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Giacinti JA, Signore AV, Jones MEB, Bourque L, Lair S, Jardine C, Stevens B, Bollinger T, Goldsmith D, Pybus M, Stasiak I, Davis R, Pople N, Nituch L, Brook RW, Ojkic D, Massé A, Dimitri-Masson G, Parsons GJ, Baker M, Yason C, Harms J, Jutha N, Neely J, Berhane Y, Lung O, French SK, Myers L, Provencher JF, Avery-Gomm S, Robertson GJ, Barychka T, Gurney KEB, Wight J, Rahman I, Hargan K, Lang AS, Montevecchi WA, Burt TV, Brown MGC, Pekarik C, Thompson T, McLaughlin A, Willie M, Wilson L, Flemming SA, Ross MV, Leafloor J, Baldwin F, Sharp C, Lewis H, Beaumont M, Hanson A, Ronconi RA, Reed E, Campbell M, Saunders M, Soos C. Avian influenza viruses in wild birds in Canada following incursions of highly pathogenic H5N1 virus from Eurasia in 2021-2022. mBio 2024; 15:e0320323. [PMID: 39012149 PMCID: PMC11323545 DOI: 10.1128/mbio.03203-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/24/2024] [Indexed: 07/17/2024] Open
Abstract
Following the detection of novel highly pathogenic avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in Newfoundland, Canada, in late 2021, avian influenza virus (AIV) surveillance in wild birds was scaled up across Canada. Herein, we present the results of Canada's Interagency Surveillance Program for Avian Influenza in Wild Birds during the first year (November 2021-November 2022) following the incursions of HPAIV from Eurasia. The key objectives of the surveillance program were to (i) identify the presence, distribution, and spread of HPAIV and other AIVs; (ii) identify wild bird morbidity and mortality associated with HPAIV; (iii) identify the range of wild bird species infected by HPAIV; and (iv) genetically characterize detected AIV. A total of 6,246 sick and dead wild birds were tested, of which 27.4% were HPAIV positive across 12 taxonomic orders and 80 species. Geographically, HPAIV detections occurred in all Canadian provinces and territories, with the highest numbers in the Atlantic and Central Flyways. Temporally, peak detections differed across flyways, though the national peak occurred in April 2022. In an additional 11,295 asymptomatic harvested or live-captured wild birds, 5.2% were HPAIV positive across 3 taxonomic orders and 19 species. Whole-genome sequencing identified HPAIV of Eurasian origin as most prevalent in the Atlantic Flyway, along with multiple reassortants of mixed Eurasian and North American origins distributed across Canada, with moderate structuring at the flyway scale. Wild birds were victims and reservoirs of HPAIV H5N1 2.3.4.4b, underscoring the importance of surveillance encompassing samples from sick and dead, as well as live and harvested birds, to provide insights into the dynamics and potential impacts of the HPAIV H5N1 outbreak. This dramatic shift in the presence and distribution of HPAIV in wild birds in Canada highlights a need for sustained investment in wild bird surveillance and collaboration across interagency partners. IMPORTANCE We present the results of Canada's Interagency Surveillance Program for Avian Influenza in Wild Birds in the year following the first detection of highly pathogenic avian influenza virus (HPAIV) H5N1 on the continent. The surveillance program tested over 17,000 wild birds, both sick and apparently healthy, which revealed spatiotemporal and taxonomic patterns in HPAIV prevalence and mortality across Canada. The significant shift in the presence and distribution of HPAIV in Canada's wild birds underscores the need for sustained investment in wild bird surveillance and collaboration across One Health partners.
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Affiliation(s)
- Jolene A. Giacinti
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
| | - Anthony V. Signore
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Megan E. B. Jones
- Canadian Wildlife Health Cooperative, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Stéphane Lair
- Canadian Wildlife Health Cooperative, Faculté de médecine vétérinaire, Université de Montréal, St-Hyacinthe, Québec, Canada
| | - Claire Jardine
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Brian Stevens
- Canadian Wildlife Health Cooperative, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Trent Bollinger
- Canadian Wildlife Health Cooperative, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Dayna Goldsmith
- Canadian Wildlife Health Cooperative, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Margo Pybus
- Alberta Environment and Parks, Edmonton, Alberta, Canada
| | - Iga Stasiak
- Saskatchewan Ministry of Environment, Saskatoon, Saskatchewan, Canada
| | - Richard Davis
- Manitoba Department of Natural Resources and Northern Development, Wildlife Branch, Dauphin, Manitoba, Canada
| | - Neil Pople
- Veterinary Diagnostic Services, Manitoba Department of Agriculture, Winnipeg, Manitoba, Canada
| | - Larissa Nituch
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Rodney W. Brook
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Peterborough, Ontario, Canada
| | - Davor Ojkic
- Animal Health Laboratory, University of Guelph, Guelph, Ontario, Canada
| | - Ariane Massé
- Ministère de l’Environnement, de la Lutte contre les changements climatiques, de la Faune et des Parcs du Québec, Québec City, Québec, Canada
| | - Gabrielle Dimitri-Masson
- Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec, Québec City, Québec, Canada
| | - Glen J. Parsons
- Wildlife Division, Nova Scotia Department of Natural Resources and Renewables, Kentville, Nova Scotia, Canada
| | - Meghan Baker
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, St. John’s, Newfoundland and Labrador, Canada
| | - Carmencita Yason
- AVC Diagnostic Services, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - Jane Harms
- Animal Health Unit, Environment Yukon, Government of Yukon, Whitehorse, Yukon, Canada
| | - Naima Jutha
- Wildlife Management Division, Department of Environment and Climate Change, Government of the Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Jon Neely
- Wildlife Operations Division, Department of Environment, Government of Nunavut, Iqaluit, Nunavut, Canada
| | - Yohannes Berhane
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Oliver Lung
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Shannon K. French
- Animal Health Strategic Planning and Research, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Lawrna Myers
- Animal Health Strategic Planning and Research, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Jennifer F. Provencher
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
| | - Stephanie Avery-Gomm
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Gregory J. Robertson
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Tatsiana Barychka
- Wildlife Research Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Mount Pearl, Newfoundland and Labrador, Canada
| | - Kirsty E. B. Gurney
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Saskatoon, Saskatchewan, Canada
| | - Jordan Wight
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Ishraq Rahman
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Kathryn Hargan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - William A. Montevecchi
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Department of Psychology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Tori V. Burt
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
- Department of Psychology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Michael G. C. Brown
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Cynthia Pekarik
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Trevor Thompson
- Wildlife Management and Regulatory Affairs Division, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, Québec, Canada
| | - Angela McLaughlin
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Government of Canada, Winnipeg, Manitoba, Canada
- Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Megan Willie
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Laurie Wilson
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Scott A. Flemming
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Megan V. Ross
- Pacific Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Delta, British Columbia, Canada
| | - Jim Leafloor
- Prairie Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Frank Baldwin
- Prairie Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Winnipeg, Manitoba, Canada
| | - Chris Sharp
- Ontario Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Hannah Lewis
- Ontario Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Ottawa, Ontario, Canada
| | - Matthieu Beaumont
- Quebec Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Québec, Québec, Canada
| | - Al Hanson
- Atlantic Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Sackville, New Brunswick, Canada
| | - Robert A. Ronconi
- Atlantic Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Sackville, New Brunswick, Canada
| | - Eric Reed
- Northern Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Yellowknife, Northwest Territories, Canada
| | - Margaret Campbell
- Northern Region Wildlife and Habitat Assessment Section, Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Whitehorse, Yukon, Canada
| | - Michelle Saunders
- Department of Lands and Natural Resources, Nunatsiavut Government, Nain, Newfoundland and Labrador, Canada
| | - Catherine Soos
- Ecotoxicology and Wildlife Health Division, Science and Technology Branch, Environment and Climate Change Canada, Government of Canada, Saskatoon, Saskatchewan, Canada
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Azeem S, Baroch J, Tewari D, Pabilonia KL, Killian M, Bradel-Tretheway B, Sun D, Ghorbani-Nezami S, Yoon KJ. Molecular Characterization of Non-H5 and Non-H7 Avian Influenza Viruses from Non-Mallard Migratory Waterbirds of the North American Flyways, 2006-2011. Pathogens 2024; 13:333. [PMID: 38668288 PMCID: PMC11054893 DOI: 10.3390/pathogens13040333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
The surveillance of migratory waterbirds (MWs) for avian influenza virus (AIV) is indispensable for the early detection of a potential AIV incursion into poultry. Surveying AIV infections and virus subtypes in understudied MW species could elucidate their role in AIV ecology. Oropharyngeal-cloacal (OPC) swabs were collected from non-mallard MWs between 2006 and 2011. OPC swabs (n = 1158) that molecularly tested positive for AIV (Cts ≤ 32) but tested negative for H5 and H7 subtypes were selected for virus isolation (VI). The selected samples evenly represented birds from all four North American flyways (Pacific, Central, Mississippi, and Atlantic). Eighty-seven low pathogenic AIV isolates, representing 31 sites in 17 states, were recovered from the samples. All isolates belonged to the North American lineage. The samples representing birds from the Central Flyway had the highest VI positive rate (57.5%) compared to those from the other flyways (10.3-17.2%), suggesting that future surveillance can focus on the Central Flyway. Of the isolates, 43.7%, 12.6%, and 10.3% were obtained from blue-winged teal, American wigeon, and American black duck species, respectively. Hatch-year MWs represented the majority of the isolates (70.1%). The most common H and N combinations were H3N8 (23.0%), H4N6 (18.4%), and H4N8 (18.4%). The HA gene between non-mallard and mallard MW isolates during the same time period shared 85.5-99.5% H3 identity and 89.3-99.7% H4 identity. Comparisons between MW (mallard and non-mallard) and poultry H3 and H4 isolates also revealed high similarity (79.0-99.0% and 88.7-98.4%), emphasizing the need for continued AIV surveillance in MWs.
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Affiliation(s)
- Shahan Azeem
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; (S.A.); (D.S.)
- Institute of Microbiology, Faculty of Veterinary Science, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan
| | - John Baroch
- Wildlife Services, Animal & Plant Health Inspection Service (APHIS), United States Department of Agriculture (USDA), Fort Collins, CO 80526, USA
| | - Deepanker Tewari
- Pennsylvania Veterinary Laboratory, Pennsylvania Department of Agriculture, Harrisburg, PA 17110, USA;
| | - Kristy L. Pabilonia
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA;
| | - Mary Killian
- National Veterinary Services Laboratories, Animal & Plant Health Inspection Service (APHIS), United States Department of Agriculture (USDA), Ames, IA 50010, USA;
| | - Birgit Bradel-Tretheway
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA 99164, USA;
| | - Dong Sun
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA; (S.A.); (D.S.)
| | - Sara Ghorbani-Nezami
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
| | - Kyoung-Jin Yoon
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA 50011, USA
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Kent CM, Bevins SN, Mullinax JM, Sullivan JD, Prosser DJ. Waterfowl show spatiotemporal trends in influenza A H5 and H7 infections but limited taxonomic variation. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2906. [PMID: 37522765 DOI: 10.1002/eap.2906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/21/2023] [Indexed: 08/01/2023]
Abstract
Influenza A viruses in wild birds pose threats to the poultry industry, wild birds, and human health under certain conditions. Of particular importance are wild waterfowl, which are the primary reservoir of low-pathogenicity influenza viruses that ultimately cause high-pathogenicity outbreaks in poultry farms. Despite much work on the drivers of influenza A virus prevalence, the underlying viral subtype dynamics are still mostly unexplored. Nevertheless, understanding these dynamics, particularly for the agriculturally significant H5 and H7 subtypes, is important for mitigating the risk of outbreaks in domestic poultry farms. Here, using an expansive surveillance database, we take a large-scale look at the spatial, temporal, and taxonomic drivers in the prevalence of these two subtypes among influenza A-positive wild waterfowl. We document spatiotemporal trends that are consistent with past work, particularly an uptick in H5 viruses in late autumn and H7 viruses in spring. Interestingly, despite large species differences in temporal trends in overall influenza A virus prevalence, we document only modest differences in the relative abundance of these two subtypes and little, if any, temporal differences among species. As such, it appears that differences in species' phenology, physiology, and behaviors that influence overall susceptibility to influenza A viruses play a much lesser role in relative susceptibility to different subtypes. Instead, species are likely to freely pass viruses among each other regardless of subtype. Importantly, despite the similarities among species documented here, individual species still may play important roles in moving viruses across large geographic areas or sustaining local outbreaks through their different migratory behaviors.
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Affiliation(s)
- Cody M Kent
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
- Department of Biology, Frostburg State University, Frostburg, Maryland, USA
| | - Sarah N Bevins
- US Department of Agriculture, Wildlife Services, National Wildlife Disease Program, Fort Collins, Colorado, USA
| | - Jennifer M Mullinax
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Jeffery D Sullivan
- US Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, USA
| | - Diann J Prosser
- US Geological Survey, Eastern Ecological Science Center, Laurel, Maryland, USA
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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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Dolinski AC, Homola JJ, Jankowski MD, Robinson JD, Owen JC. Host gene expression is associated with viral shedding magnitude in blue-winged teals (Spatula discors) infected with low-path avian influenza virus. Comp Immunol Microbiol Infect Dis 2022; 90-91:101909. [PMID: 36410069 PMCID: PMC10500253 DOI: 10.1016/j.cimid.2022.101909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
Intraspecific variation in host infectiousness affects disease transmission dynamics in human, domestic animal, and many wildlife host-pathogen systems including avian influenza virus (AIV); therefore, identifying host factors related to host infectiousness is important for understanding, controlling, and preventing future outbreaks. Toward this goal, we used RNA-seq data collected from low pathogenicity avian influenza virus (LPAIV)-infected blue-winged teal (Spatula discors) to determine the association between host gene expression and intraspecific variation in cloacal viral shedding magnitude, the transmissible fraction of virus. We found that host genes were differentially expressed between LPAIV-infected and uninfected birds early in the infection, host genes were differentially expressed between shed level groups at one-, three-, and five-days post-infection, host gene expression was associated with LPAIV infection patterns over time, and genes of the innate immune system had a positive linear relationship with cloacal viral shedding. This study provides important insights into host gene expression patterns associated with intraspecific LPAIV shedding variation and can serve as a foundation for future studies focused on the identification of host factors that drive or permit the emergence of high viral shedding individuals.
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Affiliation(s)
- Amanda C Dolinski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jared J Homola
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Mark D Jankowski
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; US Environmental Protection Agency, Region 10, Seattle, WA 98101, USA
| | - John D Robinson
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA
| | - Jennifer C Owen
- Michigan State University, Department of Fisheries and Wildlife, 480 Wilson Rd., Room 13, East Lansing, MI 48824, USA; Michigan State University, Department of Large Animal Clinical Sciences, 736 Wilson Road, East Lansing, MI 48824, USA.
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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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Ahmad S, Koh KY, Yoo DS, Lee JI. Impact of inland waters on highly pathogenic avian influenza outbreaks in neighboring poultry farms in South Korea. J Vet Sci 2022; 23:e36. [PMID: 35618317 PMCID: PMC9149499 DOI: 10.4142/jvs.21278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/20/2022] Open
Abstract
Background Since 2003, the H5 highly pathogenic avian influenza (HPAI) subtype has caused massive economic losses in the poultry industry in South Korea. The role of inland water bodies in avian influenza (AI) outbreaks has not been investigated. Identifying water bodies that facilitate risk pathways leading to the incursion of the HPAI virus (HPAIV) into poultry farms is essential for implementing specific precautionary measures to prevent viral transmission. Objectives This matched case-control study (1:4) examined whether inland waters were associated with a higher risk of AI outbreaks in the neighboring poultry farms. Methods Rivers, irrigation canals, lakes, and ponds were considered inland water bodies. The cases and controls were chosen based on the matching criteria. The nearest possible farms located within a radius of 3 km of the case farms were chosen as the control farms. The poultry farms were selected randomly, and two HPAI epidemics (H5N8 [2014–2016] and H5N6 [2016–2017]) were studied. Conditional logistic regression analysis was applied. Results Statistical analysis revealed that inland waters near poultry farms were significant risk factors for AI outbreaks. The study speculated that freely wandering wild waterfowl and small animals contaminate areas surrounding poultry farms. Conclusions Pet birds and animals raised alongside poultry birds on farm premises may wander easily to nearby waters, potentially increasing the risk of AI infection in poultry farms. Mechanical transmission of the AI virus occurs when poultry farm workers or visitors come into contact with infected water bodies or their surroundings. To prevent AI outbreaks in the future, poultry farms should adopt strict precautions to avoid contact with nearby water bodies and their surroundings.
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Affiliation(s)
- Saleem Ahmad
- Veterinary Public Health Lab, College of Veterinary Medicine, Chonnam National University, Gwangju 61216, Korea
| | - Kye-Young Koh
- Veterinary Public Health Lab, College of Veterinary Medicine, Chonnam National University, Gwangju 61216, Korea
| | - Dae-Sung Yoo
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jae-Il Lee
- Veterinary Public Health Lab, College of Veterinary Medicine, Chonnam National University, Gwangju 61216, Korea
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Bianchini EA, Bogiatto RJ, Donatello RA, Casazza ML, Ackerman JT, De La Cruz SEW, Cline TD. Host Correlates of Avian Influenza Virus Infection in Wild Waterfowl of the Sacramento Valley, California. Avian Dis 2021; 66:20-28. [DOI: 10.1637/aviandiseases-d-21-00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/15/2021] [Indexed: 11/05/2022]
Affiliation(s)
| | - Raymond J. Bogiatto
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
| | - Robin A. Donatello
- Department of Mathematics and Statistics, California State University, Chico, Chico, CA 95929
| | - Michael L. Casazza
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Joshua T. Ackerman
- United States Geological Survey, Western Ecological Research Center, Dixon Field Station, Dixon, CA 95620
| | - Susan E. W. De La Cruz
- United States Geological Survey, Western Ecological Research Center, San Francisco Bay Estuary Field Station, Vallejo, CA 94592
| | - Troy D. Cline
- Department of Biological Sciences, California State University, Chico, Chico, CA 95929
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9
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Campbell LK, Fleming-Canepa X, Webster RG, Magor KE. Tissue Specific Transcriptome Changes Upon Influenza A Virus Replication in the Duck. Front Immunol 2021; 12:786205. [PMID: 34804075 PMCID: PMC8602823 DOI: 10.3389/fimmu.2021.786205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/19/2021] [Indexed: 12/13/2022] Open
Abstract
Ducks are the natural host and reservoir of influenza A virus (IAV), and as such are permissive to viral replication while being unharmed by most strains. It is not known which mechanisms of viral control are globally regulated during infection, and which are specific to tissues during infection. Here we compare transcript expression from tissues from Pekin ducks infected with a recombinant H5N1 strain A/Vietnam 1203/04 (VN1203) or an H5N2 strain A/British Columbia 500/05 using RNA-sequencing analysis and aligning reads to the NCBI assembly ZJU1.0 of the domestic duck (Anas platyrhynchos) genome. Highly pathogenic VN1203 replicated in lungs and showed systemic dissemination, while BC500, like most low pathogenic strains, replicated in the intestines. VN1203 infection induced robust differential expression of genes all three days post infection, while BC500 induced the greatest number of differentially expressed genes on day 2 post infection. While there were many genes globally upregulated in response to either VN1203 or BC500, tissue specific gene expression differences were observed. Lungs of ducks infected with VN1203 and intestines of birds infected with BC500, tissues important in influenza replication, showed highest upregulation of pattern recognition receptors and interferon stimulated genes early in the response. These tissues also appear to have specific downregulation of inflammatory components, with downregulation of distinct sets of proinflammatory cytokines in lung, and downregulation of key components of leukocyte recruitment and complement pathways in intestine. Our results suggest that global and tissue specific regulation patterns help the duck control viral replication as well as limit some inflammatory responses in tissues involved in replication to avoid damage.
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Affiliation(s)
- Lee K Campbell
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
| | | | - Robert G Webster
- Division of Virology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Katharine E Magor
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB, Canada
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10
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Abdi HM, Mayahi M, Boroomand Z, Shoshtari A. Avian Influenza-Killed Vaccine on Tissue Distribution and Shedding of Avian Influenza Virus H9N2 in Ducklings. ARCHIVES OF RAZI INSTITUTE 2021; 76:437-444. [PMID: 34824737 PMCID: PMC8605842 DOI: 10.22092/ari.2020.342078.1452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/04/2020] [Indexed: 06/13/2023]
Abstract
Ducks play an important role in the transmission of avian influenza to poultry farms. Because of the importance of vaccination in reducing virus shedding, this study evaluated avian influenza-killed vaccine H9N2 on tissue distribution and shedding of avian influenza virus H9N2 in ducklings. One hundred-day-old ducklings were purchased and, after bleeding from 20 birds, were kept in four separate rooms under standard conditions. Groups 1 and 2 were vaccinated at 9 days, and groups 2 and 3 were challenged with 0.1 ml of allantoic fluid containing 105 EID50 (A/chicken/Iran/Aid/2013(H9)) virus intranasally at 30 days. Group 4 chicks were kept as the control group. Chicks were observed two times daily. On days 1, 3, 5, and 8 after inoculation, 3 chicks were randomly selected from each group and cloaca and trachea swabs samples were collected from each bird. Then the ducklings were euthanized and trachea, lung, spleen, intestine, liver, and brain tissue samples were collected for molecular detection. The virus was detected in the tissues and tracheal and cloacal swabs by polymerase chain reaction (PCR), and anti-AIV titres were measured by HI test. The results showed no clinical signs in the challenged groups. In the vaccinated challenged group, virus was detected only in cloacal swabs, but in the unvaccinated challenged group, virus was detected more in tracheal swabs than in cloacal swabs. In challenged-unvaccinated chicks, virus was detected in the trachea and lungs, and in challenged-vaccinated birds, virus was detected in the intestines. In conclusion, vaccinating ducks against the AI H9N2 virus reduced shedding and tissue distribution of AI viruses in challenged ducks.
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Affiliation(s)
- Haji M Abdi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - M Mayahi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Z Boroomand
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - A Shoshtari
- Department of Avian Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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11
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Gorsich EE, Webb CT, Merton AA, Hoeting JA, Miller RS, Farnsworth ML, Swafford SR, DeLiberto TJ, Pedersen K, Franklin AB, McLean RG, Wilson KR, Doherty PF. Continental-scale dynamics of avian influenza in U.S. waterfowl are driven by demography, migration, and temperature. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e2245. [PMID: 33098602 PMCID: PMC7988533 DOI: 10.1002/eap.2245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/20/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
Emerging diseases of wildlife origin are increasingly spilling over into humans and domestic animals. Surveillance and risk assessments for transmission between these populations are informed by a mechanistic understanding of the pathogens in wildlife reservoirs. For avian influenza viruses (AIV), much observational and experimental work in wildlife has been conducted at local scales, yet fully understanding their spread and distribution requires assessing the mechanisms acting at both local, (e.g., intrinsic epidemic dynamics), and continental scales, (e.g., long-distance migration). Here, we combined a large, continental-scale data set on low pathogenic, Type A AIV in the United States with a novel network-based application of bird banding/recovery data to investigate the migration-based drivers of AIV and their relative importance compared to well-characterized local drivers (e.g., demography, environmental persistence). We compared among regression models reflecting hypothesized ecological processes and evaluated their ability to predict AIV in space and time using within and out-of-sample validation. We found that predictors of AIV were associated with multiple mechanisms at local and continental scales. Hypotheses characterizing local epidemic dynamics were strongly supported, with age, the age-specific aggregation of migratory birds in an area and temperature being the best predictors of infection. Hypotheses defining larger, network-based features of the migration processes, such as clustering or between-cluster mixing explained less variation but were also supported. Therefore, our results support a role for local processes in driving the continental distribution of AIV.
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Affiliation(s)
- Erin E. Gorsich
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUnited Kingdom
- The Zeeman Institute: Systems Biology and Infectious Disease Epidemiology Research (SBIDER)University of WarwickCoventryCV4 7ALUnited Kingdom
- Department of BiologyColorado State UniversityFort CollinsColorado80521USA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColorado80521USA
| | - Colleen T. Webb
- Department of BiologyColorado State UniversityFort CollinsColorado80521USA
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColorado80521USA
| | - Andrew A. Merton
- Department of StatisticsColorado State UniversityFort CollinsColorado80521USA
| | - Jennifer A. Hoeting
- Department of StatisticsColorado State UniversityFort CollinsColorado80521USA
| | - Ryan S. Miller
- Centers for Epidemiology and Animal HealthUSDA APHIS Veterinary ServicesFort CollinsColorado80526USA
| | - Matthew L. Farnsworth
- Centers for Epidemiology and Animal HealthUSDA APHIS Veterinary ServicesFort CollinsColorado80526USA
| | - Seth R. Swafford
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
- National Wildlife Refuge SystemUS Fish and Wildlife ServiceYazoo CityMississippi39194USA
| | - Thomas J. DeLiberto
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Kerri Pedersen
- National Wildlife Disease ProgramUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
- USDA APHIS Wildlife ServicesRaleighNorth Carolina27606USA
| | - Alan B. Franklin
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Robert G. McLean
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColorado80521USA
| | - Kenneth R. Wilson
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado80521USA
| | - Paul F. Doherty
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColorado80521USA
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12
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Mateus-Anzola J, Gaytan-Cruz L, Montoya-Carrillo C, Ivan Sánchez-Betancourt J, Zarza H, Segura-Velázquez R, Ojeda-Flores R. Molecular identification and phylogenetic characterization of influenza A virus at a wildlife-livestock interface in Mexico. Transbound Emerg Dis 2020; 68:3563-3573. [PMID: 33350099 DOI: 10.1111/tbed.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 12/22/2022]
Abstract
Influenza A virus (IAV) outbreaks constitute a constant threat to public health and pose a remarkable impact on socio-economic systems worldwide. Interactions between wild and domestic birds, humans and swine can lead to spillover events. Backyard livestock systems in proximity to wetlands represent high-risk areas for viral spread. However, some gaps remain in our knowledge of IAV transmission at the wildlife-livestock interface in Mexico. Hence, the study aimed at molecular identification and phylogenetic characterization of IAV in the wild duck-backyard livestock interface at a wetland of Mexico. A total of 875 animals were tested by real-time RT-PCR (qRT-PCR). We detected IAV in 3.68% of the wild ducks sampled during the winter season 2016-2017. Nonetheless, the samples obtained from backyard poultry and swine tested negative. The highest IAV frequency (11.10%) was found in the Mexican duck (Anas diazi). Subtypes H1N1, H3N2 and H5N2 were detected. Phylogenetic analyses revealed that IAV detected in wild birds from the Lerma wetlands was mostly related to swine and poultry IAV strains previously isolated in the United States and Mexico. Except, the UIFMVZ377/H5N2 related to North American waterbirds. In conclusion, the co-circulation of three IAV subtypes in wild ducks close to backyard farms in Mexico, as well as the local identification of influenza viruses genetically related to Mexican and North American IAV strains, highlights the importance of the Lerma marshes for influenza surveillance given the close interaction among wild birds, poultry, pigs and humans.
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Affiliation(s)
- Jessica Mateus-Anzola
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Liliana Gaytan-Cruz
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Cecilia Montoya-Carrillo
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Ivan Sánchez-Betancourt
- Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Heliot Zarza
- Departamento de Ciencias Ambientales, CBS, Universidad Autónoma Metropolitana Unidad Lerma, México, México
| | - René Segura-Velázquez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Unidad de Investigación, Ciudad de México, México
| | - Rafael Ojeda-Flores
- Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, México
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13
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Dolinski AC, Jankowski MD, Fair JM, Owen JC. The association between SAα2,3Gal occurrence frequency and avian influenza viral load in mallards (Anas platyrhynchos) and blue-winged teals (Spatula discors). BMC Vet Res 2020; 16:430. [PMID: 33167978 PMCID: PMC7653716 DOI: 10.1186/s12917-020-02642-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 10/26/2020] [Indexed: 12/05/2022] Open
Abstract
Background Individual heterogeneity in pathogen load can affect disease transmission dynamics; therefore, identifying intrinsic factors responsible for variation in pathogen load is necessary for determining which individuals are prone to be most infectious. Because low pathogenic avian influenza viruses (LPAIV) preferentially bind to alpha-2,3 sialic acid receptors (SAα2,3Gal) in the intestines and bursa of Fabricius in wild ducks (Anas and Spatula spp.), we investigated juvenile mallards (Anas platyrhyncos) and blue-winged teals (Anas discors) orally inoculated with A/northern pintail/California/44221–761/2006 (H5N9) and the virus titer relationship to occurrence frequency of SAα2,3Gal in the intestines and bursa. To test the natural variation of free-ranging duck populations, birds were hatched and raised in captivity from eggs collected from nests of free-ranging birds in North Dakota, USA. Data generated from qPCR were used to quantify virus titers in cloacal swabs, ileum tissue, and bursa of Fabricius tissue, and lectin histochemistry was used to quantify the occurrence frequency of SAα2,3Gal. Linear mixed models were used to analyze infection status, species, and sex-based differences. Multiple linear regression was used to analyze the relationship between virus titer and SAα2,3Gal occurrence frequency. Results In mallards, we found high individual variation in virus titers significantly related to high variation of SAα2,3Gal in the ileum. In contrast to mallards, individual variation in teals was minimal and significant relationships between virus titers and SAα2,3Gal were not determined. Collectively, teals had both higher virus titers and a higher occurrence frequency of SAα2,3Gal compared to mallards, which may indicate a positive association between viral load and SAα2,3Gal. Statistically significant differences were observed between infected and control birds indicating that LPAIV infection may influence the occurrence frequency of SAα2,3Gal, or vice versa, but only in specific tissues. Conclusions The results of this study provide quantitative evidence that SAα2,3Gal abundance is related to LPAIV titers; thus, SAα2,3Gal should be considered a potential intrinsic factor influencing variation in LPAIV load. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02642-7.
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Affiliation(s)
- Amanda C Dolinski
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
| | - Mark D Jankowski
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.,U.S. Environmental Protection Agency, Seattle, WA, USA
| | - Jeanne M Fair
- Los Alamos National Laboratory, Biosecurity & Public Health, Los Alamos, NM, USA
| | - Jennifer C Owen
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.,Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
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14
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Ruiz S, Jimenez-Bluhm P, Di Pillo F, Baumberger C, Galdames P, Marambio V, Salazar C, Mattar C, Sanhueza J, Schultz-Cherry S, Hamilton-West C. Temporal dynamics and the influence of environmental variables on the prevalence of avian influenza virus in main wetlands in central Chile. Transbound Emerg Dis 2020; 68:1601-1614. [PMID: 32931631 DOI: 10.1111/tbed.13831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/04/2020] [Accepted: 09/06/2020] [Indexed: 11/28/2022]
Abstract
Although wild birds are considered the main reservoir of the influenza A virus (IAV) in nature, empirical investigations exploring the interaction between the IAV prevalence in these populations and environmental drivers remain scarce. Chile has a coastline of more than 4000 kilometres with hundreds of wetlands, which are important habitats for both resident and inter-hemispheric migratory species. The aim of this study was to characterize the temporal dynamics of IAV in main wetlands in central Chile and to assess the influence of environmental variables on AIV prevalence. For that purpose, four wetlands were studied from September 2015 to June 2018. Fresh faecal samples of wild birds were collected for IAV detection by real-time RT-PCR. Furthermore, a count of wild birds present at the site was performed and environmental variables, such as temperature, rainfall, vegetation coverage (Normalized Difference Vegetation Index (NDVI)) and water body size, were determined. A generalized linear mixed model was built to assess the association between IAV prevalence and explanatory variables. An overall prevalence of 4.28% ± 0.28% was detected with important fluctuations among seasons, being greater during summer (OR = 4.87, 95% CI 2.11 to 11.21) and fall (OR = 2.59, 95% CI 1.12 to 5.97). Prevalence was positively associated with minimum temperature for the month of sampling and negatively associated with water body size measured two months before sampling, and NDVI measured three months before sampling. These results contribute to the understanding of IAV ecological drivers in Chilean wetlands providing important considerations for the global surveillance of IAV.
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Affiliation(s)
- Soledad Ruiz
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile.,Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santiago, Chile.,Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Pedro Jimenez-Bluhm
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
| | - Francisca Di Pillo
- Núcleo de Investigaciones Aplicadas en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Santiago, Chile
| | - Cecilia Baumberger
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
| | - Pablo Galdames
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
| | - Victor Marambio
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
| | - Carla Salazar
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
| | - Cristian Mattar
- Laboratory for Analysis of the Biosphere (LAB), University of Chile, Santiago, Chile
| | - Juan Sanhueza
- Departamento de Ciencias Veterinarias y Salud Pública, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher Hamilton-West
- Department of Preventive Veterinary Medicine, Faculty of Veterinary Science, Universidad de Chile, Santiago, Chile
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15
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Humphreys JM, Ramey AM, Douglas DC, Mullinax JM, Soos C, Link P, Walther P, Prosser DJ. Waterfowl occurrence and residence time as indicators of H5 and H7 avian influenza in North American Poultry. Sci Rep 2020; 10:2592. [PMID: 32054908 PMCID: PMC7018751 DOI: 10.1038/s41598-020-59077-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/15/2020] [Indexed: 01/25/2023] Open
Abstract
Avian influenza (AI) affects wild aquatic birds and poses hazards to human health, food security, and wildlife conservation globally. Accordingly, there is a recognized need for new methods and tools to help quantify the dynamic interaction between wild bird hosts and commercial poultry. Using satellite-marked waterfowl, we applied Bayesian joint hierarchical modeling to concurrently model species distributions, residency times, migration timing, and disease occurrence probability under an integrated animal movement and disease distribution modeling framework. Our results indicate that migratory waterfowl are positively related to AI occurrence over North America such that as waterfowl occurrence probability or residence time increase at a given location, so too does the chance of a commercial poultry AI outbreak. Analyses also suggest that AI occurrence probability is greatest during our observed waterfowl northward migration, and less during the southward migration. Methodologically, we found that when modeling disparate facets of disease systems at the wildlife-agriculture interface, it is essential that multiscale spatial patterns be addressed to avoid mistakenly inferring a disease process or disease-environment relationship from a pattern evaluated at the improper spatial scale. The study offers important insights into migratory waterfowl ecology and AI disease dynamics that aid in better preparing for future outbreaks.
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Affiliation(s)
- John M Humphreys
- Michigan State University, East Lansing, Michigan, USA.
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, Maryland, USA.
| | - Andrew M Ramey
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | - David C Douglas
- U.S. Geological Survey, Alaska Science Center, Anchorage, Alaska, USA
| | | | - Catherine Soos
- Environment and Climate Change Canada, Ecotoxicology and Wildlife Health Division, Saskatchewan, Canada
| | - Paul Link
- Louisiana Department of Wildlife and Fisheries, Baton Rouge, Louisiana, USA
| | - Patrick Walther
- U.S. Fish and Wildlife Service, Texas Chenier Plain Refuge Complex, Anahuac, Texas, USA
| | - Diann J Prosser
- U.S. Geological Survey, Patuxent Wildlife Research Center, Laurel, Maryland, USA
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16
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Humphreys JM, Murrow JL, Sullivan JD, Prosser DJ. Seasonal occurrence and abundance of dabbling ducks across the continental United States: Joint spatio‐temporal modelling for the Genus
Anas. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12960] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- John M. Humphreys
- Michigan State University East Lansing Michigan USA
- U.S. Geological Survey, Patuxent Wildlife Research Center Laurel Maryland USA
| | | | | | - Diann J. Prosser
- U.S. Geological Survey, Patuxent Wildlife Research Center Laurel Maryland USA
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17
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Torrontegi O, Alvarez V, Acevedo P, Gerrikagoitia X, Höfle U, Barral M. Long-term avian influenza virus epidemiology in a small Spanish wetland ecosystem is driven by the breeding Anseriformes community. Vet Res 2019; 50:4. [PMID: 30654831 PMCID: PMC6337815 DOI: 10.1186/s13567-019-0623-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/20/2018] [Indexed: 11/12/2022] Open
Abstract
During 2007-2009 and 2012-2014, avian influenza virus (AIV) was studied in a wild avian community of a northern Spanish wetland using non-invasive sampling methods and host identification by COI barcoding. The aim of this longitudinal study was to evaluate AIV dynamics in a natural wetland ecosystem, taking into account both virological aspects and ecological traits of hosts. Global AIV prevalence decreased significantly during the second sampling period (0.3%) compared to the first (6.6%). Circulating subtype distributions were also different between periods, with a noteworthy H5 and H7 subtype richness during the first sampling period. Mallard Anas platyrhynchos was identified as the main AIV host, although not all positive samples could be ascribed to the host. We modelled AIV prevalence with regard to the avian host community composition and meteorological data from the wetland. Statistical analysis revealed seasonal differences in AIV detection, with higher prevalence during the breeding season compared to other phenological events. The model also shows that the lower AIV prevalence during the second study period was associated with a significant reduction of breeding Anseriformes in the wetland, revealing a long-term fluctuation of AIV prevalence driven by the breeding Anseriformes community. This longitudinal study on AIV epidemiology in a natural ecosystem reveals that although prevalence follows seasonal and annual patterns, long-term prevalence fluctuation is linked to the breeding community composition and size. These results are relevant to understanding the influence of host ecology on pathogen transmission for preventing and managing influenza emergence.
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Affiliation(s)
- Olalla Torrontegi
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Vega Alvarez
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Pelayo Acevedo
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Xeider Gerrikagoitia
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
| | - Ursula Höfle
- Grupo SaBio, Instituto de Investigación en Recursos Cinegéticos, IREC (CSIC-UCLM-JCCM), Ronda de Toledo 12, 13071 Ciudad Real, Spain
| | - Marta Barral
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Parque tecnológico de Bizkaia P-812, 48160 Derio, Bizkaia Spain
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18
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Pagano G, Johnson C, Hahn DC, Arsenault RJ. A new tool for studying waterfowl immune and metabolic responses: Molecular level analysis using kinome profiling. Ecol Evol 2018; 8:8537-8546. [PMID: 30250721 PMCID: PMC6144969 DOI: 10.1002/ece3.4370] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/16/2018] [Accepted: 06/15/2018] [Indexed: 01/03/2023] Open
Abstract
Here, we describe the design of an Anas-specific kinome peptide array that can be used to study the immunometabolic responses of mallard and American black duck to pathogens, contaminants, and environmental stress. The peptide arrays contain 2,642 unique phosphorylate-able peptide sequences representing 1,900 proteins. These proteins cover a wide array of metabolic and immunological processes, and 758 Gene Ontology Biological processes are statistically significantly represented on the duck peptide array of those 164 contain the term "metabolic" and 25 "immune." In addition, we conducted a comparison of mallard to American black duck at a genetic and proteomic level. Our results show a significant genomic and proteomic overlap between these two duck species, so that we have designed a cross-reactive peptide array capable of studying both species. This is the first reported development of a wildlife species-specific kinome peptide array.
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Affiliation(s)
- Giovanni Pagano
- Center for Bioinformatics and Computational BiologyUniversity of DelawareNewarkDelaware
| | - Casey Johnson
- Department of Animal and Food SciencesUniversity of DelawareNewarkDelaware
| | | | - Ryan J. Arsenault
- Department of Animal and Food SciencesUniversity of DelawareNewarkDelaware
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Zenouzi R, Liwinski T, Yamamura J, Weiler-Normann C, Sebode M, Keller S, Lohse AW, Schramm C. Follow-up magnetic resonance imaging/3D-magnetic resonance cholangiopancreatography in patients with primary sclerosing cholangitis: challenging for experts to interpret. Aliment Pharmacol Ther 2018; 48:169-178. [PMID: 29741240 DOI: 10.1111/apt.14797] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 02/19/2018] [Accepted: 04/18/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND In patients with primary sclerosing cholangitis follow-up magnetic resonance imaging (MRI) with magnetic resonance cholangiopancreatography (MRCP) is performed by many centres, particularly for the early detection of biliary malignancies and strictures. Clinically meaningful MRI-based definitions of primary sclerosing cholangitis related complications are, however, lacking. AIM To investigate how primary sclerosing cholangitis experts interpret follow-up MRI/MRCP with a focus on conclusions that may impact clinical decision-making in primary sclerosing cholangitis. METHODS Within the International Primary Sclerosing Cholangitis Study Group, an online survey on 16 real-life primary sclerosing cholangitis cases including clinical and biochemical information as well as a T2-weighted liver MRI/3D-MRCP was conducted. The interpretation of images and subsequent recommendations were assessed using a multiple-choice questionnaire. An inter-rater reliability calculation (Fleiss' kappa) was performed and factors potentially affecting the interpretation of magnetic resonance images were analysed using generalised linear mixed-effect models. RESULTS Forty-four members/associates of the International Primary Sclerosing Cholangitis Study Group (median experience in the care of primary sclerosing cholangitis patients: 14 years) completed the survey. The MRI interpretation significantly varied among the participants. The lowest agreement was found with respect to the indication to perform subsequent endoscopic retrograde cholangiopancreatography (ERCP; Κ = 0.12, 95%CI 0.11-0.14). Elevated total bilirubin was the variable with the strongest effect on the rate of suspected dominant strictures, cholangiocarcinoma or ERCP recommendations. Liver cirrhosis did not prevent participants from recommending ERCP. Overall, the survey participants' recommendations contrasted the real-life management and outcome. CONCLUSIONS In primary sclerosing cholangitis, the interpretation of follow-up MRI/3D-MRCP significantly varies even among experts and seems to be primarily affected by bilirubin levels. Generally accepted MRI-based definitions of primary sclerosing cholangitis-related complications are urgently needed.
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Affiliation(s)
- R Zenouzi
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - T Liwinski
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - J Yamamura
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - C Weiler-Normann
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - M Sebode
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - S Keller
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - A W Lohse
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - C Schramm
- 1st Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
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Galletti G, Santi A, Guberti V, Paternoster G, Licata E, Loli Piccolomini L, Procopio A, Tamba M. A method to identify the areas at risk for the introduction of avian influenza virus into poultry flocks through direct contact with wild ducks. Transbound Emerg Dis 2018; 65:1033-1038. [PMID: 29473322 DOI: 10.1111/tbed.12838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 11/30/2022]
Abstract
Wild dabbling ducks are the main reservoir for avian influenza (AI) viruses and pose an ongoing threat to commercial poultry flocks. Combining the (i) size of that population, (ii) their flight distances and (iii) their AI prevalence, the density of AI-infected dabbling ducks (DID) was calculated as a risk factor for the introduction of AI viruses into poultry holdings of Emilia-Romagna region, Northern Italy. Data on 747 poultry holdings and on 39 AI primary outbreaks notified in Emilia-Romagna between 2000 and 2017 were used to validate that risk factor. A multivariable Bayesian logistic regression was performed to assess whether DID could be associated with the occurrence of AI primary outbreaks. DID value, being an outdoor flock, hobby poultry trading, species reared, length of cycle and flock size were used as explanatory variables. Being an outdoor poultry flock was significantly associated with a higher risk of AI outbreak occurrence. The probability of DID to be a risk factor for AI virus introduction was estimated to be 90%. A DID cut-off of 0.23 was identified to define high-risk areas for AI virus introduction. Using this value, the high-risk area covers 43% of the region. Seventy-four per cent of the primary AI outbreaks have occurred in that area, containing 39% of the regional poultry holdings. Poultry holdings located in areas with a high DID value should be included in a risk-based surveillance programme aimed at AI early detection.
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Affiliation(s)
- G Galletti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Brescia, Italy
| | - A Santi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Brescia, Italy
| | - V Guberti
- Institute for Environmental Protection and Research, Ozzano nell'Emilia, Italy
| | - G Paternoster
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Brescia, Italy
| | - E Licata
- Local Health Unit of Modena Province - Public Health Department, Modena, Italy
| | - L Loli Piccolomini
- Regione Emilia-Romagna, Service of Collective Prevention and Public Health, Bologna, Italy
| | - A Procopio
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Brescia, Italy
| | - M Tamba
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna "Bruno Ubertini", Brescia, Italy
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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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