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Warren CJ, Brookes SM, Arnold ME, Irvine RM, Hansen RDE, Brown IH, Banyard AC, Slomka MJ. Assessment of Survival Kinetics for Emergent Highly Pathogenic Clade 2.3.4.4 H5Nx Avian Influenza Viruses. Viruses 2024; 16:889. [PMID: 38932181 PMCID: PMC11209063 DOI: 10.3390/v16060889] [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: 04/05/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
High pathogenicity avian influenza viruses (HPAIVs) cause high morbidity and mortality in poultry species. HPAIV prevalence means high numbers of infected wild birds could lead to spill over events for farmed poultry. How these pathogens survive in the environment is important for disease maintenance and potential dissemination. We evaluated the temperature-associated survival kinetics for five clade 2.3.4.4 H5Nx HPAIVs (UK field strains between 2014 and 2021) incubated at up to three temperatures for up to ten weeks. The selected temperatures represented northern European winter (4 °C) and summer (20 °C); and a southern European summer temperature (30 °C). For each clade 2.3.4.4 HPAIV, the time in days to reduce the viral infectivity by 90% at temperature T was established (DT), showing that a lower incubation temperature prolonged virus survival (stability), where DT ranged from days to weeks. The fastest loss of viral infectivity was observed at 30 °C. Extrapolation of the graphical DT plots to the x-axis intercept provided the corresponding time to extinction for viral decay. Statistical tests of the difference between the DT values and extinction times of each clade 2.3.4.4 strain at each temperature indicated that the majority displayed different survival kinetics from the other strains at 4 °C and 20 °C.
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Affiliation(s)
- Caroline J. Warren
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
| | - Sharon M. Brookes
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
| | - Mark E. Arnold
- Department of Epidemiological Sciences, Animal and Plant Health Agency, Sutton Bonington, Loughborough LE12 5RB, UK;
| | - Richard M. Irvine
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
- Office of the Chief Veterinary Officer (OCVO), Welsh Government, Cathays Park, Cardiff CF10 3NQ, UK
| | - Rowena D. E. Hansen
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
- Veterinary Advice Services, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency, (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Ashley C. Banyard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency, (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Marek J. Slomka
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK; (S.M.B.); (R.M.I.); (R.D.E.H.); (I.H.B.); (A.C.B.)
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2
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Kok A, Scheuer R, Bestebroer TM, Burke DF, Wilks SH, Spronken MI, de Meulder D, Lexmond P, Pronk M, Smith DJ, Herfst S, Fouchier RAM, Richard M. Characterization of A/H7 influenza virus global antigenic diversity and key determinants in the hemagglutinin globular head mediating A/H7N9 antigenic evolution. mBio 2023; 14:e0048823. [PMID: 37565755 PMCID: PMC10655666 DOI: 10.1128/mbio.00488-23] [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: 02/23/2023] [Accepted: 04/26/2023] [Indexed: 08/12/2023] Open
Abstract
IMPORTANCE A/H7 avian influenza viruses cause outbreaks in poultry globally, resulting in outbreaks with significant socio-economical impact and zoonotic risks. Occasionally, poultry vaccination programs have been implemented to reduce the burden of these viruses, which might result in an increased immune pressure accelerating antigenic evolution. In fact, evidence for antigenic diversification of A/H7 influenza viruses exists, posing challenges to pandemic preparedness and the design of vaccination strategies efficacious against drifted variants. Here, we performed a comprehensive analysis of the global antigenic diversity of A/H7 influenza viruses and identified the main substitutions in the hemagglutinin responsible for antigenic evolution in A/H7N9 viruses isolated between 2013 and 2019. The A/H7 antigenic map and knowledge of the molecular determinants of their antigenic evolution add value to A/H7 influenza virus surveillance programs, the design of vaccines and vaccination strategies, and pandemic preparedness.
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Affiliation(s)
- Adinda Kok
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rachel Scheuer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Theo M. Bestebroer
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - David F. Burke
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Samuel H. Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Monique I. Spronken
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dennis de Meulder
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Pascal Lexmond
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mark Pronk
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Derek J. Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sander Herfst
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands
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3
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Teitelbaum CS, Masto NM, Sullivan JD, Keever AC, Poulson RL, Carter DL, Blake-Bradshaw AG, Highway CJ, Feddersen JC, Hagy HM, Gerhold RW, Cohen BS, Prosser DJ. North American wintering mallards infected with highly pathogenic avian influenza show few signs of altered local or migratory movements. Sci Rep 2023; 13:14473. [PMID: 37660131 PMCID: PMC10475108 DOI: 10.1038/s41598-023-40921-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/18/2023] [Indexed: 09/04/2023] Open
Abstract
Avian influenza viruses pose a threat to wildlife and livestock health. The emergence of highly pathogenic avian influenza (HPAI) in wild birds and poultry in North America in late 2021 was the first such outbreak since 2015 and the largest outbreak in North America to date. Despite its prominence and economic impacts, we know relatively little about how HPAI spreads in wild bird populations. In January 2022, we captured 43 mallards (Anas platyrhynchos) in Tennessee, USA, 11 of which were actively infected with HPAI. These were the first confirmed detections of HPAI H5N1 clade 2.3.4.4b in the Mississippi Flyway. We compared movement patterns of infected and uninfected birds and found no clear differences; infected birds moved just as much during winter, migrated slightly earlier, and migrated similar distances as uninfected birds. Infected mallards also contacted and shared space with uninfected birds while on their wintering grounds, suggesting ongoing transmission of the virus. We found no differences in body condition or survival rates between infected and uninfected birds. Together, these results show that HPAI H5N1 clade 2.3.4.4b infection was unrelated to body condition or movement behavior in mallards infected at this location during winter; if these results are confirmed in other seasons and as HPAI H5N1 continues to evolve, they suggest that these birds could contribute to the maintenance and dispersal of HPAI in North America. Further research on more species across larger geographic areas and multiple seasons would help clarify potential impacts of HPAI on waterfowl and how this emerging disease spreads at continental scales, across species, and potentially between wildlife and domestic animals.
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Affiliation(s)
- Claire S Teitelbaum
- Akima Systems Engineering, Herndon, VA, USA.
- Contractor to U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA.
- Bay Area Environmental Research Institute and NASA Ames Research Center, Moffett Field, CA, USA.
| | - Nicholas M Masto
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Jeffery D Sullivan
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA
| | - Allison C Keever
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Deborah L Carter
- Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | | | - Cory J Highway
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | | | - Heath M Hagy
- U.S. Fish and Wildlife Service, National Wildlife Refuge System, Stanton, TN, USA
| | - Richard W Gerhold
- University of Tennessee College of Veterinary Medicine, Knoxville, TN, USA
| | - Bradley S Cohen
- College of Arts and Sciences, Tennessee Technological University, Cookeville, TN, USA
| | - Diann J Prosser
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, USA
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4
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [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] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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5
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Hill SC, François S, Thézé J, Smith AL, Simmonds P, Perrins CM, van der Hoek L, Pybus OG. Impact of host age on viral and bacterial communities in a waterbird population. THE ISME JOURNAL 2023; 17:215-226. [PMID: 36319706 PMCID: PMC9860062 DOI: 10.1038/s41396-022-01334-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.
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Affiliation(s)
- Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Sarah François
- Department of Biology, University of Oxford, Oxford, UK.
| | - Julien Thézé
- Department of Biology, University of Oxford, Oxford, UK
- UMR EPIA, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Adrian L Smith
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | | | - Lia van der Hoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver G Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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6
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Wille M, Lisovski S, Roshier D, Ferenczi M, Hoye BJ, Leen T, Warner S, Fouchier RAM, Hurt AC, Holmes EC, Klaassen M. Strong host phylogenetic and ecological effects on host competency for avian influenza in Australian wild birds. Proc Biol Sci 2023; 290:20222237. [PMID: 36651046 PMCID: PMC9845974 DOI: 10.1098/rspb.2022.2237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Host susceptibility to parasites is mediated by intrinsic and external factors such as genetics, ecology, age and season. While waterfowl are considered central to the reservoir community for low pathogenic avian influenza A viruses (LPAIV), the role of host phylogeny has received limited formal attention. Herein, we analysed 12 339 oropharyngeal and cloacal swabs and 10 826 serum samples collected over 11 years from wild birds in Australia. As well as describing age and species-level differences in prevalence and seroprevalence, we reveal that host phylogeny is a key driver in host range. Seasonality effects appear less pronounced than in the Northern Hemisphere, while annual variations are potentially linked to El Niño-Southern Oscillation. Our study provides a uniquely detailed insight into the evolutionary ecology of LPAIV in its avian reservoir community, defining distinctive processes on the continent of Australia and expanding our understanding of LPAIV globally.
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Affiliation(s)
- Michelle Wille
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia,WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia,Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Simeon Lisovski
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - David Roshier
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Marta Ferenczi
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Bethany J. Hoye
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia
| | - Trent Leen
- Geelong Field and Game, Geelong, VIC 3340, Australia,Wetlands Environmental Taskforce, Field and Game Australia, Seymour, VIC 3660, Australia
| | - Simone Warner
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, VIC 3083, Australia
| | - Ron A. M. Fouchier
- Department of Viroscience, Erasmus Medical Centre, Rotterdam 3015GE, The Netherlands
| | - Aeron C. Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC 3000, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, VIC 3217, Australia,Victorian Wader Study Group, Thornbury, Victoria 3071, Australia,Australasian Wader Studies Group, Curtin, ACT 2605, Australia
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7
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Teitelbaum CS, Ackerman JT, Hill MA, Satter JM, Casazza ML, De La Cruz SEW, Boyce WM, Buck EJ, Eadie JM, Herzog MP, Matchett EL, Overton CT, Peterson SH, Plancarte M, Ramey AM, Sullivan JD, Prosser DJ. Avian influenza antibody prevalence increases with mercury contamination in wild waterfowl. Proc Biol Sci 2022; 289:20221312. [PMID: 36069010 PMCID: PMC9449466 DOI: 10.1098/rspb.2022.1312] [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: 07/06/2022] [Accepted: 08/15/2022] [Indexed: 11/12/2022] Open
Abstract
Environmental contamination is widespread and can negatively impact wildlife health. Some contaminants, including heavy metals, have immunosuppressive effects, but prior studies have rarely measured contamination and disease simultaneously, which limits our understanding of how contaminants and pathogens interact to influence wildlife health. Here, we measured mercury concentrations, influenza infection, influenza antibodies and body condition in 749 individuals from 11 species of wild ducks overwintering in California. We found that the odds of prior influenza infection increased more than fivefold across the observed range of blood mercury concentrations, while accounting for species, age, sex and date. Influenza infection prevalence was also higher in species with higher average mercury concentrations. We detected no relationship between influenza infection and body fat content. This positive relationship between influenza prevalence and mercury concentrations in migratory waterfowl suggests that immunotoxic effects of mercury contamination could promote the spread of avian influenza along migratory flyways, especially if influenza has minimal effects on bird health and mobility. More generally, these results show that the effects of environmental contamination could extend beyond the geographical area of contamination itself by altering the prevalence of infectious diseases in highly mobile hosts.
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Affiliation(s)
- Claire S. Teitelbaum
- Akima Systems Engineering, Herndon, VA, USA
- Contractor to U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
| | - Joshua T. Ackerman
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Mason A. Hill
- U.S. Geological Survey Western Ecological Research Center, San Francisco Bay Estuary Field Station, Moffett Field, CA, USA
| | - Jacqueline M. Satter
- UC Davis College of Agricultural and Environmental Sciences, Department of Wildlife, Fish, and Conservation Biology, Davis, CA, USA
| | - Michael L. Casazza
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Susan E. W. De La Cruz
- U.S. Geological Survey Western Ecological Research Center, San Francisco Bay Estuary Field Station, Moffett Field, CA, USA
| | | | - Evan J. Buck
- U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
| | - John M. Eadie
- UC Davis College of Agricultural and Environmental Sciences, Department of Wildlife, Fish, and Conservation Biology, Davis, CA, USA
| | - Mark P. Herzog
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Elliott L. Matchett
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Cory T. Overton
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | - Sarah H. Peterson
- U.S. Geological Survey Western Ecological Research Center, Dixon Field Station, Dixon, CA, USA
| | | | - Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center, Anchorage, AK, USA
| | | | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center, Laurel, MD, USA
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8
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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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9
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Alkie TN, Lopes S, Hisanaga T, Xu W, Suderman M, Koziuk J, Fisher M, Redford T, Lung O, Joseph T, Himsworth CG, Brown IH, Bowes V, Lewis NS, Berhane Y. A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways. Virus Evol 2022; 8:veac077. [PMID: 36105667 PMCID: PMC9463990 DOI: 10.1093/ve/veac077] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/06/2022] [Accepted: 08/22/2022] [Indexed: 08/14/2023] Open
Abstract
From 2016 to 2020, high pathogenicity avian influenza (HPAI) H5 viruses circulated in Asia, Europe, and Africa, causing waves of infections and the deaths of millions of wild and domestic birds and presenting a zoonotic risk. In late 2021, H5N1 HPAI viruses were isolated from poultry in Canada and also retrospectively from a great black-backed gull (Larus marinus), raising concerns that the spread of these viruses to North America was mediated by migratory wild bird populations. In February and April 2022, H5N1 HPAI viruses were isolated from a bald eagle (Haliaeetus leucocephalus) and broiler chickens in British Columbia, Canada. Phylogenetic analysis showed that the virus from bald eagle was genetically related to H5N1 HPAI virus isolated in Hokkaido, Japan, in January 2022. The virus identified from broiler chickens was a reassortant H5N1 HPAI virus with unique constellation genome segments containing PB2 and NP from North American lineage LPAI viruses, and the remaining gene segments were genetically related to the original Newfoundland-like H5N1 HPAI viruses detected in November and December 2021 in Canada. This is the first report of H5 HPAI viruses' introduction to North America from the Pacific and the North Atlantic-linked flyways and highlights the expanding risk of genetically distinct virus introductions from different geographical locations and the potential for local reassortment with both the American lineage LPAI viruses in wild birds and with both Asian-like and European-like H5 HPAI viruses. We also report the presence of some amino acid substitutions across each segment that might contribute to the replicative efficiency of these viruses in mammalian host, evade adaptive immunity, and pose a potential zoonotic risk.
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Affiliation(s)
- Tamiru N Alkie
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Sara Lopes
- Department of Pathobiology and Population Sciences, Hawkshead Campus, The Royal Veterinary College Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
| | - Tamiko Hisanaga
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Wanhong Xu
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Matthew Suderman
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Janice Koziuk
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Mathew Fisher
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
| | - Tony Redford
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
- Department of Biological Sciences, University of Manitoba, 50 Sifton Rd., Winnipeg, Manitoba R3T 2M5, Canada
| | - Tomy Joseph
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Chelsea G Himsworth
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
- Canadian Wildlife Health Cooperative British Columbia, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
- School of Population and Public Health, University of British Columbia, 2206 E Mall, Vancouver, British Columbia V6T 1Z3, Canada
| | - Ian H Brown
- International Reference Laboratory for AI, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Victoria Bowes
- Animal Health Centre, BC Ministry of Agriculture and Food, 1767 Angus Campbell Road, Abbotsford, British Columbia V3G 2M3, Canada
| | - Nicola S Lewis
- Department of Pathobiology and Population Sciences, Hawkshead Campus, The Royal Veterinary College Hawkshead Lane, North Mymms, Hatfield, Hertfordshire AL9 7TA, UK
- International Reference Laboratory for AI, Animal and Plant Health Agency-Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, 1015 Arlington Street, Winnipeg, Manitoba R3E 3M4, Canada
- Department of Animal Science, University of Manitoba, Chancellors Cir, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Dr., Saskatoon, Saskatchewan S7N 5B4, Canada
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10
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Spatiotemporal changes in influenza A virus prevalence among wild waterfowl inhabiting the continental United States throughout the annual cycle. Sci Rep 2022; 12:13083. [PMID: 35906292 PMCID: PMC9338306 DOI: 10.1038/s41598-022-17396-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 07/25/2022] [Indexed: 11/08/2022] Open
Abstract
Avian influenza viruses can pose serious risks to agricultural production, human health, and wildlife. An understanding of viruses in wild reservoir species across time and space is important to informing surveillance programs, risk models, and potential population impacts for vulnerable species. Although it is recognized that influenza A virus prevalence peaks in reservoir waterfowl in late summer through autumn, temporal and spatial variation across species has not been fully characterized. We combined two large influenza databases for North America and applied spatiotemporal models to explore patterns in prevalence throughout the annual cycle and across the continental United States for 30 waterfowl species. Peaks in prevalence in late summer through autumn were pronounced for dabbling ducks in the genera Anas and Spatula, but not Mareca. Spatially, areas of high prevalence appeared to be related to regional duck density, with highest predicted prevalence found across the upper Midwest during early fall, though further study is needed. We documented elevated prevalence in late winter and early spring, particularly in the Mississippi Alluvial Valley. Our results suggest that spatiotemporal variation in prevalence outside autumn staging areas may also represent a dynamic parameter to be considered in IAV ecology and associated risks.
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11
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Should I stay, should I go, or something in between? The potential for parasite-mediated and age-related differential migration strategies. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10190-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AbstractSeasonal long-distance migratory behaviour of trillions of animals may in part have evolved to reduce parasite infection risk, and the fitness costs that may come with these infections. This may apply to a diversity of vertebrate migration strategies that can sometimes be observed within species and may often be age-dependent. Herein we review some common age-related variations in migration strategy, discussing why in some animal species juveniles preferentially forego or otherwise rearrange their migrations as compared to adults, potentially as an either immediate (proximate) or anticipatory (ultimate) response to infection risk and disease. We notably focus on the phenomenon of “oversummering”, where juveniles abstain from migration to the breeding grounds. This strategy is particularly prevalent amongst migratory shorebirds and has thus far received little attention as a strategy to reduce parasite infection rate, while comparative intra-specific research approaches have strong potential to elucidate the drivers of differential behavioural strategies.
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12
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Bichet C, Régis C, Gilot-Fromont E, Cohas A. Variations in immune parameters with age in a wild rodent population and links with survival. Ecol Evol 2022; 12:e9094. [PMID: 35845372 PMCID: PMC9273568 DOI: 10.1002/ece3.9094] [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: 05/19/2021] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 12/02/2022] Open
Abstract
Recent findings suggest that immune functions do not unidirectionally deteriorate with age but that a potentially adaptive remodeling, where functions of the immune system get downregulated while others get upregulated with age could also occur. Scarce in wild populations, longitudinal studies are yet necessary to properly understand the patterns and consequences of age variations of the immune system in the wild. Meanwhile, it is challenging to understand if the observed variations in immune parameters with age are due to changes at the within‐individual level or to selective (dis)appearance of individuals with peculiar immune phenotypes. Thanks to a long‐term and longitudinal monitoring of a wild Alpine marmot population, we aimed to understand within‐ and between‐individual variation in the immune phenotype with age, in order to improve our knowledge about the occurrence and the evolutionary consequences of such age variations in the wild. To do so, we recorded the age‐specific leukocyte concentration and leukocyte profile in repeatedly sampled dominant individuals. We then tested whether the potential changes with age were attributable to within‐individual variations and/or selective (dis)appearance. Finally, we investigated if the leukocyte concentration and profiles were correlated to the probability of death at a given age. The leukocyte concentration was stable with age, but the relative number of lymphocytes decreased, while the relative number of neutrophils increased, over the course of an individual's life. Moreover, between individuals of the same age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Therefore, selective disappearance seems to play a role in the age variations of the immune parameters in this population. Further investigations linking age variations in immune phenotype to individual fitness are needed to understand whether remodeling of the immune system with age could or could not be adaptive.
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Affiliation(s)
- Coraline Bichet
- Centre d'Etudes Biologiques de Chizé CNRS-La Rochelle Université Villiers-en-Bois France.,Institut für Vogelforschung "Vogelwarte Helgoland" (Institute of Avian Research) Wilhelmshaven Germany.,UMR-CNRS 5558, Laboratoire Biométrie et Biologie Évolutive Université Claude Bernard Lyon 1 Villeurbanne France
| | - Corinne Régis
- UMR-CNRS 5558, Laboratoire Biométrie et Biologie Évolutive Université Claude Bernard Lyon 1 Villeurbanne France
| | - Emmanuelle Gilot-Fromont
- UMR-CNRS 5558, Laboratoire Biométrie et Biologie Évolutive Université Claude Bernard Lyon 1 Villeurbanne France.,Université de Lyon, VetAgro Sup Marcy-l'Etoile France
| | - Aurélie Cohas
- UMR-CNRS 5558, Laboratoire Biométrie et Biologie Évolutive Université Claude Bernard Lyon 1 Villeurbanne France.,Institut Universitaire de France (IUF) Paris France
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13
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Stallknecht DE, Fojtik A, Carter DL, Crum-Bradley JA, Perez DR, Poulson RL. Naturally Acquired Antibodies to Influenza A Virus in Fall-Migrating North American Mallards. Vet Sci 2022; 9:214. [PMID: 35622742 PMCID: PMC9148056 DOI: 10.3390/vetsci9050214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/15/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Although waterfowl are the primary reservoir for multiple subtypes of influenza A virus (IAV), our understanding of population immunity in naturally infected waterfowl is poorly understood. Population immunity may be an important driver of seasonal subtype predominance in waterfowl populations and may affect the potential for establishment of introduced IAV such as the Eurasian-like A/Goose/Guangdong/1/1996 lineage in these populations. Here, we examine the prevalence of naturally acquired antibodies to nucleoprotein (NP), hemagglutinin (H3, H4, H5), and neuraminidase (N1, N2, N6, N8) in early migrating mallards (Anas platyrhynchos) sampled in Northwest Minnesota during staging and early fall migration in September 2014, 2015, 2017, and 2018. Serologic results were compared to historic and contemporary virus isolation results from these same study sites. The prevalence of antibodies to NP ranged from 60.8−76.1% in hatch-year (HY) birds and from 86.0−92.7% in after-hatch-year (AHY, >1-year-old) mallards indicating a high level of previous infection with IAV early in the fall migration season. Neutralizing antibodies were detected against H3, H4, and H5 in all years as were antibodies to N1, N2, N6, and N8. A high proportion of NP seropositive ducks tested positive for antibodies to multiple HA and NA subtypes, and this was more common in the AHY age class. Antibody prevalence to the HA and NA subtypes included in this study were consistent with the predominance of H4N6 in these populations during all years and reflected a broadening of the antibody response with age. Additional work is needed to document the longevity of these immune responses, if and how they correlate with protection against IAV transmission, infection, and disease, and if, as detected in this study, they adequately describe the true extent of exposure to IAV or specific HA or NA subtypes.
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Affiliation(s)
- David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, 589 D.W. Brooks Drive, Athens, GA 30602, USA; (D.E.S.); (A.F.); (D.L.C.); (J.A.C.-B.)
| | - Alinde Fojtik
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, 589 D.W. Brooks Drive, Athens, GA 30602, USA; (D.E.S.); (A.F.); (D.L.C.); (J.A.C.-B.)
| | - Deborah L. Carter
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, 589 D.W. Brooks Drive, Athens, GA 30602, USA; (D.E.S.); (A.F.); (D.L.C.); (J.A.C.-B.)
| | - Jo Anne Crum-Bradley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, 589 D.W. Brooks Drive, Athens, GA 30602, USA; (D.E.S.); (A.F.); (D.L.C.); (J.A.C.-B.)
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA;
| | - Daniel R. Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, 953 College Station Road, Athens, GA 30602, USA;
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, 589 D.W. Brooks Drive, Athens, GA 30602, USA; (D.E.S.); (A.F.); (D.L.C.); (J.A.C.-B.)
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14
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Tudeka CK, Aning GK, Naazie A, Botchway PK, Amuzu-Aweh EN, Agbenyegah GK, Enyetornye B, Fiadzomor D, Saelao P, Wang Y, Kelly TR, Gallardo R, Dekkers JCM, Lamont SJ, Zhou H, Kayang BB. Response of three local chicken ecotypes of Ghana to lentogenic and velogenic Newcastle disease virus challenge. Trop Anim Health Prod 2022; 54:134. [PMID: 35266056 DOI: 10.1007/s11250-022-03124-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/18/2022] [Indexed: 11/25/2022]
Abstract
This study was carried out to assess the response of three Ghanaian local chicken ecotypes to LaSota (lentogenic) and virulent field strains of Newcastle disease virus (NDV). Local chickens sampled from the Interior Savannah (IS), Forest (FO) and Coastal Savannah (CS) agro-ecological zones were bred and their offspring were challenged with LaSota NDV at 4 weeks of age. The LaSota challenge was replicated four times with different chicken groups. A total of 1438 chicks comprising 509 Coastal Savannah, 518 Forest and 411 Interior Savannah ecotypes were used. Pre- and post-challenge anti-NDV antibody titre levels were determined via ELISA assays. A second trial was conducted by introducing sick birds infected with virulent NDV to a flock of immunologically naïve chickens at 4 weeks old. Body weights were measured pre- and post-infection. Sex of the chickens was determined using a molecular method. In both trials, there was no significant difference among ecotypes in body weight and growth rate. In the LaSota trial, anti-NDV antibody titre did not differ by ecotype or sex. However, there was a positive linear relationship between body weight and antibody titre. In the velogenic NDV trial, survivability and lesion scores were similar among the three ecotypes. This study confirms that a relatively high dose of LaSota (NDV) challenge has no undesirable effect on Ghanaian local chicken ecotypes. All three Ghanaian local chicken ecotypes were susceptible to velogenic NDV challenge. Resistance to NDV by Ghanaian local chickens appears to be determined more by the individual's genetic makeup than by their ecotype.
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Affiliation(s)
- Christopher K Tudeka
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Livestock and Poultry Research Centre, University of Ghana, P.O. Box LG 38, Legon, Accra, Ghana
| | - George K Aning
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- School of Veterinary Medicine, University of Ghana, P.O. Box LG 68, Legon, Accra, Ghana
| | - Augustine Naazie
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Princess K Botchway
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Esinam N Amuzu-Aweh
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Godwin K Agbenyegah
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Animal Production Directorate, Ministry of Food and Agriculture, Accra, Ghana
| | - Ben Enyetornye
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- School of Veterinary Medicine, University of Ghana, P.O. Box LG 68, Legon, Accra, Ghana
| | - Diana Fiadzomor
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana
| | - Perot Saelao
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Ying Wang
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Terra R Kelly
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Rodrigo Gallardo
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Jack C M Dekkers
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Susan J Lamont
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Huaijun Zhou
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA
- Department of Animal Science, University of California Davis, Davis, CA, 95616, USA
| | - Boniface B Kayang
- Department of Animal Science, University of Ghana, P.O. Box LG 226, Legon, Accra, Ghana.
- Feed the Future Innovation Lab for Genomics To Improve Poultry, Department of Animal Science, University of California, Davis, CA, 95616, USA.
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15
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Ineson KM, Hill NJ, Clark DE, MacKenzie KG, Whitney JJ, Laskaris Y, Ronconi RA, Ellis JC, Giroux JF, Lair S, Stevens S, Puryear WB, Runstadler JA. Age and season predict influenza A virus dynamics in urban gulls: consequences for natural hosts in unnatural landscapes. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2497. [PMID: 34783416 DOI: 10.1002/eap.2497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/01/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Gulls are ubiquitous in urban areas due to a growing reliance on anthropogenic feeding sites, which has led to changes in their abundance, distribution, and migration ecology, with implications for disease transmission. Gulls offer a valuable model for testing hypotheses regarding the dynamics of influenza A virus (IAV) - for which gulls are a natural reservoir in urban areas. We sampled sympatric populations of Ring-billed (Larus delawarensis), Herring (L. argentatus), and Great Black-backed Gulls (L. marinus) along the densely populated Atlantic rim of North America to understand how IAV transmission is influenced by drivers such as annual cycle, host species, age, habitat type, and their interplay. We found that horizontal transmission, rather than vertical transmission, played an outsized role in the amplification of IAV due to the convergence of gulls from different breeding grounds and age classes. We detected overlapping effects of age and season in our prevalence model, identifying juveniles during autumn as the primary drivers of the seasonal epidemic in gulls. Gulls accumulated immunity over their lifespan, however short-term fluctuations in seroprevalence were observed, suggesting that migration may impose limits on the immune system to maintain circulating antibodies. We found that gulls in coastal urban habitats had higher viral prevalence than gulls captured inland, correlating with higher richness of waterbird species along the coast, a mechanism supported by our movement data. The peak in viral prevalence in newly fledged gulls that are capable of long-distance movement has important implications for the spread of pathogens to novel hosts during the migratory season as well as for human health as gulls increasingly utilize urban habitats.
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Affiliation(s)
- Katherine M Ineson
- Department of Natural Resources & the Environment, University of New Hampshire, Durham, New Hampshire, 03824, USA
| | - Nichola J Hill
- Department of Biology, University of Massachusetts, Boston, Massachusetts, 02125, USA
| | - Daniel E Clark
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Kenneth G MacKenzie
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Jillian J Whitney
- Division of Water Supply Protection, Massachusetts Department of Conservation and Recreation, West Boylston, Massachusetts, 01583, USA
| | - Yianni Laskaris
- US Fish and Wildlife Service, Galloway, New Jersey, 08205, USA
| | - Robert A Ronconi
- Canadian Wildlife Service, Environment and Climate Change Canada, Dartmouth, Nova Scotia, B2Y 2N6, Canada
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, Kennett Square, Pennsylvania, 19348, USA
| | - Jean-François Giroux
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, Québec, H3C 3P8, Canada
| | - Stéphane Lair
- Centre québécois sur la santé des animaux sauvages/Canadian Wildlife Health Cooperative, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, J2S 2M2, Canada
| | - Skyler Stevens
- Division of Mathematics, Physical, and Natural Sciences, University of New Mexico, Gallup, New Mexico, 87301, USA
| | - Wendy B Puryear
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts, 01536, USA
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University, North Grafton, Massachusetts, 01536, USA
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16
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Correia-Gomes C, Henry MK, Reeves A, Sparks N. Management and biosecurity practices by small to medium egg producers in Scotland. Br Poult Sci 2021; 62:499-508. [PMID: 33611987 DOI: 10.1080/00071668.2021.1894635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. Information about procedures and biosecurity practices used by small and medium egg producers (SMEPs) is scarce. Anecdotal evidence suggests that biosecurity in such enterprises may be poor, as personnel and equipment move freely between sites and this may be compounded by personnel working on commercial units who keep their own poultry.2. To fill this knowledge gap, a questionnaire was designed and implemented targeting SMEPs in Scotland. Small enterprises were defined as egg producers that have ≥50 laying hens but <350 laying hens; while medium enterprises were defined as egg producers that have ≥350 laying hens but ≤32 000 laying hens. The questionnaire consisted of a total of 56 questions divided into multiple sections, covering the characteristics of the primary keeper, location of the enterprise and size of the flocks, husbandry, marketing of products and health/biosecurity.3. The questionnaire was posted to 375 holdings at the beginning of March 2017 and the survey remained open until the end of May 2017. In total 90 questionnaires were received by the cut-off date of which 76 questionnaires were from SMEPs. Forty were small enterprises and 36 were medium enterprises. For three questionnaires, it was not possible to identify the enterprise type.4. Differences were observed between SMEPs in terms of reported biosecurity and management practices, with medium enterprises reporting the adoption of more biosecurity measures than small enterprises. Furthermore, SMEPs behave differently from backyard poultry keepers and large commercial companies in terms of disease risk.5. In conclusion, it is important to ensure that SMEPs are considered in contingency plans and disease control programmes and that engagement with them is promoted so that the uptake of relevant information, such as awareness of disease control programmes, is optimised.
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Affiliation(s)
- C Correia-Gomes
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Scotland's Rural College (SRUC), Inverness, Scotland
| | - M K Henry
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Scotland's Rural College (SRUC), Inverness, Scotland
| | - A Reeves
- Epidemiology Research Unit, Department of Veterinary and Animal Science, Scotland's Rural College (SRUC), Inverness, Scotland
| | - N Sparks
- South and West, Scotland's Rural College (SRUC), Parkgate Dumfries, Scotland
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17
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Highly Pathogenic Avian Influenza Viruses at the Wild-Domestic Bird Interface in Europe: Future Directions for Research and Surveillance. Viruses 2021; 13:v13020212. [PMID: 33573231 PMCID: PMC7912471 DOI: 10.3390/v13020212] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Highly pathogenic avian influenza (HPAI) outbreaks in wild birds and poultry are no longer a rare phenomenon in Europe. In the past 15 years, HPAI outbreaks—in particular those caused by H5 viruses derived from the A/Goose/Guangdong/1/1996 lineage that emerged in southeast Asia in 1996—have been occuring with increasing frequency in Europe. Between 2005 and 2020, at least ten HPAI H5 incursions were identified in Europe resulting in mass mortalities among poultry and wild birds. Until 2009, the HPAI H5 virus outbreaks in Europe were caused by HPAI H5N1 clade 2.2 viruses, while from 2014 onwards HPAI H5 clade 2.3.4.4 viruses dominated outbreaks, with abundant genetic reassortments yielding subtypes H5N1, H5N2, H5N3, H5N4, H5N5, H5N6 and H5N8. The majority of HPAI H5 virus detections in wild and domestic birds within Europe coincide with southwest/westward fall migration and large local waterbird aggregations during wintering. In this review we provide an overview of HPAI H5 virus epidemiology, ecology and evolution at the interface between poultry and wild birds based on 15 years of avian influenza virus surveillance in Europe, and assess future directions for HPAI virus research and surveillance, including the integration of whole genome sequencing, host identification and avian ecology into risk-based surveillance and analyses.
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18
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Escalera-Zamudio M, Golden M, Gutiérrez B, Thézé J, Keown JR, Carrique L, Bowden TA, Pybus OG. Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nat Commun 2020; 11:5511. [PMID: 33139731 PMCID: PMC7608645 DOI: 10.1038/s41467-020-19364-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/12/2020] [Indexed: 01/30/2023] Open
Abstract
Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. We combine phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein structure. Our resulting mutational panel may help to reveal new links between virulence evolution and other traits, and raises the possibility of predicting aspects of AIV evolution.
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Affiliation(s)
| | - Michael Golden
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | | | - Julien Thézé
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | - Jeremy Russell Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
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19
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Lam SS, Tjørnløv RS, Therkildsen OR, Christensen TK, Madsen J, Daugaard-Petersen T, Ortiz JMC, Peng W, Charbonneaux M, Rivas EI, Garbus SE, Lyngs P, Siebert U, Dietz R, Maier-Sam K, Lierz M, Tombre IM, Andersen-Ranberg EU, Sonne C. Seroprevalence of avian influenza in Baltic common eiders (Somateria mollissima) and pink-footed geese (Anser brachyrhynchus). ENVIRONMENT INTERNATIONAL 2020; 142:105873. [PMID: 32585505 DOI: 10.1016/j.envint.2020.105873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
Blood plasma was collected during 2016-2018 from healthy incubating eiders (Somateria molissima, n = 183) in three Danish colonies, and healthy migrating pink-footed geese (Anser brachyrhynchus, n = 427) at their spring roost in Central Norway (Svalbard breeding population) and their novel flyway through the Finnish Baltic Sea (Russian breeding population). These species and flyways altogether represent terrestrial, brackish and marine ecosystems spanning from the Western to the Eastern and Northern part of the Baltic Sea. Plasma of these species was analysed for seroprevalence of specific avian influenza A (AI) antibodies to obtain information on circulating AI serotypes and exposure. Overall, antibody prevalence was 55% for the eiders and 47% for the pink-footed geese. Of AI-antibody seropositive birds, 12% (22/183) of the eiders and 3% (12/427) of the pink-footed geese had been exposed to AI of the potentially zoonotic serotypes H5 and/or H7 virus. AI seropositive samples selected at random (n = 33) showed a low frequency of serotypes H1, H6 and H9. Future projects should aim at sampling and isolating AI virus to characterize dominant serotypes and virus strains (PCR). This will increase our understanding of how AI exposure may affect health, breeding and population viability of Baltic common eiders and pink-footed geese as well as the potential spill-over to humans (zoonotic potential).
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Affiliation(s)
- Su Shiung Lam
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China; Pyrolysis Technology Research Group, Institute of Tropical Aquaculture and Fisheries (Akuatrop), Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.
| | - Rune Skjold Tjørnløv
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | | | | | - Jesper Madsen
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | - Tobias Daugaard-Petersen
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | | | - Wanxi Peng
- Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Maël Charbonneaux
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | - Esteban Iglesias Rivas
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Svend-Erik Garbus
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Peter Lyngs
- Christiansø Scientific Field Station, Christiansø 97, DK-3760 Gudhjem, Denmark
| | - Ursula Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, GE-25761 Büsum, Germany.
| | - Rune Dietz
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | - Kristina Maier-Sam
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig-University Giessen, Frankfurter Str. 91-93, GE-35392 Giessen, Germany.
| | - Michael Lierz
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus-Liebig-University Giessen, Frankfurter Str. 91-93, GE-35392 Giessen, Germany.
| | - Ingunn M Tombre
- Department of Arctic Ecology, The Fram Centre, Norwegian Institute for Nature Research (NINA), P.O. Box 6606 Langnes, N-9296 Tromso, Norway.
| | - Emilie U Andersen-Ranberg
- University of Copenhagen, Department of Clinical Veterinary Sciences, Dyrlægevej 16, DK-1870 Frederiksberg C, Denmark.
| | - Christian Sonne
- Aarhus University, Department of Bioscience, Arctic Research Centre (ARC), Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark; Henan Province Engineering Research Center for Biomass Value-added Products, School of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
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20
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Wille M, Lisovski S, Risely A, Ferenczi M, Roshier D, Wong FYK, Breed AC, Klaassen M, Hurt AC. Serologic Evidence of Exposure to Highly Pathogenic Avian Influenza H5 Viruses in Migratory Shorebirds, Australia. Emerg Infect Dis 2020; 25:1903-1910. [PMID: 31538564 PMCID: PMC6759277 DOI: 10.3201/eid2510.190699] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) H5Nx viruses of the goose/Guangdong/96 lineage continue to cause outbreaks in poultry and wild birds globally. Shorebirds, known reservoirs of avian influenza viruses, migrate from Siberia to Australia along the East-Asian-Australasian Flyway. We examined whether migrating shorebirds spending nonbreeding seasons in Australia were exposed to HPAI H5 viruses. We compared those findings with those for a resident duck species. We screened >1,500 blood samples for nucleoprotein antibodies and tested positive samples for specific antibodies against 7 HPAI H5 virus antigens and 2 low pathogenicity avian influenza H5 virus antigens. We demonstrated the presence of hemagglutinin inhibitory antibodies against HPAI H5 virus clade 2.3.4.4 in the red-necked stint (Calidris ruficolis). We did not find hemagglutinin inhibitory antibodies in resident Pacific black ducks (Anas superciliosa). Our study highlights the potential role of long-distance migratory shorebirds in intercontinental spread of HPAI H5 viruses.
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21
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Wille M, Shi M, Klaassen M, Hurt AC, Holmes EC. Virome heterogeneity and connectivity in waterfowl and shorebird communities. THE ISME JOURNAL 2019; 13:2603-2616. [PMID: 31239538 PMCID: PMC6775988 DOI: 10.1038/s41396-019-0458-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 05/27/2019] [Indexed: 11/09/2022]
Abstract
Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.
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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.
| | - 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, Australia
| | - Marcel Klaassen
- Centre for Integrative Ecology, Deakin University, Geelong, Australia
| | - Aeron C Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia.
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22
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Peters A, Delhey K, Nakagawa S, Aulsebrook A, Verhulst S. Immunosenescence in wild animals: meta‐analysis and outlook. Ecol Lett 2019; 22:1709-1722. [DOI: 10.1111/ele.13343] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 05/30/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Anne Peters
- School of Biological Sciences Monash University Clayton Vic. 3800 Australia
| | - Kaspar Delhey
- School of Biological Sciences Monash University Clayton Vic. 3800 Australia
| | - Shinichi Nakagawa
- School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW 2052 Australia
| | - Anne Aulsebrook
- School of Biological Sciences Monash University Clayton Vic. 3800 Australia
- School of BioSciences University of Melbourne Parkville Vic. 3010 Australia
| | - Simon Verhulst
- Groningen Institute for Evolutionary Life Sciences University of Groningen 9747 AGGroningen The Netherlands
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23
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Hill SC, Hansen R, Watson S, Coward V, Russell C, Cooper J, Essen S, Everest H, Parag KV, Fiddaman S, Reid S, Lewis N, Brookes SM, Smith AL, Sheldon B, Perrins CM, Brown IH, Pybus OG. Comparative micro-epidemiology of pathogenic avian influenza virus outbreaks in a wild bird population. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180259. [PMID: 31056057 PMCID: PMC6553603 DOI: 10.1098/rstb.2018.0259] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2019] [Indexed: 12/13/2022] Open
Abstract
Understanding the epidemiological dynamics of highly pathogenic avian influenza virus (HPAIV) in wild birds is crucial for guiding effective surveillance and control measures. The spread of H5 HPAIV has been well characterized over large geographical and temporal scales. However, information about the detailed dynamics and demographics of individual outbreaks in wild birds is rare and important epidemiological parameters remain unknown. We present data from a wild population of long-lived birds (mute swans; Cygnus olor) that has experienced three outbreaks of related H5 HPAIVs in the past decade, specifically, H5N1 (2007), H5N8 (2016) and H5N6 (2017). Detailed demographic data were available and intense sampling was conducted before and after the outbreaks; hence the population is unusually suitable for exploring the natural epidemiology, evolution and ecology of HPAIV in wild birds. We show that key epidemiological features remain remarkably consistent across multiple outbreaks, including the timing of virus incursion and outbreak duration, and the presence of a strong age-structure in morbidity that likely arises from an equivalent age-structure in immunological responses. The predictability of these features across a series of outbreaks in a complex natural population is striking and contributes to our understanding of HPAIV in wild birds. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.
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Affiliation(s)
- Sarah C. Hill
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Rowena Hansen
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Samantha Watson
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Vivien Coward
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Christine Russell
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Jayne Cooper
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Steve Essen
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Holly Everest
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Kris V. Parag
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Steven Fiddaman
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Scott Reid
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Nicola Lewis
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
- The Royal Veterinary College, Royal College Street, London, UK
| | - Sharon M. Brookes
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Adrian L. Smith
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Ben Sheldon
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Christopher M. Perrins
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency – Weybridge, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Oliver G. Pybus
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK
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24
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Wille M, Latorre-Margalef N, Tolf C, Halpin R, Wentworth D, Fouchier RAM, Raghwani J, Pybus OG, Olsen B, Waldenström J. Where do all the subtypes go? Temporal dynamics of H8-H12 influenza A viruses in waterfowl. Virus Evol 2018; 4:vey025. [PMID: 30151242 PMCID: PMC6101617 DOI: 10.1093/ve/vey025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Influenza A virus (IAV) is ubiquitous in waterfowl. In the northern hemisphere IAV prevalence is highest during the autumn and coincides with a peak in viral subtype diversity. Although haemagglutinin subtypes H1-H12 are associated with waterfowl hosts, subtypes H8-H12 are detected very infrequently. To better understand the role of waterfowl in the maintenance of these rare subtypes, we sequenced H8-H12 viruses isolated from Mallards (Anas platyrhynchos) from 2002 to 2009. These rare viruses exhibited varying ecological and phylodynamic features. The Eurasian clades of H8 and H12 phylogenies were dominated by waterfowl sequences; mostly viruses sequenced in this study. H11, once believed to be a subtype that infected charadriiformes (shorebirds), exhibited patterns more typical of common virus subtypes. Finally, subtypes H9 and H10, which have maintained lineages in poultry, showed markedly different patterns: H10 was associated with all possible NA subtypes and this drove HA lineage diversity within years. Rare viruses belonging to subtypes H8-H12 were highly reassorted, indicating that these rare subtypes are part of the broader IAV pool. Our results suggest that waterfowl play a role in the maintenance of these rare subtypes, but we recommend additional sampling of non-traditional hosts to better understand the reservoirs of these rare viruses.
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Affiliation(s)
- Michelle Wille
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Neus Latorre-Margalef
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden.,Department of Biology, Lund University, Ecology Building, 223 62 Lund, Sweden
| | - Conny Tolf
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Rebecca Halpin
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, MD, USA
| | - David Wentworth
- Department of Infectious Disease, J. Craig Venter Institute, Rockville, MD, USA
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jayna Raghwani
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford OX1 3SY, UK
| | - Björn Olsen
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Jonas Waldenström
- Center for Ecology and Evolution in Microbial Model Systems, Linnaeus University, SE-391 82 Kalmar, Sweden
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25
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Lickfett TM, Clark E, Gehring TM, Alm EW. Detection of Influenza A viruses at migratory bird stopover sites in Michigan, USA. Infect Ecol Epidemiol 2018; 8:1474709. [PMID: 29805786 PMCID: PMC5965024 DOI: 10.1080/20008686.2018.1474709] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/25/2018] [Indexed: 11/04/2022] Open
Abstract
Introduction: Influenza A viruses have the potential to cause devastating illness in humans and domestic poultry. Wild birds are the natural reservoirs of Influenza A viruses and migratory birds are implicated in their global dissemination. High concentrations of this virus are excreted in the faeces of infected birds and faecal contamination of shared aquatic habitats can lead to indirect transmission among birds via the faecal-oral route. The role of migratory birds in the spread of avian influenza has led to large-scale surveillance efforts of circulating avian influenza viruses through direct sampling of live and dead wild birds. Environmental monitoring of bird habitats using molecular detection methods may provide additional information on the persistence of influenza virus at migratory stopover sites distributed across large spatial scales. Materials and methods: In the current study, faecal and water samples were collected at migratory stopover sites and evaluated for Influenza A by real-time quantitative reverse transcriptase PCR. Results and Discussion: This study found that Influenza A was detected at 53% of the evaluated stopover sites, and 7% and 4.8% of the faecal and water samples, respectively, tested positive for Influenza A virus. Conclusion: Environmental monitoring detected Influenza A at stopover sites used by migratory birds.
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Affiliation(s)
- Todd M Lickfett
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.,Region 6 Ecological Services, U.S. Fish and Wildlife Service, Lakewood, CO, USA
| | - Erica Clark
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA.,Silver Spring, MD, USA
| | - Thomas M Gehring
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
| | - Elizabeth W Alm
- Department of Biology and Institute for Great Lakes Research, Central Michigan University, Mount Pleasant, MI, USA
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26
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van Dijk JGB, Verhagen JH, Wille M, Waldenström J. Host and virus ecology as determinants of influenza A virus transmission in wild birds. Curr Opin Virol 2018; 28:26-36. [DOI: 10.1016/j.coviro.2017.10.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/11/2017] [Accepted: 10/17/2017] [Indexed: 10/18/2022]
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Abstract
Waterbirds are the main reservoir for low pathogenic avian influenza A viruses (LPAIV), from which occasional spillover to poultry occurs. When circulating among poultry, LPAIV may become highly pathogenic avian influenza A viruses (HPAIV). In recent years, the epidemiology of HPAIV viruses has changed drastically. HPAIV H5N1 are currently endemic among poultry in a number of countries. In addition, global spread of HPAIV H5Nx viruses has resulted in major outbreaks among wild birds and poultry worldwide. Using data collected during these outbreaks, the role of migratory birds as a vector became increasingly clear. Here we provide an overview of current data about various aspects of the changing role of wild birds in the epidemiology of avian influenza A viruses.
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28
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Spivey TJ, Lindberg MS, Meixell BW, Smith KR, Puryear WB, Davis KR, Runstadler JA, Stallknecht DE, Ramey AM. Maintenance of influenza A viruses and antibody response in mallards (Anas platyrhynchos) sampled during the non-breeding season in Alaska. PLoS One 2017; 12:e0183505. [PMID: 28837606 PMCID: PMC5570339 DOI: 10.1371/journal.pone.0183505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/04/2017] [Indexed: 11/25/2022] Open
Abstract
Prevalence of influenza A virus (IAV) infections in northern-breeding waterfowl has previously been reported to reach an annual peak during late summer or autumn; however, little is known about IAV infection dynamics in waterfowl populations persisting at high-latitude regions such as Alaska, during winter. We captured mallards (Anas platyrhynchos) throughout the non-breeding season (August–April) of 2012–2015 in Fairbanks and Anchorage, the two largest cities in Alaska, to assess patterns of IAV infection and antibody production using molecular methods and a standard serologic assay. In addition, we used virus isolation, genetic sequencing, and a virus microneutralization assay to characterize viral subtypes and to evaluate the immune response of mallards captured on multiple occasions through time. We captured 923 mallards during three successive sampling years: Fairbanks in 2012/13 and 2013/14, and Anchorage in 2014/15. Prevalence varied by age, season, and year/site with high and relatively stable estimates throughout the non-breeding season. Infected birds were detected in all locations/seasons except early-winter in Fairbanks during 2013/14. IAVs with 17 combinations of hemagglutinin (H1–5, H7–9, H11, H12) and neuraminidase (N1–6, N8, N9) subtypes were isolated. Antibodies to IAVs were detected throughout autumn and winter for all sampling locations and years, however, seroprevalence was higher among adults and varied among years. Mallards exhibited individual heterogeneity with regard to immune response, providing instances of both seroconversion and seroreversion to detected viral subtypes. The probability that an individual transitioned from one serostatus to another varied by age, with juvenile mallards having higher rates of seroconversion and seroreversion than adults. Our study provides evidence that a diversity of IAVs circulate in populations of mallards wintering at urban locations in Alaska, and we suggest waterfowl wintering at high-latitudes may play an important role in maintenance of viruses across breeding seasons.
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Affiliation(s)
- Timothy J. Spivey
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
- * E-mail:
| | - Mark S. Lindberg
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
- Institute of Arctic Biology, University of Alaska, Fairbanks, Alaska, United States of America
| | - Brandt W. Meixell
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
| | - Kyle R. Smith
- Alaska Department of Fish and Game, Anchorage, Alaska, United States of America
| | - Wendy B. Puryear
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Kimberly R. Davis
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan A. Runstadler
- Department of Biological Engineering & Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - David E. Stallknecht
- College of Veterinary Medicine, Department of Population Health, University of Georgia, Athens, Georgia, United States of America
| | - Andrew M. Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, United States of America
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Hurst CJ. Of Ducks and Men: Ecology and Evolution of a Zoonotic Pathogen in a Wild Reservoir Host. MODELING THE TRANSMISSION AND PREVENTION OF INFECTIOUS DISEASE 2017. [PMCID: PMC7123570 DOI: 10.1007/978-3-319-60616-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A hallmark of disease is that most pathogens are able to infect more than one host species. However, for most pathogens, we still have a limited understanding of how this affects epidemiology, persistence and virulence of infections—including several zoonotic pathogens that reside in wild animal reservoirs and spillover into humans. In this chapter, we review the current knowledge of mallard (Anas platyrhynchos) as host for pathogens. This species is widely distributed, often occupying habitats close to humans and livestock, and is an important game bird species and the ancestor to domestic ducks—thereby being an excellent model species to highlight aspects of the wildlife, domestic animal interface and the relevance for human health. We discuss mallard as host for a range of pathogens but focus more in depth of it as a reservoir host for influenza A virus (IAV). Over the last decades, IAV research has surged, prompted in part to the genesis and spread of highly pathogenic virus variants that have been devastating to domestic poultry and caused a number of human spillover infections. The aim of this chapter is to synthesise and review the intricate interactions of virus, host and environmental factors governing IAV epidemiology and evolution.
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