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Rong-Bao Gao
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Da-Yan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yue-Long Shu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China. .,Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, 102206, China.
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16
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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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17
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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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18
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Cunha MV, Inácio J, Freimanis G, Fusaro A, Granberg F, Höper D, King DP, Monne I, Orton R, Rosseel T. Next-generation sequencing in veterinary medicine: how can the massive amount of information arising from high-throughput technologies improve diagnosis, control, and management of infectious diseases? Methods Mol Biol 2014; 1247:415-36. [PMID: 25399113 PMCID: PMC7123048 DOI: 10.1007/978-1-4939-2004-4_30] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of high-throughput molecular technologies and associated bioinformatics has dramatically changed the capacities of scientists to produce, handle, and analyze large amounts of genomic, transcriptomic, and proteomic data. A clear example of this step-change is represented by the amount of DNA sequence data that can be now produced using next-generation sequencing (NGS) platforms. Similarly, recent improvements in protein and peptide separation efficiencies and highly accurate mass spectrometry have promoted the identification and quantification of proteins in a given sample. These advancements in biotechnology have increasingly been applied to the study of animal infectious diseases and are beginning to revolutionize the way that biological and evolutionary processes can be studied at the molecular level. Studies have demonstrated the value of NGS technologies for molecular characterization, ranging from metagenomic characterization of unknown pathogens or microbial communities to molecular epidemiology and evolution of viral quasispecies. Moreover, high-throughput technologies now allow detailed studies of host-pathogen interactions at the level of their genomes (genomics), transcriptomes (transcriptomics), or proteomes (proteomics). Ultimately, the interaction between pathogen and host biological networks can be questioned by analytically integrating these levels (integrative OMICS and systems biology). The application of high-throughput biotechnology platforms in these fields and their typical low-cost per information content has revolutionized the resolution with which these processes can now be studied. The aim of this chapter is to provide a current and prospective view on the opportunities and challenges associated with the application of massive parallel sequencing technologies to veterinary medicine, with particular focus on applications that have a potential impact on disease control and management.
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Affiliation(s)
- Mónica V. Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, IP and Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Inácio
- Instituto Nacional de Investigação Agrária e Veterinária, IP, Lisboa, Portugal and School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
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Quiñones-Mateu ME, Avila S, Reyes-Teran G, Martinez MA. Deep sequencing: becoming a critical tool in clinical virology. J Clin Virol 2014; 61:9-19. [PMID: 24998424 DOI: 10.1016/j.jcv.2014.06.013] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/12/2014] [Accepted: 06/14/2014] [Indexed: 02/07/2023]
Abstract
Population (Sanger) sequencing has been the standard method in basic and clinical DNA sequencing for almost 40 years; however, next-generation (deep) sequencing methodologies are now revolutionizing the field of genomics, and clinical virology is no exception. Deep sequencing is highly efficient, producing an enormous amount of information at low cost in a relatively short period of time. High-throughput sequencing techniques have enabled significant contributions to multiples areas in virology, including virus discovery and metagenomics (viromes), molecular epidemiology, pathogenesis, and studies of how viruses to escape the host immune system and antiviral pressures. In addition, new and more affordable deep sequencing-based assays are now being implemented in clinical laboratories. Here, we review the use of the current deep sequencing platforms in virology, focusing on three of the most studied viruses: human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza virus.
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Affiliation(s)
- Miguel E Quiñones-Mateu
- University Hospital Translational Laboratory, University Hospitals Case Medical Center, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
| | - Santiago Avila
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Gustavo Reyes-Teran
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico; Centro de Investigaciones en Enfermedades Infecciosas, Mexico City, Mexico
| | - Miguel A Martinez
- Fundació irsicaixa, Universitat Autònoma de Barcelona, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
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20
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Sharshov K, Sivay M, Liu D, Pantin-Jackwood M, Marchenko V, Durymanov A, Alekseev A, Damdindorj T, Gao GF, Swayne DE, Shestopalov A. Molecular characterization and phylogenetics of a reassortant H13N8 influenza virus isolated from gulls in Mongolia. Virus Genes 2014; 49:237-49. [DOI: 10.1007/s11262-014-1083-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 05/02/2014] [Indexed: 11/29/2022]
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21
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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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The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing. PLoS One 2013; 8:e76144. [PMID: 24086702 PMCID: PMC3784409 DOI: 10.1371/journal.pone.0076144] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 08/20/2013] [Indexed: 12/31/2022] Open
Abstract
Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides) and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.
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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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What's in a strain? Viral metagenomics identifies genetic variation and contaminating circoviruses in laboratory isolates of pigeon paramyxovirus type 1. Virus Res 2013; 171:186-93. [DOI: 10.1016/j.virusres.2012.11.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/21/2022]
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DNase SISPA-next generation sequencing confirms Schmallenberg virus in Belgian field samples and identifies genetic variation in Europe. PLoS One 2012; 7:e41967. [PMID: 22848676 PMCID: PMC3407049 DOI: 10.1371/journal.pone.0041967] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 06/28/2012] [Indexed: 01/02/2023] Open
Abstract
In 2011, a novel Orthobunyavirus was identified in cattle and sheep in Germany and the Netherlands. This virus was named Schmallenberg virus (SBV). Later, presence of the virus was confirmed using real time RT-PCR in cases of congenital malformations of bovines and ovines in several European countries, including Belgium. In the absence of specific sequencing protocols for this novel virus we confirmed its presence in RT-qPCR positive field samples using DNase SISPA-next generation sequencing (NGS), a virus discovery method based on random amplification and next generation sequencing. An in vitro transcribed RNA was used to construct a standard curve allowing the quantification of viral RNA in the field samples. Two field samples of aborted lambs containing 7.66 and 7.64 log10 RNA copies per µL total RNA allowed unambiguous identification of SBV. One sample yielded 192 SBV reads covering about 81% of the L segment, 56% of the M segment and 13% of the S segment. The other sample resulted in 8 reads distributed over the L and M segments. Three weak positive field samples (one from an aborted calf, two from aborted lambs) containing virus quantities equivalent to 4.27–4.89 log10 RNA copies per µL did not allow identification using DNase SISPA-NGS. This partial sequence information was compared to the whole genome sequence of SBV isolated from bovines in Germany, identifying several sequence differences. The applied viral discovery method allowed the confirmation of SBV in RT-qPCR positive brain samples. However, the failure to confirm SBV in weak PCR-positive samples illustrates the importance of the selection of properly targeted and fresh field samples in any virus discovery method. The partial sequences derived from the field samples showed several differences compared to the sequences from bovines in Germany, indicating sequence divergence within the epidemic.
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