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Raghwani J, Faust CL, François S, Nguyen D, Marsh K, Raulo A, Hill SC, Parag KV, Simmonds P, Knowles SCL, Pybus OG. Seasonal dynamics of the wild rodent faecal virome. Mol Ecol 2023; 32:4763-4776. [PMID: 36367339 PMCID: PMC7614976 DOI: 10.1111/mec.16778] [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: 04/21/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.
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Affiliation(s)
- Jayna Raghwani
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | - Christina L. Faust
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | | | - Dung Nguyen
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Kirsty Marsh
- School of BiosciencesUniversity of ExeterExeterUK
| | - Aura Raulo
- Department of BiologyUniversity of OxfordOxfordUK
- University of TurkuTurkuFinland
| | - Sarah C. Hill
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | | | - Peter Simmonds
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Oliver G. Pybus
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
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2
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Naguib MM, Eriksson P, Jax E, Wille M, Lindskog C, Bröjer C, Krambrich J, Waldenström J, Kraus RHS, Larson G, Lundkvist Å, Olsen B, Järhult JD, Ellström P. A Comparison of Host Responses to Infection with Wild-Type Avian Influenza Viruses in Chickens and Tufted Ducks. Microbiol Spectr 2023; 11:e0258622. [PMID: 37358408 PMCID: PMC10434033 DOI: 10.1128/spectrum.02586-22] [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: 07/28/2022] [Accepted: 05/31/2023] [Indexed: 06/27/2023] Open
Abstract
Cross-species transmission of influenza A virus (IAV) from wild waterfowl to poultry is the first step in a chain of events that can ultimately lead to exposure and infection of humans. Herein, we study the outcome of infection with eight different mallard-origin IAV subtypes in two different avian hosts: tufted ducks and chickens. We found that infection and shedding patterns as well as innate immune responses were highly dependent on viral subtypes, host species, and inoculation routes. For example, intraoesophageal inoculation, commonly used in mallard infection experiments, resulted in no infections in contrast to oculonasal inoculation, suggesting a difference in transmission routes. Despite H9N2 being endemic in chickens, inoculation of mallard-origin H9N2 failed to cause viable infection beyond 1 day postinfection in our study design. The innate immune responses were markedly different in chickens and tufted ducks, and despite the presence of retinoic acid-inducible gene-I (RIG-I) in tufted duck transcriptomes, it was neither up nor downregulated in response to infection. Overall, we have revealed the heterogeneity of infection patterns and responses in two markedly different avian hosts following a challenge with mallard-origin IAV. These virus-host interactions provide new insights into important aspects of interspecies transmission of IAV. IMPORTANCE Our current findings highlight important aspects of IAV infection in birds that have implications for our understanding of its zoonotic ecology. In contrast to mallards where the intestinal tract is the main site of IAV replication, chickens and tufted ducks show limited or no signs of intestinal infection suggesting that the fecal-oral transmission route might not apply to all bird IAV host species. Our results indicate that mallard-origin IAVs undergo genetic changes upon introduction into new hosts, suggesting rapid adaptation to a new environment. However, similar to the mallard, chickens and tufted ducks show a limited immune response to infection with low pathogenic avian influenza viruses. These findings and future studies in different IAV hosts are important for our understanding of barriers to IAV transmission between species and ultimately from the wild reservoir to humans.
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Affiliation(s)
- Mahmoud M. Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Per Eriksson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Elinor Jax
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Michelle Wille
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Caroline Bröjer
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Uppsala, Sweden
| | - Janina Krambrich
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Robert H. S. Kraus
- Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Göran Larson
- Department of Laboratory Medicine, University of Gothenburg, Gothenburg, Sweden
- Laboratory of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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3
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Abdelwhab EM, Mettenleiter TC. Zoonotic Animal Influenza Virus and Potential Mixing Vessel Hosts. Viruses 2023; 15:980. [PMID: 37112960 PMCID: PMC10145017 DOI: 10.3390/v15040980] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Influenza viruses belong to the family Orthomyxoviridae with a negative-sense, single-stranded segmented RNA genome. They infect a wide range of animals, including humans. From 1918 to 2009, there were four influenza pandemics, which caused millions of casualties. Frequent spillover of animal influenza viruses to humans with or without intermediate hosts poses a serious zoonotic and pandemic threat. The current SARS-CoV-2 pandemic overshadowed the high risk raised by animal influenza viruses, but highlighted the role of wildlife as a reservoir for pandemic viruses. In this review, we summarize the occurrence of animal influenza virus in humans and describe potential mixing vessel or intermediate hosts for zoonotic influenza viruses. While several animal influenza viruses possess a high zoonotic risk (e.g., avian and swine influenza viruses), others are of low to negligible zoonotic potential (e.g., equine, canine, bat and bovine influenza viruses). Transmission can occur directly from animals, particularly poultry and swine, to humans or through reassortant viruses in "mixing vessel" hosts. To date, there are less than 3000 confirmed human infections with avian-origin viruses and less than 7000 subclinical infections documented. Likewise, only a few hundreds of confirmed human cases caused by swine influenza viruses have been reported. Pigs are the historic mixing vessel host for the generation of zoonotic influenza viruses due to the expression of both avian-type and human-type receptors. Nevertheless, there are a number of hosts which carry both types of receptors and can act as a potential mixing vessel host. High vigilance is warranted to prevent the next pandemic caused by animal influenza viruses.
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Affiliation(s)
- Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Thomas C. Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany
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4
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Blue-Winged Teals in Guatemala and Their Potential Role in the Ecology of H14 Subtype Influenza a Viruses. Viruses 2023; 15:v15020483. [PMID: 36851697 PMCID: PMC9961055 DOI: 10.3390/v15020483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Wild aquatic birds are considered the natural hosts of 16 HA (H1-H16) and 9 NA (N1-N9) subtypes of influenza A viruses (FLUAV) found in different combinations. H14 FLUAVs are rarely detected in nature. Since 2011, H14 FLUAVs have been consistently detected in Guatemala, leading to the largest collection of this subtype from a single country. All H14 FLUAVs in Guatemala were detected from blue-winged teal samples. In this report, 17 new full-length H14 FLUAV genome sequences detected from 2014 until 2019 were analyzed and compared to all published H14 sequences, including Guatemala, North America, and Eurasia. The H14 FLUAVs identified in Guatemala were mostly associated with the N3 subtype (n = 25), whereas the rest were paired with either N4 (n = 7), N5 (n = 4), N6 (n = 1), and two mixed infections (N3/N5 n = 2, and N2/N3 n = 1). H14 FLUAVs in Guatemala belong to a distinct H14 lineage in the Americas that is evolving independently from the Eurasian H14 lineage. Of note, the ORF of the H14 HA segments showed three distinct motifs at the cleavage site, two of these containing arginine instead of lysine in the first and fourth positions, not previously described in other countries. The effects of these mutations on virus replication, virulence, and/or transmission remain unknown and warrant further studies.
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Petherbridge G, Gadzhiev AA, Shestopalov АМ, Alekseev AY, Sharshov KA, Daudova MG. An early warning system for highly pathogenic viruses borne by waterbird species and related dynamics of climate change in the Caspian Sea region: Outlines of a concept. SOUTH OF RUSSIA: ECOLOGY, DEVELOPMENT 2022. [DOI: 10.18470/1992-1098-2022-2-233-263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aim. Formulation of the outlines of the concept of ViEW (Viral Early Warning) which is intended as a long term system of multidisciplinary transboundary cooperation between specialist institutions of all five Caspian region states to research, regularly monitor and share data about the generation, transmission and epidemiology of avian‐borne pathogens and their vectors in the region, and the ways climate change may affect these processes.Material and Methods. The concept is based on the multidisciplinary experience of the authors in researching the processes incorporated in the ViEW concept and on an in‐depth survey of the literature involved.Results. The outlines of the ViEW concept are presented in this study for review and comment by interested parties and stakeholders.Conclusion. Review of activities and opinions of specialists and organizations with remits relating to the development, establishment and maintenance of ViEW, indicates that such a system is a necessity for global animal and human health because of the role that the Caspian region plays in the mass migration of species of waterbird known as vectors for avian influenza and the already evident impacts of climate change on their phenologies. Waterbirds frequenting the Caspian Sea littorals and their habitats together constitute a major potential global hotspot or High Risk region for the generation and transmission of highly pathogenic avian influenza viruses and other dangerous zoonotic diseases.
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Affiliation(s)
| | | | - А. М. Shestopalov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - A. Yu. Alekseev
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - K. A. Sharshov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
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6
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Gulyaeva M, Badmaeva E, Yurchenko K, Sharshov K, Sobolev I, Bi Y, Chen J, Shi W, Diulin I, Dorzhiev T, Shestopalov A. Monitoring of Potentially Emerging Pathogens in Wild Birds at Baikal Lake Basin in 2019. ECOHEALTH 2022; 19:335-341. [PMID: 36018399 DOI: 10.1007/s10393-022-01614-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Marina Gulyaeva
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060.
- Novosibirsk State University, Pirogova St., 2, Novosibirsk, Russia, 630090.
| | | | - Kseniya Yurchenko
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060
| | - Kirill Sharshov
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060
| | - Ivan Sobolev
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060
| | - Yuhai Bi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jianjun Chen
- Wuhan Institute of Virology, Chinese Academy of Sciences, 44 Xiaohongshan, Wuhan, 430071, Hubei, People's Republic of China
| | - Weifeng Shi
- Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271016, People's Republic of China
| | - Iliya Diulin
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060
| | | | - Alexander Shestopalov
- FSBSI "The Federal Research Center of Fundamental and Translational Medicine", Timakova str., 2, Novosibirsk, Russia, 630060
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7
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Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evol 2022; 8:veac074. [PMID: 36128050 PMCID: PMC9477075 DOI: 10.1093/ve/veac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/12/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
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Affiliation(s)
- Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | - Jayna Ragwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala SE751 85, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
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8
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Wille M, Grillo V, Ban de Gouvea Pedroso S, Burgess GW, Crawley A, Dickason C, Hansbro PM, Hoque MA, Horwood PF, Kirkland PD, Kung NYH, Lynch SE, Martin S, McArthur M, O’Riley K, Read AJ, Warner S, Hoye BJ, Lisovski S, Leen T, Hurt AC, Butler J, Broz I, Davies KR, Mileto P, Neave MJ, Stevens V, Breed AC, Lam TTY, Holmes EC, Klaassen M, Wong FYK. Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathog 2022; 18:e1010150. [PMID: 35536868 PMCID: PMC9089890 DOI: 10.1371/journal.ppat.1010150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/13/2022] [Indexed: 12/03/2022] Open
Abstract
Most of our understanding of the ecology and evolution of avian influenza A virus (AIV) in wild birds is derived from studies conducted in the northern hemisphere on waterfowl, with a substantial bias towards dabbling ducks. However, relevant environmental conditions and patterns of avian migration and reproduction are substantially different in the southern hemisphere. Through the sequencing and analysis of 333 unique AIV genomes collected from wild birds collected over 15 years we show that Australia is a global sink for AIV diversity and not integrally linked with the Eurasian gene pool. Rather, AIV are infrequently introduced to Australia, followed by decades of isolated circulation and eventual extinction. The number of co-circulating viral lineages varies per subtype. AIV haemagglutinin (HA) subtypes that are rarely identified at duck-centric study sites (H8-12) had more detected introductions and contemporary co-circulating lineages in Australia. Combined with a lack of duck migration beyond the Australian-Papuan region, these findings suggest introductions by long-distance migratory shorebirds. In addition, on the available data we found no evidence of directional or consistent patterns in virus movement across the Australian continent. This feature corresponds to patterns of bird movement, whereby waterfowl have nomadic and erratic rainfall-dependant distributions rather than consistent intra-continental migratory routes. Finally, we detected high levels of virus gene segment reassortment, with a high diversity of AIV genome constellations across years and locations. These data, in addition to those from other studies in Africa and South America, clearly show that patterns of AIV dynamics in the Southern Hemisphere are distinct from those in the temperate north.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | | | | | - Graham W. Burgess
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | | | | | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, Australia
| | - Md. Ahasanul Hoque
- Chattogram (previously Chittagong) Veterinary and Animal Sciences University, Khulshi, Bangladesh
| | - Paul F. Horwood
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Peter D. Kirkland
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Nina Yu-Hsin Kung
- Animal Biosecurity & Welfare, Biosecurity Queensland, Department of Agriculture and Fisheries, Health Food Science Precinct, Coopers Plains, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Sue Martin
- Department of Primary Industries, Parks, Water and Environment, Hobart, Australia
| | - Michaela McArthur
- Department of Primary Industries and Regional Development, Kensington, Australia
| | - Kim O’Riley
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Andrew J. Read
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Trent Leen
- Geelong Field & Game, Geelong, Australia
- Wetlands Environmental Taskforce, Field & Game Australia, Seymour, Australia
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Jeff Butler
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Ivano Broz
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Kelly R. Davies
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Patrick Mileto
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Matthew J. Neave
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Vicky Stevens
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
| | - Andrew C. Breed
- Department of Agriculture, Water and the Environment, Canberra, Australia
- University of Queensland, St. Lucia, Australia
| | - Tommy T. Y. Lam
- State Key Laboratory of Emerging Infectious Diseases, School of Public Health, The University of Hong Kong, Hong Kong, PR China
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Frank Y. K. Wong
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, Australia
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9
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Tang L, Tang W, Ming L, Gu J, Qian K, Li X, Wang T, He G. Characterization of Avian Influenza Virus H10-H12 Subtypes Isolated from Wild Birds in Shanghai, China from 2016 to 2019. Viruses 2020; 12:E1085. [PMID: 32992999 PMCID: PMC7600165 DOI: 10.3390/v12101085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
H10, H11 and H12 (H10-H12) subtypes of the avian influenza virus (AIV) are associated with waterfowl. Although these subtypes of AIV are infrequently detected in nature, they can undergo reassortment with other AIV subtypes. Few H10-H12 subtypes of AIV have been isolated from wild birds in China. In this study, 12 AIV isolates of H10-H12 subtypes were identified via routine surveillance of wild birds in Shanghai, China from 2016 to 2019, including two H10, three H11 and seven H12 isolates. Sequence and phylogenetic analyses revealed that the genomic segments of the 12 isolates are highly diverse. These 12 isolates are closely related to those in the Eurasian lineage and share a high degree of sequence identity with those from wild birds and domestic ducks in countries in the East Asian-Australasian Flyway, including Japan, Korea, Bangladesh, Vietnam and China. However, parts of the genomic segments of two H12N2 isolates (NH112319-H12N2 and NH101807-H12N2) belong to the North American lineage, suggesting intercontinental reassortment among H12 AIVs in Eurasia and North American. To better understand the ecological and phylodynamic features of H10-H12 subtypes in wild birds, a large-scale surveillance of AIVs in wild birds is warranted.
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Affiliation(s)
- Ling Tang
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
| | - Wangjun Tang
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
| | - Le Ming
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
| | - Jianming Gu
- Pudong District Forestry Station of Shanghai, Shanghai 200120, China; (J.G.); (K.Q.)
| | - Kai Qian
- Pudong District Forestry Station of Shanghai, Shanghai 200120, China; (J.G.); (K.Q.)
| | - Xiaofang Li
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
| | - Tianhou Wang
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
- Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200063, China
| | - Guimei He
- Laboratory of Wildlife Epidemic Diseases, School of Life Sciences, East China Normal University, Shanghai 200063, China; (L.T.); (W.T.); (L.M.); (X.L.); (T.W.)
- Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200063, China
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10
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Yang H, Carney PJ, Chang JC, Stevens J. Molecular characterization and three-dimensional structures of avian H8, H11, H14, H15 and swine H4 influenza virus hemagglutinins. Heliyon 2020; 6:e04068. [PMID: 32529072 PMCID: PMC7281811 DOI: 10.1016/j.heliyon.2020.e04068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/25/2020] [Accepted: 05/21/2020] [Indexed: 11/08/2022] Open
Abstract
Of the eighteen hemagglutinin (HA) subtypes (H1–H18) that have been identified in bats and aquatic birds, many HA subtypes have been structurally characterized. However, several subtypes (H8, H11 and H12) still require characterization. To better understand all of these HA subtypes at the molecular level, HA structures from an A(H4N6) (A/swine/Missouri/A01727926/2015), an A(H8N4) (A/turkey/Ontario/6118/1968), an A(H11N9) (A/duck/Memphis/546/1974), an A(H14N5) A/mallard/Gurjev/263/1982, and an A(H15N9) (A/wedge-tailed shearwater/Western Australia/2576/1979 were determined by X-ray crystallography at 2.2Å, 2.3Å, 2.8Å, 3.0Å and 2.5Å resolution, respectively. The interactions between these viruses and host receptors were studied utilizing glycan-binding analyses with their recombinant HA. The data show that all avian HAs retain their strict binding preference to avian receptors, whereas swine H4 has a weak human receptor binding. The molecular characterization and structural analyses of the HA from these zoonotic influenza viruses not only provide a deeper appreciation and understanding of the structure of all HA subtypes, but also re-iterate why continuous global surveillance is needed.
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Affiliation(s)
- Hua Yang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Paul J Carney
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jessie C Chang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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11
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Sharshov K, Mine J, Sobolev I, Kurskaya O, Dubovitskiy N, Kabilov M, Alikina T, Nakayama M, Tsunekuni R, Derko A, Prokopyeva E, Alekseev A, Shchelkanov M, Druzyaka A, Gadzhiev A, Uchida Y, Shestopalov A, Saito T. Characterization and Phylodynamics of Reassortant H12Nx Viruses in Northern Eurasia. Microorganisms 2019; 7:microorganisms7120643. [PMID: 31816947 PMCID: PMC6956379 DOI: 10.3390/microorganisms7120643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/19/2019] [Accepted: 11/30/2019] [Indexed: 11/16/2022] Open
Abstract
Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Northern Eurasia and studied their characteristics. H12N2 from the Far East region was a double reassortant containing hemagglutinin (HA), non-structural (NS) and nucleoprotein (NP) segments of the American lineage and others from the classical Eurasian avian-like lineage. H12N5 viruses contain Eurasian lineage segments. We suggest a phylogeographical scheme for reassortment events associated with geographical groups of aquatic birds and their migration flyways. The H12N2 virus is of particular interest as this subtype has been found in common teal in the Russian Far East region, and it has a strong relation to North American avian influenza virus lineages, clearly showing that viral exchange of segments between the two continents does occur. Our results emphasize the importance of Avian Influenza Virus (AIV) surveillance in Northern Eurasia for the annual screening of virus characteristics, including the genetic constellation of rare virus subtypes, to understand the evolutionary ecology of AIV.
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Affiliation(s)
- Kirill Sharshov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
- Correspondence: ; Tel.: +7-960-794-2136; Fax: +7-383-333-6456
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ivan Sobolev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Olga Kurskaya
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Nikita Dubovitskiy
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Tatiana Alikina
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Momoko Nakayama
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Anastasiya Derko
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Elena Prokopyeva
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Alexander Alekseev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Michael Shchelkanov
- School of Biomedicine, Far Eastern Federal University, 690091 Vladivostok, Russia;
- Laboratory of Virology, Federal Scientific Center of East Asia Terrestrial Biodiversity, 690022 Vladivostok, Russia
- Laboratory of marine microbiota, National Scientific Center o Marine Biology, 690041 Vladivostok, Russia
| | - Alexey Druzyaka
- Laboratory of behavioral ecology, Institute of Animal Systematics and Ecology, 630091 Novosibirsk, Russia;
| | - Alimurad Gadzhiev
- Department of Ecology, Dagestan State University, 367000 Makhachkala, Russia;
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Alexander Shestopalov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
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12
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Susceptibility of Chickens to Low Pathogenic Avian Influenza (LPAI) Viruses of Wild Bird- and Poultry-Associated Subtypes. Viruses 2019; 11:v11111010. [PMID: 31683727 PMCID: PMC6893415 DOI: 10.3390/v11111010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Analysis of low pathogenic avian influenza (LPAI) viruses circulating in the Netherlands in a previous study revealed associations of specific hemagglutinin (HA) and neuraminidase (NA) subtypes with wild bird or poultry hosts. In this study, we identified putative host associations in LPAI virus internal proteins. We show that LPAI viruses isolated from poultry more frequently carried the allele A variant of the nonstructural protein (NS) gene, compared to wild bird viruses. We determined the susceptibility of chickens to wild bird–associated subtypes H3N8 and H4N6 and poultry-associated subtypes H8N4 and H9N2, carrying either NS allele A or B, in an infection experiment. We observed variations in virus shedding and replication patterns, however, these did not correlate with the predicted wild bird- or poultry-associations of the viruses. The experiment demonstrated that LPAI viruses of wild bird-associated subtypes can replicate in chickens after experimental infection, despite their infrequent detection in poultry. Although the NS1 protein is known to play a role in immune modulation, no differences were detected in the limited innate immune response to LPAI virus infection. This study contributes to a better understanding of the infection dynamics of LPAI viruses in chickens.
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13
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Cross-Reactive Antibodies Binding to the Influenza Virus Subtype H11 Hemagglutinin. Pathogens 2019; 8:pathogens8040199. [PMID: 31640141 PMCID: PMC6963512 DOI: 10.3390/pathogens8040199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/13/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
H11 subtype influenza viruses were isolated from a wide range of bird species and one strain also was isolated from swine. In an effort to generate reagents for a chimeric H11/1 hemagglutinin-based universal influenza virus vaccine candidate, we produced 28 monoclonal antibodies that recognize the H11 HA subtype. Here we characterized these antibodies in terms of binding breadth and functionality. We found that the antibodies bind broadly to North American and Eurasian lineage isolates and also show broad neutralizing activity, suggesting that immunogenic epitopes on the H11 head domain are not under strong pressure from immunity in the natural reservoir. Furthermore, we found that the antibodies were highly hemagglutination inhibition active against the homologous chimeric H11/1N1 virus, but approximately 50% lost this activity when tested against a virus expressing the same the full length H11 HA of which the head domain is present on cH11/1 HA. Furthermore, while strong neutralizing activity was found to a genetically distant North American lineage H11 isolate, little hemagglutination inhibition activity was detected. This suggests that small structural changes between wild type H11 and cH11/1 as well as between Eurasian and North American lineage H11 HAs can strongly influence the functionality of the isolated monoclonal antibodies.
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14
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Liu J, Zhou L, Lv J, Zou Y, Wang T. Two novel reassortant H11N8 avian influenza viruses occur in wild birds found in East Dongting Lake, China. Arch Virol 2019; 164:1405-1410. [DOI: 10.1007/s00705-019-04168-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 01/19/2019] [Indexed: 11/28/2022]
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15
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Eriksson P, Lindskog C, Lorente-Leal V, Waldenström J, González-Acuna D, Järhult JD, Lundkvist Å, Olsen B, Jourdain E, Ellström P. Attachment Patterns of Human and Avian Influenza Viruses to Trachea and Colon of 26 Bird Species - Support for the Community Concept. Front Microbiol 2019; 10:815. [PMID: 31057520 PMCID: PMC6482220 DOI: 10.3389/fmicb.2019.00815] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/01/2019] [Indexed: 12/23/2022] Open
Abstract
Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.
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Affiliation(s)
- Per Eriksson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Victor Lorente-Leal
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | | | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Björn Olsen
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Elsa Jourdain
- UMR0346 - EPIA, INRA, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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16
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Naguib MM, Verhagen JH, Samy A, Eriksson P, Fife M, Lundkvist Å, Ellström P, Järhult JD. Avian influenza viruses at the wild-domestic bird interface in Egypt. Infect Ecol Epidemiol 2019; 9:1575687. [PMID: 30815236 PMCID: PMC6383604 DOI: 10.1080/20008686.2019.1575687] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
Wild birds of the orders Anseriformes (mainly ducks, geese and swans) and Charadriiformes (mainly gulls, terns and waders) constitute the natural reservoir for low pathogenic avian influenza (LPAI) viruses. In Egypt, highly pathogenic avian influenza (HPAI) H5N1 and LPAI H9N2 viruses are endemic in domestic poultry, forming a threat to animal and human health and raising questions about the routes of introduction and mechanisms of persistence. Recently, HPAI H5N8 virus was also introduced into Egyptian domestic birds. Here we review the literature on the role of wild birds in the introduction and endemicity of avian influenza viruses in Egypt. Dabbling ducks in Egypt harbor an extensive LPAI virus diversity and may constitute the route of introduction for HPAI H5N1 and HPAI H5N8 viruses into Egypt through migration, however their role in the endemicity of HPAI H5N1, LPAI H9N2 and potentially other avian influenza virus (AIV) strains - by means of reassortment of viral genes - is less clear. Strengthened surveillance programs, in both domestic and wild birds, that include all LPAI virus subtypes and full genome sequencing are needed to better assess the wild-domestic bird interface and form a basis for evidence-based measures to limit and prevent AIV transmission between wild and domestic birds.
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Affiliation(s)
- Mahmoud M. Naguib
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
| | - Josanne H. Verhagen
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Ahmed Samy
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Giza, Egypt
- Genetics and Genomics, The Pirbright Institute, Surrey, UK
| | - Per Eriksson
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Mark Fife
- Genetics and Genomics, The Pirbright Institute, Surrey, UK
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Patrik Ellström
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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17
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Wille M, Eden JS, Shi M, Klaassen M, Hurt AC, Holmes EC. Virus-virus interactions and host ecology are associated with RNA virome structure in wild birds. Mol Ecol 2018; 27:5263-5278. [PMID: 30375075 PMCID: PMC6312746 DOI: 10.1111/mec.14918] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
Little is known about the factors that shape the ecology of RNA viruses in nature. Wild birds are an important case in point, as other than influenza A virus, avian samples are rarely tested for viruses, especially in the absence of overt disease. Using bulk RNA-sequencing ("meta-transcriptomics"), we revealed the viral diversity present in Australian wild birds through the lens of the ecological factors that may determine virome structure and abundance. A meta-transcriptomic analysis of four Anseriformes (waterfowl) and Charadriiformes (shorebird) species sampled in temperate and arid Australia revealed the presence of 27 RNA virus genomes, 18 of which represent newly described species. The viruses identified included a previously described gammacoronavirus and influenza A viruses. Additionally, we identified novel virus species from the families Astroviridae, Caliciviridae, Reoviridae, Rhabdoviridae, Picobirnaviridae and Picornaviridae. We noted differences in virome structure that reflected underlying differences in location and influenza A infection status. Red-necked Avocets (Recurvirostra novaehollandiae) from Australia's arid interior possessed the greatest viral diversity and abundance, markedly higher than individuals sampled in temperate Australia. In Ruddy Turnstones (Arenaria interpres) and dabbling ducks (Anas spp.), viral abundance and diversity were higher and more similar in hosts that were positive for influenza A infection compared to those that were negative for this virus, despite samples being collected on the same day and from the same location. This study highlights the extent and diversity of RNA viruses in wild birds and lays the foundation for understanding the factors that determine virome structure in wild populations.
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Affiliation(s)
- Michelle Wille
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.,The Westmead Institute for Medical Research, Centre for Virus Research, Sydney, New South Wales, Australia
| | - Mang Shi
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
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