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Lee LKF, Hipfner JM, Frankfurter G, Cray C, Pearson SF, Fiorello C, Clyde NMT, Hudson SA, Parker SE, Stallknecht DE, Furst E, Haman KH. Baseline health parameters of rhinoceros auklets ( Cerorhinca monocerata) using serum protein electrophoresis, acute phase proteins, and biochemistry. Front Vet Sci 2024; 11:1379980. [PMID: 38983768 PMCID: PMC11231077 DOI: 10.3389/fvets.2024.1379980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/20/2024] [Indexed: 07/11/2024] Open
Abstract
Clinical metrics of baseline health in sentinel seabird species can offer insight into marine ecosystem dynamics, individual and population health, and assist in wildlife rehabilitation and conservation efforts. Protein electrophoresis is useful for detecting changes in acute phase proteins and immunoglobulin levels that may indicate subtle inflammatory responses and/or infectious disease. Serum biochemistry can highlight nutritional status, metabolic derangements, and organ injury and function. However, baseline values for such health parameters are largely unknown for many seabird species. Therefore, the objective of this study is to establish baseline clinical health reference intervals for serum protein electrophoresis, acute phase proteins including serum amyloid A and haptoglobin, and biochemistry parameters in the rhinoceros auklet (Cerorhinca monocerata), a key sentinel species in the North Pacific. From 2013 to 2019, 178 wild, apparently healthy breeding adult rhinoceros auklets were captured across four breeding colonies in British Columbia, Canada (Lucy Island, Pine Island, Triangle Islands, and SGang Gwaay) and from one colony in Washington, United States (Protection Island). Reference intervals were calculated for protein electrophoresis fractions and acute phase proteins (n = 163), and serum biochemistry (n = 35) following established guidelines by the American Society of Veterinary Clinical Pathology. Animals were also assessed for the presence of antibodies to the influenza A virus. Approximately 48% (70/147) of sampled birds were seropositive for influenza A virus, with a prevalence of 50% (6/12) in 2013, 75% (47/63) in 2014, and 24% (17/72) in 2019. This work provides clinical baseline health metrics of a key North Pacific sentinel species to help inform marine ecosystem monitoring, recovery, and rehabilitation efforts in the Pacific Northwest.
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Affiliation(s)
- Lisa K F Lee
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - J Mark Hipfner
- Wildlife Research Division, Environment and Climate Change Canada, Delta, BC, Canada
| | - Greg Frankfurter
- School of Veterinary Medicine, Karen C. Drayer Wildlife Health Center, Davis, CA, United States
| | - Carolyn Cray
- Division of Comparative Pathology, Department of Pathology and Laboratory Medicine, Miller School of Medicine, Miami, FL, United States
| | - Scott F Pearson
- Wildlife Program, Science Division, Washington Department of Fish and Wildlife, Olympia, WA, United States
| | | | - Nikolas M T Clyde
- Wildlife Research Division, Environment and Climate Change Canada, Delta, BC, Canada
| | - Sarah A Hudson
- Wildlife Research Division, Environment and Climate Change Canada, Delta, BC, Canada
| | - Sarah E Parker
- Centre for Applied Epidemiology, Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - David E Stallknecht
- Department of Population Health, Southeastern Cooperative Wildlife Disease Study, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | | | - Katherine H Haman
- Wildlife Program, Science Division, Washington Department of Fish and Wildlife, Olympia, WA, United States
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2
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024:gkae528. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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3
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Miki M, Obara RD, Nishimura K, Shishido T, Ikenaka Y, Oka R, Sato K, Nakayama SMM, Kimura T, Kobayashi A, Aoshima K, Saito K, Hiono T, Isoda N, Sakoda Y. FOUR-WEEK ORAL ADMINISTRATION OF BALOXAVIR MARBOXIL AS AN ANTI-INFLUENZA VIRUS DRUG SHOWS NO TOXICITY IN CHICKENS. J Zoo Wildl Med 2024; 55:313-321. [PMID: 38875188 DOI: 10.1638/2023-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2024] [Indexed: 06/16/2024] Open
Abstract
High pathogenicity avian influenza is an acute zoonotic disease with high mortality in birds caused by a high pathogenicity avian influenza virus (HPAIV). Recently, HPAIV has rapidly spread worldwide and has killed many wild birds, including endangered species. Baloxavir marboxil (BXM), an anti-influenza agent used for humans, was reported to reduce mortality and virus secretion from HPAIV-infected chickens (Gallus domesticus, order Galliformes) at a dosage of ≥2.5 mg/kg when administered simultaneously with viral challenge. Application of this treatment to endangered birds requires further information on potential avian-specific toxicity caused by repeated exposure to BXM over the long term. To obtain information of potential avian-specific toxicity, a 4-wk oral repeated-dose study of BXM was conducted in chickens (n = 6 or 7 per group), which are commonly used as laboratory avian species. The study was conducted in reference to the human pharmaceutical guidelines for nonclinical repeated-dose drug toxicity studies to evaluate systemic toxicity and exposure. No adverse changes were observed in any organs examined, and dose proportional increases in systemic exposure to active pharmaceutical ingredients were noted from 12.5 to 62.5 mg/kg per day. BXM showed no toxicity to chickens at doses of up to 62.5 mg/kg per day, at which systemic exposure was approximately 71 times higher than systemic exposure at 2.5 mg/kg, the reported efficacious dosage amount, in HPAIV-infected chickens. These results also suggest that BXM could be considered safe for treating HPAIV-infected endangered birds due to its high safety margin compared with the efficacy dose. The data in this study could contribute to the preservation of endangered birds by using BXM as a means of protecting biodiversity.
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Affiliation(s)
- Mariko Miki
- Shionogi & Co, Ltd, Toyonaka 561-0825, Japan,
| | | | | | | | - Yoshinori Ikenaka
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2531, South Africa
| | - Ryoko Oka
- Shionogi & Co, Ltd, Toyonaka 561-0825, Japan
| | - Kenji Sato
- Shionogi & Co, Ltd, Toyonaka 561-0825, Japan
| | - Shouta M M Nakayama
- Laboratory of Toxicology, Department of Environmental Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- Biomedical Sciences Department, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Kimura
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
| | - Atsushi Kobayashi
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
| | - Keisuke Aoshima
- Laboratory of Comparative Pathology, Department of Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
| | - Keisuke Saito
- Institute for Raptor Biomedicine Japan, Kushiro 084-0922, Japan
| | - Takahiro Hiono
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo 001-0020, Japan
| | - Norikazu Isoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo 001-0020, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-ku, Sapporo 060-0818, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Kita-Ku, Sapporo 001-0020, Japan
- Hokkaido University Institute for Vaccine Research and Development, Hokkaido University, Kita-ku, Sapporo 001-0021, Japan
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4
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Lean FZX, Falchieri M, Furman N, Tyler G, Robinson C, Holmes P, Reid SM, Banyard AC, Brown IH, Man C, Núñez A. Highly pathogenic avian influenza virus H5N1 infection in skua and gulls in the United Kingdom, 2022. Vet Pathol 2024; 61:421-431. [PMID: 38140946 DOI: 10.1177/03009858231217224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The reemergence of the highly pathogenic avian influenza virus (HPAIV) subtype H5N1 in the United Kingdom in 2021-2022 has caused unprecedented epizootic events in wild birds and poultry. During the summer of 2022, there was a shift in virus transmission dynamics resulting in increased HPAIV infection in seabirds, and consequently, a profound impact on seabird populations. To understand the pathological impact of HPAIV in seabirds, we evaluated the virus antigen distribution and associated pathological changes in the tissues of great skua (Stercorarius skua, n = 8), long-tailed skua (Stercorarius longicaudus, n = 1), European herring gull (Larus argentatus, n = 5), and black-headed gull (Chroicocephalus ridibundus, n = 4), which succumbed to natural infection of HPAIV during the summer of 2022. Cases were collected from Shetland, including Scatness (mainland), No Ness (mainland), Clumlie (mainland), Hermaness (island), Fair Isle (island), Noss (island), and the West Midlands, South East, and South West of England. Grossly, gizzard ulceration was observed in one great skua and pancreatic necrosis was observed in 4 herring gulls, with intralesional viral antigen detected subsequently. Microscopical analysis revealed neuro-, pneumo-, lymphoid-, and cardiomyotropism of HPAIV H5N1, with the most common virus-associated pathological changes being pancreatic and splenic necrosis. Examination of the reproductive tract of the great skua revealed HPAIV-associated oophoritis and salpingitis, and virus replication within the oviductal epithelium. The emergence of HPAIV in seabirds Stercorariidae and Laridae, particularly during summer 2022, has challenged the dogma of HPAIV dynamics, posing a significant threat to wild bird life with potential implications for the reproductive performance of seabirds of conservation importance.
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Affiliation(s)
- Fabian Z X Lean
- Animal and Plant Health Agency, Weybridge, UK
- Royal Veterinary College, Hertfordshire, UK
| | | | | | | | | | - Paul Holmes
- APHA Shrewsbury Veterinary Investigation Centre, UK
| | | | | | - Ian H Brown
- Animal and Plant Health Agency, Weybridge, UK
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5
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Feoktistova S, Sayganova M, Trutneva K, Glazova O, Blagodatski AS, Shevkova L, Navoikova A, Anisimov Y, Albert E, Mityaeva O, Volchkov P, Deviatkin A. Abundant Intra-Subtype Reassortment Revealed in H13N8 Influenza Viruses. Viruses 2024; 16:568. [PMID: 38675910 PMCID: PMC11054967 DOI: 10.3390/v16040568] [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: 03/04/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Influenza A viruses (IAVs) pose a serious threat to global health. On the one hand, these viruses cause seasonal flu outbreaks in humans. On the other hand, they are a zoonotic infection that has the potential to cause a pandemic. The most important natural reservoir of IAVs are waterfowl. In this study, we investigated the occurrence of IAV in birds in the Republic of Buryatia (region in Russia). In 2020, a total of 3018 fecal samples were collected from wild migratory birds near Lake Baikal. Of these samples, 11 were found to be positive for the H13N8 subtype and whole-genome sequencing was performed on them. All samples contained the same virus with the designation A/Unknown/Buryatia/Arangatui-1/2020. To our knowledge, virus A/Unknown/Buryatia/Arangatui-1/2020 is the first representative of the H13N8 subtype collected on the territory of Russia, the sequence of which is available in the GenBank database. An analysis of reassortments based on the genome sequences of other known viruses has shown that A/Unknown/Buryatia/Arangatui-1/2020 arose as a result of reassortment. In addition, a reassortment most likely occurred several decades ago between the ancestors of the viruses recently collected in China, the Netherlands, the United States and Chile. The presence of such reassortment emphasizes the ongoing evolution of the H13N8 viruses distributed in Europe, North and East Asia, North and South America and Australia. This study underscores the importance of the continued surveillance and research of less-studied influenza subtypes.
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Affiliation(s)
- Sofia Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Marya Sayganova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Kseniya Trutneva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Glazova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Artem S. Blagodatski
- Federal State Budget Institution of Science Institute of Theoretical and Experimental Biophysics, 142290 Pushchino, Russia;
| | - Liudmila Shevkova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Anna Navoikova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Yuriy Anisimov
- Baikalsky State Nature Biosphere Reserve, 671220 Tankhoi, Russia;
| | - Eugene Albert
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
| | - Olga Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Pavel Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Department of Fundamental Medicine, Lomonosov Moscow State University, 119992 Moscow, Russia
- The Moscow Clinical Scientific Center (MCSC) Named after A.S. Loginov, 111123 Moscow, Russia
| | - Andrey Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, 125315 Moscow, Russia; (M.S.); (K.T.); (O.G.); (L.S.); (A.N.); (E.A.); (O.M.); (P.V.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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Shi J, Meng L, Xia S, Liu S, Zhou L. Habitat Suitability and Determinants for Anatidae in Multi-Watershed Composite Wetlands in Anhui, China. Animals (Basel) 2024; 14:1010. [PMID: 38612249 PMCID: PMC11010902 DOI: 10.3390/ani14071010] [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: 01/27/2024] [Revised: 03/13/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Habitat suitability analysis is essential in habitat and species conservation. Anatidae are known for their migratory behaviour, high population density, and wide distribution range. Understanding their habitat utilzation and influencing factors is crucial in targeted conservation and management. In this study, we collected Anatidae diversity data, including the number of species, through field surveys from October 2021 to March 2022 and thirty habitat variables through an online database in Anhui Province, China. By using MaxEnt, we simulated the habitat suitability of twenty-one Anatidae species, revealing potential distribution sites in Anhui Province. Generalized linear mixed models (GLMM) were employed to identify factors affecting the distribution of geese and ducks. The results showed that high-suitability habitats were predominantly located in the large lakes of the Yangtze River floodplain. The GLMM analysis showed significant correlations between Anatidae richness and altitude, distribution of farmland, and human footprint. In addition, ducks were more sensitive to the human interference factor than geese. In summary, the lakes in the Yangtze River floodplain emerged as the most important Anatidae habitats in Anhui Province due to their abundant wetland resources, flat terrain, and high distribution of farmlands. These findings provide a scientific basis for the development of relevant conservation strategies and measures, aiding in wildlife epidemic monitoring, prevention, and control.
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Affiliation(s)
- Jiye Shi
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.S.); (L.M.); (S.X.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi 247230, China
| | - Lei Meng
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.S.); (L.M.); (S.X.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi 247230, China
| | - Shanshan Xia
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.S.); (L.M.); (S.X.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi 247230, China
| | - Song Liu
- Anhui General Station of Wildlife Monitoring of Epidemic Sources and Disease, Hefei 230088, China;
| | - Lizhi Zhou
- School of Resources and Environmental Engineering, Anhui University, Hefei 230601, China; (J.S.); (L.M.); (S.X.)
- Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei 230601, China
- Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi 247230, China
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7
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583560. [PMID: 38559265 PMCID: PMC10979853 DOI: 10.1101/2024.03.08.583560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L. Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Gene S. Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Karen G. Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L. Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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8
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Li Y, An Q, Sun Z, Gao X, Wang H. Multifaceted analysis of temporal and spatial distribution and risk factors of global poultry HPAI-H5N1, 2005-2023. Animal 2024; 18:101085. [PMID: 38364655 DOI: 10.1016/j.animal.2024.101085] [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: 10/22/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/18/2024] Open
Abstract
The purpose of this study was to analyze the characteristics of occurrence and spread of highly pathogenic avian influenza H5N1 (HPAI-H5N1) globally, understand its spatiotemporal characteristics, investigate the risk factors influencing outbreaks, and identify high-risk areas for disease occurrence. We collected the data on global poultry HPAI-H5N1 outbreaks from January 2005 to April 2023, and conducted a thorough analysis of the spatial and temporal characteristics of the disease through time series decomposition and directional distribution analysis. Additionally, an ecological niche model was established to explore the major factors influencing the occurrence of HPAI-H5N1 and to pinpoint high-risk areas. Our findings revealed that HPAI-H5N1 outbreaks were cyclical, and seasonal, exhibiting a rising trend, with a predominant northwest-southeast transmission direction. The ecological niche model highlighted that species factors and economic trade factors are critical in influencing the outbreak of HPAI-H5N1. Variables such as chicken and duck density, population density, isothermality, and road density, contributed to importantly risk of outbreaks. High-risk areas for HPAI-H5N1 occurrence were primarily identified in Europe, West Africa, Southeast Asia, and Southeast China. This study provided valuable insights into the spatial and temporal distribution characteristics and risk factors of global poultry HPAI-H5N1 outbreaks. The identification of high-risk areas provides essential information that can be used to develop more effective prevention and control policies.
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Affiliation(s)
- Yuepeng Li
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Qi An
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Zhuo Sun
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Xiang Gao
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China
| | - Hongbin Wang
- Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment, College of Veterinary Medicine, Northeast Agricultural University, Harbin, People's Republic of China.
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Poudel A, Sharma S, Dhital K, Bhandari S, Rajbhandari PG, Napit R, Puri D, Karmacharya DB. Antimicrobial stewardship hindered by inadequate biosecurity and biosafety practices, and inappropriate antibiotics usage in poultry farms of Nepal-A pilot study. PLoS One 2024; 19:e0296911. [PMID: 38427679 PMCID: PMC10906820 DOI: 10.1371/journal.pone.0296911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 12/19/2023] [Indexed: 03/03/2024] Open
Abstract
Nepal's poultry industry has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers. As a result, farms often suffer from sporadic and regular outbreaks of many diseases, impacting production and creating public health challenges. Poor management practices, including overuse of antibiotics for prophylaxis and therapeutics, can enhance the spread of poultry diseases by propagating antimicrobial resistance (AMR) that is threatening poultry and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts: Ramechhap, Nuwakot, Sindhupalchowk, and Kavre. Risk assessment and AMR stewardship evaluation questionnaires were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified the highest BBCM score of 67% obtained by Sindhupalchowk farm 4 and the lowest of 12% by Kavre farm 3. Most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Lowest scores were obtained for personnel safety standard (42.4%) and rodent control (3.1%). At least one of the screened pathogens were detected in all farms. Mycoplasma gallisepticum was the most common pathogen detected in all but three farms, followed by Mycoplasma synoviae. More than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as "Watch" and "Restrict" by the WHO were frequently used by the farmers to treat bacterial infections in their farms.
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Affiliation(s)
- Ajit Poudel
- One Health Division, Biovac Nepal, Nala, Nepal
- One Health Division, Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | | | - Shova Bhandari
- One Health Division, Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | | | - Rajindra Napit
- One Health Division, Biovac Nepal, Nala, Nepal
- One Health Division, Center for Molecular Dynamics Nepal, Kathmandu, Nepal
| | - Dhiraj Puri
- One Health Division, Biovac Nepal, Nala, Nepal
| | - Dibesh B. Karmacharya
- One Health Division, Biovac Nepal, Nala, Nepal
- One Health Division, Center for Molecular Dynamics Nepal, Kathmandu, Nepal
- Department of Biological Sciences, University of Queensland, Brisbane, Australia
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Lin S, Zhang Y, Yang J, Yang L, Li X, Bo H, Liu J, Tan M, Zhu W, Wang D, Shu Y. Cross-Species Transmission Potential of H4 Avian Influenza Viruses in China: Epidemiological and Evolutionary Study. Viruses 2024; 16:353. [PMID: 38543719 PMCID: PMC10974465 DOI: 10.3390/v16030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 05/23/2024] Open
Abstract
H4 avian influenza viruses (AIVs) have been widely detected in live poultry markets in China. However, the potential public health impact of H4 AIVs remains largely uncertain. Here, we fully analyzed the distribution and phylogenetic relationship of H4 AIVs in China. We obtained 31 isolates of H4 viruses in China during 2009-2022 through surveillance in poultry-associated environments, such as live poultry markets and poultry farms. Genomic sequence analysis together with publicly available data revealed that frequent reassortment and introduction of H4 AIV from wild birds to poultry may have occurred. We identified 62 genotypes among 127 whole genome sequences of H4 viruses in China, indicating that H4 AIVs had great genetic diversity in China. We also investigated molecular markers and found that drug resistance mutations frequently occurred in the M2 protein and a few mutations related to receptor binding and the host signature in H4 AIVs. Our study demonstrates the cross-species transmission potential of H4 AIVs in China and provides some reference significance for its risk assessment.
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Affiliation(s)
- Shuxia Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Ye Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jiaying Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Hong Bo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza, Key Laboratory for Medical Virology, National Health Commission, Beijing 102206, China; (Y.Z.)
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China; (S.L.)
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510006, China
- Key Laboratory of Pathogen Infection Prevention and Control (MOE), State Key Laboratory of Respiratory Health and Multimorbidity, National Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 102629, China
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11
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Kuchinski KS, Coombe M, Mansour SC, Cortez GAP, Kalhor M, Himsworth CG, Prystajecky NA. Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats. Appl Environ Microbiol 2024; 90:e0084223. [PMID: 38259077 PMCID: PMC10880596 DOI: 10.1128/aem.00842-23] [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: 05/23/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Diverse influenza A viruses (IAVs) circulate in wild birds, including highly pathogenic strains that infect poultry and humans. Consequently, surveillance of IAVs in wild birds is a cornerstone of agricultural biosecurity and pandemic preparedness. Surveillance is traditionally done by testing wild birds directly, but obtaining these specimens is labor intensive, detection rates can be low, and sampling is often biased toward certain avian species. As a result, local incursions of dangerous IAVs are rarely detected before outbreaks begin. Testing environmental specimens from wild bird habitats has been proposed as an alternative surveillance strategy. These specimens are thought to contain diverse IAVs deposited by a broad range of avian hosts, including species that are not typically sampled by surveillance programs. To enable this surveillance strategy, we developed a targeted genomic sequencing method for characterizing IAVs in these challenging environmental specimens. It combines custom hybridization probes, unique molecular index-based library construction, and purpose-built bioinformatic tools, allowing IAV genomic material to be enriched and analyzed with single-fragment resolution. We demonstrated our method on 90 sediment specimens from wetlands around Vancouver, Canada. We recovered 2,312 IAV genome fragments originating from all eight IAV genome segments. Eleven hemagglutinin subtypes and nine neuraminidase subtypes were detected, including H5, the current global surveillance priority. Our results demonstrate that targeted genomic sequencing of environmental specimens from wild bird habitats could become a valuable complement to avian influenza surveillance programs.IMPORTANCEIn this study, we developed genome sequencing tools for characterizing avian influenza viruses in sediment from wild bird habitats. These tools enable an environment-based approach to avian influenza surveillance. This could improve early detection of dangerous strains in local wild birds, allowing poultry producers to better protect their flocks and prevent human exposures to potential pandemic threats. Furthermore, we purposefully developed these methods to contend with viral genomic material that is diluted, fragmented, incomplete, and derived from multiple strains and hosts. These challenges are common to many environmental specimens, making these methods broadly applicable for genomic pathogen surveillance in diverse contexts.
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Affiliation(s)
- Kevin S. Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Coombe
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Sarah C. Mansour
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabrielle Angelo P. Cortez
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marzieh Kalhor
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea G. Himsworth
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Natalie A. Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Provincial Health Services Authority, Vancouver, British Columbia, Canada
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12
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Fair JM, Al-Hmoud N, Alrwashdeh M, Bartlow AW, Balkhamishvili S, Daraselia I, Elshoff A, Fakhouri L, Javakhishvili Z, Khoury F, Muzyka D, Ninua L, Tsao J, Urushadze L, Owen J. Transboundary determinants of avian zoonotic infectious diseases: challenges for strengthening research capacity and connecting surveillance networks. Front Microbiol 2024; 15:1341842. [PMID: 38435695 PMCID: PMC10907996 DOI: 10.3389/fmicb.2024.1341842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
As the climate changes, global systems have become increasingly unstable and unpredictable. This is particularly true for many disease systems, including subtypes of highly pathogenic avian influenzas (HPAIs) that are circulating the world. Ecological patterns once thought stable are changing, bringing new populations and organisms into contact with one another. Wild birds continue to be hosts and reservoirs for numerous zoonotic pathogens, and strains of HPAI and other pathogens have been introduced into new regions via migrating birds and transboundary trade of wild birds. With these expanding environmental changes, it is even more crucial that regions or counties that previously did not have surveillance programs develop the appropriate skills to sample wild birds and add to the understanding of pathogens in migratory and breeding birds through research. For example, little is known about wild bird infectious diseases and migration along the Mediterranean and Black Sea Flyway (MBSF), which connects Europe, Asia, and Africa. Focusing on avian influenza and the microbiome in migratory wild birds along the MBSF, this project seeks to understand the determinants of transboundary disease propagation and coinfection in regions that are connected by this flyway. Through the creation of a threat reduction network for avian diseases (Avian Zoonotic Disease Network, AZDN) in three countries along the MBSF (Georgia, Ukraine, and Jordan), this project is strengthening capacities for disease diagnostics; microbiomes; ecoimmunology; field biosafety; proper wildlife capture and handling; experimental design; statistical analysis; and vector sampling and biology. Here, we cover what is required to build a wild bird infectious disease research and surveillance program, which includes learning skills in proper bird capture and handling; biosafety and biosecurity; permits; next generation sequencing; leading-edge bioinformatics and statistical analyses; and vector and environmental sampling. Creating connected networks for avian influenzas and other pathogen surveillance will increase coordination and strengthen biosurveillance globally in wild birds.
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Affiliation(s)
- Jeanne M. Fair
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Nisreen Al-Hmoud
- Bio-Safety and Bio-Security Center, Royal Scientific Society, Amman, Jordan
| | - Mu’men Alrwashdeh
- Bio-Safety and Bio-Security Center, Royal Scientific Society, Amman, Jordan
| | - Andrew W. Bartlow
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | | | - Ivane Daraselia
- Center of Wildlife Disease Ecology, Ilia State University, Tbilisi, Georgia
| | | | | | - Zura Javakhishvili
- Center of Wildlife Disease Ecology, Ilia State University, Tbilisi, Georgia
| | - Fares Khoury
- Department of Biology and Biotechnology, American University of Madaba, Madaba, Jordan
| | - Denys Muzyka
- National Scientific Center, Institute of Experimental and Clinical Veterinary Medicine, Kharkiv, Ukraine
| | | | - Jean Tsao
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States
| | - Lela Urushadze
- National Center for Disease Control and Public Health (NCDC) of Georgia, Tbilisi, Georgia
| | - Jennifer Owen
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, United States
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Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024; 15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [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: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Highly pathogenic avian influenza virus (HPAIV) A H5, particularly clade 2.3.4.4, has caused worldwide outbreaks in domestic poultry, occasional spillover to humans, and increasing deaths of diverse species of wild birds since 2014. Wild bird migration is currently acknowledged as an important ecological process contributing to the global dispersal of HPAIV H5. However, this mechanism has not been quantified using bird movement data from different species, and the timing and location of exposure of different species is unclear. We sought to explore these questions through phylodynamic analyses based on empirical data of bird movement tracking and virus genome sequences of clade 2.3.4.4 and 2.3.2.1. First, we demonstrate that seasonal bird migration can explain salient features of the global dispersal of clade 2.3.4.4. Second, we detect synchrony between the seasonality of bird annual cycle phases and virus lineage movements. We reveal the differing exposed bird orders at geographical origins and destinations of HPAIV H5 clade 2.3.4.4 lineage movements, including relatively under-discussed orders. Our study provides a phylodynamic framework that links the bird movement ecology and genomic epidemiology of avian influenza; it highlights the importance of integrating bird behavior and life history in avian influenza studies.
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Affiliation(s)
- Qiqi Yang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Ben Wang
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Phillipe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Lu Dong
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Tong Mu
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA
| | - R Alex Wiebe
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Fengyi Guo
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Sang Woo Park
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Nicola Lewis
- Animal and Plant Health Agency-Weybridge, OIE/FAO International Reference Laboratory for Avian Influenza, Swine Influenza and Newcastle Disease Virus, Department of Virology, Addlestone, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
| | | | - Sumali Bajaj
- Department of Biology, University of Oxford, Oxford, UK
| | - Yachang Cheng
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luojun Yang
- Institute for Disease Modeling, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yuki Haba
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Bingying Li
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China
| | - Guogang Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, National Bird Banding Center of China, Beijing, China
| | - Oliver G Pybus
- Department of Pathobiology and Population Science, Royal Veterinary College, London, UK
- Department of Biology, University of Oxford, Oxford, UK
| | - Huaiyu Tian
- State Key Laboratory of Remote Sensing Science, Center for Global Change and Public Health, Faculty of Geographical Science, Beijing Normal University, Beijing, China.
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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14
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Olawuyi K, Orole O, Meseko C, Monne I, Shittu I, Bianca Z, Fusaro A, Inuwa B, Akintola R, Ibrahim J, Muhammad M. Detection of clade 2.3.4.4 highly pathogenic avian influenza H5 viruses in healthy wild birds in the Hadeji-Nguru wetland, Nigeria 2022. Influenza Other Respir Viruses 2024; 18:e13254. [PMID: 38314064 PMCID: PMC10837781 DOI: 10.1111/irv.13254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 02/06/2024] Open
Abstract
Background The introduction of multiple avian influenza virus (AIV) subtypes into Nigeria has resulted in several poultry outbreaks purportedly linked to trade and wild birds. The role of wild birds in perpetuating AIV in Nigeria was, therefore, elucidated. Methods A cross-sectional study was conducted among wild aquatic bird species at the Hadejia-Nguru wetlands in Northeastern Nigeria between March and April 2022. A total of 452 swabs (226 cloacae and 226 oropharyngeal) were collected using a mist net to capture the birds. These samples were tested by RT-qPCR, followed by sequencing. Results Highly pathogenic AIV of the H5N1 subtype was identified in clinically healthy wild bird species, namely, African jacana, ruff, spur-winged goose, squared-tailed nightjar, white-faced whistling ducks, and white stork. A prevalence of 11.1% (25/226) was recorded. Phylogenetic analysis of the complete HA gene segment indicated the presence of clade 2.3.4.4b. However, these H5N1 viruses characterized from these wild birds cluster separately from the H5N1 viruses characterized in Nigerian poultry since early 2021. Specifically, the viruses form two distinct genetic groups both linked with the Eurasian H5N1 gene pool but likely resulting from two distinct introductions of the virus in the region. Whole-genome characterization of the viruses reveals the presence of mammalian adaptive marker E627K in two Afro-tropical resident aquatic ducks. This has zoonotic potential. Conclusion Our findings highlight the key role of surveillance in wild birds to monitor the diversity of viruses in this area, provide the foundations of epidemiological understanding, and facilitate risk assessment.
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Affiliation(s)
- Kayode Olawuyi
- National Veterinary Research InstituteVomNigeria
- Department of MicrobiologyFederal University of LafiaLafiaNigeria
| | - Olukayode Orole
- Department of MicrobiologyFederal University of LafiaLafiaNigeria
| | | | - Isabella Monne
- Istituto Zooprofilattico Sperimentale delle VeneziePadovaItaly
| | | | - Zecchin Bianca
- Istituto Zooprofilattico Sperimentale delle VeneziePadovaItaly
| | - Alice Fusaro
- Istituto Zooprofilattico Sperimentale delle VeneziePadovaItaly
| | - Bitrus Inuwa
- National Veterinary Research InstituteVomNigeria
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15
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Nagy A, Stará M, Černíková L, Kličková E, Horák O, Hofmannová L, Sedlák K. Enzootic Circulation, Massive Gull Mortality and Poultry Outbreaks during the 2022/2023 High-Pathogenicity Avian Influenza H5N1 Season in the Czech Republic. Viruses 2024; 16:221. [PMID: 38399998 PMCID: PMC10892573 DOI: 10.3390/v16020221] [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: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
In 2022/2023, Europe experienced its third consecutive season of high-pathogenicity avian influenza. During this period, the Czech Republic was again severely affected. For the first time, the number of culled birds approached one million, which was three times higher than in previous seasons. In parallel to the outbreaks in poultry, mass die-offs of gulls were also observed. In the present study, we performed whole-genome sequencing and phylogenetic analysis of 137 H5N1 strains collected in the Czech Republic in 2022/2023 (94.6% of all outbreaks or locations). The analysis revealed four distinct genotypes: AB, CH, BB and AF. Phylogenetic analysis suggested that the AF genotype persisted from the previous H5N1 season without reassortment. In addition, the genotype BB, which was detected mainly in gulls, showed a noticeable strain diversity at the local level. This virus was also responsible for a single outbreak in commercially bred turkeys. Finally, an interesting spatio-temporal cluster with three co-circulating H5N1 genotypes, AB, CH and AF, was identified with no evidence of intrasubtype reassortment. Highly sensitive molecular surveillance and the timely sharing of genomic sequences and associated metadata could greatly assist in tracking the spread and detecting molecular changes associated with the increased virulence of this potentially zoonotic pathogen.
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Affiliation(s)
- Alexander Nagy
- State Veterinary Institute Prague, Sídlištní 136/24, 165 03 Prague, Czech Republic; (M.S.); (L.Č.); (E.K.); (O.H.); (L.H.); (K.S.)
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16
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Grace D, Knight-Jones TJD, Melaku A, Alders R, Jemberu WT. The Public Health Importance and Management of Infectious Poultry Diseases in Smallholder Systems in Africa. Foods 2024; 13:411. [PMID: 38338547 PMCID: PMC10855203 DOI: 10.3390/foods13030411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
Poultry diseases pose major constraints on smallholder production in Africa, causing high flock mortality and economic hardship. Infectious diseases, especially viral diseases like Newcastle disease and highly pathogenic avian influenza (HPAI) and bacterial diseases, especially colibacillosis and salmonellosis, are responsible for most chicken losses, with downstream effects on human nutrition and health. Beyond production impacts, poultry diseases directly harm public health if zoonotic, can give rise to epidemics and pandemics, and facilitate antimicrobial resistance through treatment attempts. HPAI, campylobacteriosis, and salmonellosis are the priority zoonoses. Sustainable solutions for poultry health remain elusive despite recognition of the problem. This review summarises current knowledge on major poultry diseases in smallholder systems, their impacts, and options for prevention and control. We find biosecurity, vaccination, good husbandry, and disease-resistant breeds can reduce disease burden, but practical limitations exist in implementing these measures across smallholder systems. Treatment is often inefficient for viral diseases, and treatment for bacterial diseases risks antimicrobial resistance. Ethnoveterinary practices offer accessible alternatives but require more rigorous evaluation. Multisectoral collaboration and policies that reach smallholder poultry keepers are essential to alleviate disease constraints. Successful control will improve livelihoods, nutrition, and gender equity for millions of rural families. This review concludes that sustainable, scalable solutions for smallholder poultry disease control remain a critical unmet need in Africa.
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Affiliation(s)
- Delia Grace
- Natural Resources Institute (NRI), Chatham ME4 4TB, UK
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709, Kenya
| | | | - Achenef Melaku
- Department of Veterinary Pharmacy, University of Gondar, Gondar P.O. Box 196, Ethiopia;
| | - Robyn Alders
- Development Policy Centre, Australian National University, Acton, Canberra 2601, Australia;
| | - Wudu T. Jemberu
- International Livestock Research Institute (ILRI), Addis Ababa P.O. Box 5689, Ethiopia or (W.T.J.)
- Department of Veterinary Epidemiology and Public Health, University of Gondar, Gondar P.O. Box 196, Ethiopia
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17
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Min KD, Yoo DS. Ecological drivers for poultry farms predisposed to highly pathogenic avian influenza virus infection during the initial phase of the six outbreaks between 2010-2021: a nationwide study in South Korea. Front Vet Sci 2023; 10:1278852. [PMID: 38130434 PMCID: PMC10733472 DOI: 10.3389/fvets.2023.1278852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Background Highly pathogenic avian influenza (HPAI) has caused substantial economic losses worldwide. An understanding of the environmental drivers that contribute to spillover transmission from wild birds to poultry farms is important for predicting areas at risk of introduction and developing risk-based surveillance strategies. We conducted an epidemiological study using data from six HPAI outbreak events in South Korea. Materials and methods An aggregate-level study design was implemented using third-level administrative units in South Korea. Only regions with high natural reservoir suitability were included. The incidence of HPAI at chicken and duck farms during the initial phase (30 and 45 days after the first case) of each outbreak event was used as the outcome variable, assuming that cross-species transmission from wild birds was the dominant exposure leading to infection. Candidate environmental drivers were meteorological factors, including temperature, precipitation, humidity, and altitude, as well as the proportion of protected area, farm density, deforestation level, and predator species richness. Logistic regression models were implemented; conditional autoregression models were used in cases of spatial autocorrelation of residuals. Results Lower temperature, higher farm density, and lower predator species richness were significantly associated with a higher risk of HPAI infection on chicken farms. Lower temperature, higher proportion of protected area, and lower predator species richness were significantly associated with a higher risk of HPAI infection on duck farms. Conclusion The predicted dominant transmission routes on chicken and duck farms were horizontal and spillover, respectively. These results reveal a potential protective effect of predator species richness against HPAI outbreaks. Further studies are required to confirm a causal relationship.
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Affiliation(s)
- Kyung-Duk Min
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Republic of Korea
| | - Dae-sung Yoo
- College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
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18
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Xu X, Chen Q, Tan M, Liu J, Li X, Yang L, Shu Y, Wang D, Zhu W. Epidemiology, evolution, and biological characteristics of H6 avian influenza viruses in China. Emerg Microbes Infect 2023; 12:2151380. [PMID: 36440484 PMCID: PMC9788695 DOI: 10.1080/22221751.2022.2151380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
H6 avian influenza virus (AIV) is one of the most prevalent AIV subtypes in birds globally. To investigate the current situation and characteristics of H6 AIVs circulating in China, we analysed the epidemiology, genetic evolution and pathogenic features of this subtype. During 2000-2021, H6 subtype AIVs spread widely through Southern China and presented high host diversity. On analysing 171 H6 viruses isolated during 2009-2021, dynamic reassortments were observed among H6 and other co-circulating AIV subtypes, and these generated a total of 16 different genotypes. A few H6N6 strains possessed L226 and S228 mutations of hemagglutinin (H3 numbering), which may enhance the affinity of H6 viruses to human receptors. H6N6 viruses also exhibited divergent pathogenicity and growth profiles in vivo and in vitro. Some of the H6N6 viruses could infect mice without mammalian adaptation, and even caused death in this species. Therefore, our study demonstrated that the H6 AIVs posed a potential threat to human health and highlighted the urgent need for continued surveillance and evaluation of the H6 influenza viruses circulating in the field.
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Affiliation(s)
- Xiaohao Xu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Min Tan
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Jia Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Xiyan Li
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Lei Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China,Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China, Yuelong Shu School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong, People’s Republic of China; Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China,Dayan Wang National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
| | - Wenfei Zhu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China,Wenfei Zhu National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention; WHO Collaborating Center for Reference and Research on Influenza; Key Laboratory for Medical Virology, National Health and Family Planning Commission, Beijing, People’s Republic of China
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19
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Sun W, Zhao M, Yu Z, Li Y, Zhang X, Feng N, Wang T, Wang H, He H, Zhao Y, Yang S, Xia X, Gao Y. Cross-species infection potential of avian influenza H13 viruses isolated from wild aquatic birds to poultry and mammals. Emerg Microbes Infect 2023; 12:e2184177. [PMID: 36877121 PMCID: PMC10013326 DOI: 10.1080/22221751.2023.2184177] [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: 03/07/2023]
Abstract
Wild aquatic birds are the primary hosts of H13 avian influenza viruses (AIVs). Herein, we performed a genetic analysis of two H13 AIVs isolated from wild birds in China and evaluated their infection potential in poultry to further explore the potential for transmission from wild aquatic birds to poultry. Our results showed that the two strains belong to different groups, one strain (A/mallard/Dalian/DZ-137/2013; abbreviated as DZ137) belongs to Group I, whereas the other strain (A/Eurasian Curlew/Liaoning/ZH-385/2014; abbreviated as ZH385) belongs to Group III. In vitro experiments showed that both DZ137 and ZH385 can replicate efficiently in chicken embryo fibroblast cells. We found that these H13 AIVs can also efficiently replicate in mammalian cell lines, including human embryonic kidney cells and Madin-Darby canine kidney cells. In vivo experiments showed that DZ137 and ZH385 can infect 1-day-old specific pathogen-free (SPF) chickens, and that ZH385 has a higher replication ability in chickens than DZ137. Notably, only ZH385 can replicate efficiently in 10-day-old SPF chickens. However, neither DZ137 nor ZH385 can replicate well in turkeys and quails. Both DZ137 and ZH385 can replicate in 3-week-old mice. Serological surveillance of poultry showed a 4.6%-10.4% (15/328-34/328) antibody-positive rate against H13 AIVs in farm chickens. Our findings indicate that H13 AIVs have the replication ability in chickens and mice and may have a risk of crossing the host barrier from wild aquatic birds to poultry or mammals in the future.
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Affiliation(s)
- Weiyang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Menglin Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, People's Republic of China
| | - Yuanguo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Xinghai Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Hongmei Wang
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Ji'nan, People's Republic of China
| | - Hongbin He
- Key Laboratory of Animal Resistant Biology of Shandong, Ruminant Disease Research Center, College of Life Science, Shandong Normal University, Ji'nan, People's Republic of China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yang'zhou, People's Republic of China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Chang'chun, People's Republic of China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yang'zhou, People's Republic of China
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20
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Wang Y, Wang M, Zhang H, Zhao C, Zhang Y, Shen J, Sun X, Xu H, Xie Y, Gao X, Cui P, Chu D, Li Y, Liu W, Peng P, Deng G, Guo J, Li X. Prevalence, evolution, replication and transmission of H3N8 avian influenza viruses isolated from migratory birds in eastern China from 2017 to 2021. Emerg Microbes Infect 2023; 12:2184178. [PMID: 36913241 PMCID: PMC10013397 DOI: 10.1080/22221751.2023.2184178] [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: 02/24/2023]
Abstract
The continued evolution and emergence of novel influenza viruses in wild and domestic animals poses an increasing public health risk. Two human cases of H3N8 avian influenza virus infection in China in 2022 have caused public concern regarding the risk of transmission between birds and humans. However, the prevalence of H3N8 avian influenza viruses in their natural reservoirs and their biological characteristics are largely unknown. To elucidate the potential threat of H3N8 viruses, we analyzed five years of surveillance data obtained from an important wetland region in eastern China and evaluated the evolutionary and biological characteristics of 21 H3N8 viruses isolated from 15,899 migratory bird samples between 2017 and 2021. Genetic and phylogenetic analyses showed that the H3N8 viruses circulating in migratory birds and ducks have evolved into different branches and have undergone complicated reassortment with viruses in waterfowl. The 21 viruses belonged to 12 genotypes, and some strains induced body weight loss and pneumonia in mice. All the tested H3N8 viruses preferentially bind to avian-type receptors, although they have acquired the ability to bind human-type receptors. Infection studies in ducks, chickens and pigeons demonstrated that the currently circulating H3N8 viruses in migratory birds have a high possibility of infecting domestic waterfowl and a low possibility of infecting chickens and pigeons. Our findings imply that circulating H3N8 viruses in migratory birds continue to evolve and pose a high infection risk in domestic ducks. These results further emphasize the importance of avian influenza surveillance at the wild bird and poultry interface.
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Affiliation(s)
- Yanwen Wang
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Mengjing Wang
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Hong Zhang
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Conghui Zhao
- Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin, People's Republic of China
| | - Yaping Zhang
- Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin, People's Republic of China
| | - Jinyan Shen
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Xiaohong Sun
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Hongke Xu
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Yujiao Xie
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Xinxin Gao
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Pengfei Cui
- Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin, People's Republic of China
| | - Dong Chu
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang, People's Republic of China
| | - Yubao Li
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Wenqiang Liu
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Peng Peng
- Biological Disaster Control and Prevention Center, National Forestry and Grassland Administration, Shenyang, People's Republic of China
| | - Guohua Deng
- Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, State Key Laboratory of Veterinary Biotechnology, National Poultry Laboratory Animal Resource Center, Harbin, People's Republic of China
| | - Jing Guo
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
| | - Xuyong Li
- College of Agronomy, Liaocheng University, Liaocheng, People's Republic of China
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21
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Rizal FA, Ho KL, Omar AR, Tan WS, Mariatulqabtiah AR, Iqbal M. Sequence Analysis of the Malaysian Low Pathogenic Avian Influenza Virus Strain H5N2 from Duck. Genes (Basel) 2023; 14:1973. [PMID: 37895321 PMCID: PMC10606931 DOI: 10.3390/genes14101973] [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: 09/27/2023] [Revised: 10/19/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023] Open
Abstract
The avian influenza viruses (AIV) of the H5 subtype have the ability to mutate from low pathogenic (LPAI) to highly pathogenic (HPAI), which can cause high mortality in poultry. Little is known about the pathogenic switching apart from the mutations at the haemagglutinin cleavage site, which significantly contributes to the virus virulence switching phenomenon. Therefore, this study aimed to compare the molecular markers in the haemagglutinin (HA), neuraminidase (NA), and matrix (M) genes of a locally isolated LPAI AIV strain H5N2 from Malaysia with the reference HPAI strains using bioinformatics approaches, emphasising the pathogenic properties of the viral genes. First, the H5N2 strain A/Duck/Malaysia/8443/2004 was propagated in SPF eggs. The viral presence was verified by haemagglutination assay, RT-PCR, and sequencing. Results showed successful amplifications of HA (1695 bp), NA (1410 bp), and M (1019 bp) genes. The genes were sequenced and the deduced amino acid sequences were analysed computationally using MEGA 11 and NetNGlyc software. Analysis of the HA protein showed the absence of the polybasic cleavage motif, but presence of two amino acid residues that are known to affect pathogenicity. There were also two glycosylation sites (glycosites) compared to the reference HPAI viruses, which had three or more at the HA globular head domain. No NA stalk deletion was detected but the haemadsorbing and active centres of the studied NA protein were relatively similar to the reference HPAI H5N2 isolates of duck but not chicken origins. Six NA glycosites were also identified. Finally, we observed a consistent M1 and M2 amino acid sequences between our LPAI isolate with the other HPAI H5N1 or H5N2 reference proteins. These data demonstrate distinct characteristics of the Malaysian LPAI H5N2, compared to HPAI H5N2 or H5N1 from ducks or chickens, potentially aiding the epidemiological research on genetic dynamics of circulating AIV in poultry.
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Affiliation(s)
- Fatin Ahmad Rizal
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abdul Rahman Omar
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Abdul Razak Mariatulqabtiah
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Munir Iqbal
- Avian Influenza and Newcastle Disease Group, The Pirbright Institute, Woking GU24 0NF, UK
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22
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Taylor LU, Ronconi RA, Spina HA, Jones MEB, Ogbunugafor CB, Ayala AJ. Limited Outbreak of Highly Pathogenic Influenza A(H5N1) in Herring Gull Colony, Canada, 2022. Emerg Infect Dis 2023; 29:2150-2154. [PMID: 37619593 PMCID: PMC10521612 DOI: 10.3201/eid2910.230536] [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] [Indexed: 08/26/2023] Open
Abstract
In summer 2022, highly pathogenic influenza A(H5N1) virus reached the herring gull (Larus argentatus subspecies smithsonianus) breeding colony on Kent Island, New Brunswick, Canada. Real-time monitoring revealed a self-limiting outbreak with low mortality. Proactive seabird surveillance is crucial for monitoring such limited outbreaks, protecting seabirds, and tracing zoonotic transmission routes.
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23
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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24
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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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25
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Xie R, Edwards KM, Wille M, Wei X, Wong SS, Zanin M, El-Shesheny R, Ducatez M, Poon LLM, Kayali G, Webby RJ, Dhanasekaran V. The episodic resurgence of highly pathogenic avian influenza H5 virus. Nature 2023; 622:810-817. [PMID: 37853121 DOI: 10.1038/s41586-023-06631-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023]
Abstract
Highly pathogenic avian influenza (HPAI) H5N1 activity has intensified globally since 2021, increasingly causing mass mortality in wild birds and poultry and incidental infections in mammals1-3. However, the ecological and virological properties that underscore future mitigation strategies still remain unclear. Using epidemiological, spatial and genomic approaches, we demonstrate changes in the origins of resurgent HPAI H5 and reveal significant shifts in virus ecology and evolution. Outbreak data show key resurgent events in 2016-2017 and 2020-2021, contributing to the emergence and panzootic spread of H5N1 in 2021-2022. Genomic analysis reveals that the 2016-2017 epizootics originated in Asia, where HPAI H5 reservoirs are endemic. In 2020-2021, 2.3.4.4b H5N8 viruses emerged in African poultry, featuring mutations altering HA structure and receptor binding. In 2021-2022, a new H5N1 virus evolved through reassortment in wild birds in Europe, undergoing further reassortment with low-pathogenic avian influenza in wild and domestic birds during global dissemination. These results highlight a shift in the HPAI H5 epicentre beyond Asia and indicate that increasing persistence of HPAI H5 in wild birds is facilitating geographic and host range expansion, accelerating dispersion velocity and increasing reassortment potential. As earlier outbreaks of H5N1 and H5N8 were caused by more stable genomic constellations, these recent changes reflect adaptation across the domestic-bird-wild-bird interface. Elimination strategies in domestic birds therefore remain a high priority to limit future epizootics.
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Affiliation(s)
- Ruopeng Xie
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kimberly M Edwards
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Michelle Wille
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
- Department of Microbiology and Immunology, at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiaoman Wei
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sook-San Wong
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mark Zanin
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Mariette Ducatez
- IHAP, Université de Toulouse, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Ecole Nationale Vétérinaire de Toulouse, Toulouse, France
| | - Leo L M Poon
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Immunology & Infection, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | | | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
- HKU-Pasteur Research Pole, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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26
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Saavedra I, Rabadán-González J, Aragonés D, Figuerola J. Can Citizen Science Contribute to Avian Influenza Surveillance? Pathogens 2023; 12:1183. [PMID: 37764991 PMCID: PMC10535995 DOI: 10.3390/pathogens12091183] [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: 07/03/2023] [Revised: 09/01/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Global change is an important driver of the increase in emerging infectious diseases in recent decades. In parallel, interest in nature has increased, and different citizen science platforms have been developed to record wildlife observations from the general public. Some of these platforms also allow registering the observations of dead or sick birds. Here, we test the utility of live, sick and dead observations of birds recorded on the platform Observation.org for the early detection of highly pathogenic avian influenza virus (HPAIV) outbreaks in the wild in Belgium and The Netherlands. There were no significant differences in the morbidity/mortality rate through Observation.org one to four weeks in advance. However, the results show that the HPAIV outbreaks officially reported by the World Organisation for Animal Health (WOAH) overlapped in time with sudden increases in the records of sick and dead birds in the wild. In addition, in two of the five main HPAIV outbreaks recorded between 2016 and 2021, wild Anseriformes mortality increased one to two months before outbreak declaration. Although we cannot exclude that this increase was related to other causes such as other infectious diseases, we propose that Observation.org is a useful nature platform to complement animal health surveillance in wild birds. We propose possible approaches to improve the utility of the platform for pathogen surveillance in wildlife and discuss the potential for HPAIV outbreak detection systems based on citizen science to complement current surveillance programs of health authorities.
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Affiliation(s)
- Irene Saavedra
- Consejo Superior de Investigaciones Científicas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
| | | | - David Aragonés
- Remote Sensing and GIS Laboratory (LAST-EBD), Consejo Superior de Investigaciones Cientificas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
| | - Jordi Figuerola
- Consejo Superior de Investigaciones Científicas, Estación Biológica de Doñana, C/Américo Vespucio 26, E-41092 Sevilla, Spain;
- CIBER Epidemiology and Public Health (CIBERESP), E-28028 Madrid, Spain
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Gamble A. Disease ecology: When a GPS logger tells you more than a blood sample. Curr Biol 2023; 33:R907-R909. [PMID: 37699348 DOI: 10.1016/j.cub.2023.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Long-term movement tracking revealed sublethal effects of avian influenza infection in vultures, adding an important element to our understanding of the subtleties of the feedback loop between host movement and pathogen transmission.
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Affiliation(s)
- Amandine Gamble
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow G12 8QQ, Scotland, UK; Department of Public and Ecosystem Health, Cornell University, Ithaca, NY 14853, USA.
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28
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Li S, Jing T, Zhu F, Chen Y, Yao X, Tang X, Zuo C, Liu M, Xie Y, Jiang Y, Wang Y, Li D, Li L, Gao S, Chen D, Zhao H, Ma W. Genetic Analysis of Orf Virus (ORFV) Strains Isolated from Goats in China: Insights into Epidemiological Characteristics and Evolutionary Patterns. Virus Res 2023; 334:199160. [PMID: 37402415 PMCID: PMC10410590 DOI: 10.1016/j.virusres.2023.199160] [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: 03/08/2023] [Revised: 06/14/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Contagious ecthyma (CE) is an acute infectious zoonosis caused by orf virus (ORFV) that mainly infects sheep and goats and causes obvious lesions and low market value of livestock, resulting in huge economic losses for farmers. In this study, two strains of ORFV were isolated from Shaanxi Province and Yunnan Province in China, named FX and LX. The two ORFVs were located in the major clades of domestic strains respectively, and exhibited distinct sequence homology. We analyzed the genetic data of core genes (B2L, F1L, VIR, ORF109) and variable genes (GIF, ORF125 and vIL-10) of ORFV to investigate its epidemiological and evolutionary characteristics. The sequences from 2007 to 2018 constituted the majority of the viral population, predominantly concentrated in India and China. Most genes were clustered into SA00-like type and IA82-like type, and the hotspots in East and South Asia were identified in the ORFV transmission trajectories. For these genes, VIR had the highest substitution rate of 4.85 × 10-4, both VIR and vIL-10 suffered the positive selection pressure during ORFV evolution. Many motifs associated with viral survival were distributed among ORFVs. In addition, some possible viral epitopes have been predicted, which still require validation in vivo and in vitro. This work gives more insight into the prevalence and phylogenetic relationships of existing orf viruses and facilitate better vaccine design.
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Affiliation(s)
- Shaofei Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Tian Jing
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Fang Zhu
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yiming Chen
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Xiaoting Yao
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Xidian Tang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Chenxiang Zuo
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Mingjie Liu
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yanfei Xie
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yuecai Jiang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yunpeng Wang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Dengliang Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Lulu Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Shikong Gao
- Shenmu Animal Husbandry Development Center, Shenmu, Shaanxi Province 719399, China
| | - Dekun Chen
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
| | - Huiying Zhao
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
| | - Wentao Ma
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
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29
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Alkie TN, Byrne AMP, Jones MEB, Mollett BC, Bourque L, Lung O, James J, Yason C, Banyard AC, Sullivan D, Signore AV, Lang AS, Baker M, Dawe B, Brown IH, Berhane Y. Recurring Trans-Atlantic Incursion of Clade 2.3.4.4b H5N1 Viruses by Long Distance Migratory Birds from Northern Europe to Canada in 2022/2023. Viruses 2023; 15:1836. [PMID: 37766243 PMCID: PMC10536465 DOI: 10.3390/v15091836] [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: 07/30/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
In December 2022 and January 2023, we isolated clade 2.3.4.4b H5N1 high-pathogenicity avian influenza (HPAI) viruses from six American crows (Corvus brachyrhynchos) from Prince Edward Island and a red fox (Vulpes vulpes) from Newfoundland, Canada. Using full-genome sequencing and phylogenetic analysis, these viruses were found to fall into two distinct phylogenetic clusters: one group containing H5N1 viruses that had been circulating in North and South America since late 2021, and the other one containing European H5N1 viruses reported in late 2022. The transatlantic re-introduction for the second time by pelagic/Icelandic bird migration via the same route used during the 2021 incursion of Eurasian origin H5N1 viruses into North America demonstrates that migratory birds continue to be the driving force for transcontinental dissemination of the virus. This new detection further demonstrates the continual long-term threat of H5N1 viruses for poultry and mammals and the subsequent impact on various wild bird populations wherever these viruses emerge. The continual emergence of clade 2.3.4.4b H5Nx viruses requires vigilant surveillance in wild birds, particularly in areas of the Americas, which lie within the migratory corridors for long-distance migratory birds originating from Europe and Asia. Although H5Nx viruses have been detected at higher rates in North America since 2021, a bidirectional flow of H5Nx genes of American origin viruses to Europe has never been reported. In the future, coordinated and systematic surveillance programs for HPAI viruses need to be launched between European and North American agencies.
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Affiliation(s)
- Tamiru N. Alkie
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Alexander M. P. Byrne
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Megan E. B. Jones
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Benjamin C. Mollett
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
| | - Laura Bourque
- Canadian Wildlife Health Cooperative, Atlantic Region, Charlottetown, PE C1A 4P3, Canada; (M.E.B.J.); (L.B.)
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Joe James
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Carmencita Yason
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE C1A 4P3, Canada;
| | - Ashley C. Banyard
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Daniel Sullivan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Anthony V. Signore
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
| | - Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada;
| | - Meghan Baker
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Beverly Dawe
- Animal Health Division, Department of Fisheries, Forestry and Agriculture, Government of Newfoundland and Labrador, Provincial Agriculture Building, 204 Brookfield Road, St. John’s, NL A1E 0B2, Canada; (M.B.); (B.D.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, 10 Addlestone, Surrey KT15 3NB, UK; (A.M.P.B.); (B.C.M.); (J.J.); (A.C.B.)
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health 12 Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
| | - Yohannes Berhane
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3R2, Canada; (T.N.A.); (O.L.); (D.S.); (A.V.S.)
- Department of Veterinary Pathology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Salve BG, Kurian AM, Vijay N. Concurrent loss of ciliary genes WDR93 and CFAP46 in phylogenetically distant birds. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230801. [PMID: 37621660 PMCID: PMC10445033 DOI: 10.1098/rsos.230801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
The respiratory system is the primary route of infection for many contagious pathogens. Mucociliary clearance of inhaled pathogens is an important innate defence mechanism sustained by the rhythmic movement of epithelial cilia. To counter host defences, viral pathogens target epithelial cells and cilia. For instance, the avian influenza virus that targets ciliated cells modulates the expression of WDR93, a central ciliary apparatus C1d projection component. Lineage-specific prevalence of such host defence genes results in differential susceptibility. In this study, the comparative analysis of approximately 500 vertebrate genomes from seven taxonomic classes spanning 73 orders confirms the widespread conservation of WDR93 across these different vertebrate groups. However, we established loss of the WDR93 in landfowl, geese and other phylogenetically independent bird species due to gene-disrupting changes. The lack of WDR93 transcripts in species with gene loss in contrast to its expression in species with an intact gene confirms gene loss. Notably, species with WDR93 loss have concurrently lost another C1d component, CFAP46, through large segmental deletions. Understanding the consequences of such gene loss may provide insight into their role in host-pathogen interactions and benefit global pathogen surveillance efforts by prioritizing species missing host defence genes and identifying putative zoonotic reservoirs.
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Affiliation(s)
- Buddhabhushan Girish Salve
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Amia Miriam Kurian
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
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31
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Gass JD, Hill NJ, Damodaran L, Naumova EN, Nutter FB, Runstadler JA. Ecogeographic Drivers of the Spatial Spread of Highly Pathogenic Avian Influenza Outbreaks in Europe and the United States, 2016-Early 2022. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6030. [PMID: 37297634 PMCID: PMC10252585 DOI: 10.3390/ijerph20116030] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/10/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
H5Nx highly pathogenic avian influenza (HPAI) viruses of clade 2.3.4.4 have caused outbreaks in Europe among wild and domestic birds since 2016 and were introduced to North America via wild migratory birds in December 2021. We examined the spatiotemporal extent of HPAI viruses across continents and characterized ecological and environmental predictors of virus spread between geographic regions by constructing a Bayesian phylodynamic generalized linear model (phylodynamic-GLM). The findings demonstrate localized epidemics of H5Nx throughout Europe in the first several years of the epizootic, followed by a singular branching point where H5N1 viruses were introduced to North America, likely via stopover locations throughout the North Atlantic. Once in the United States (US), H5Nx viruses spread at a greater rate between US-based regions as compared to prior spread in Europe. We established that geographic proximity is a predictor of virus spread between regions, implying that intercontinental transport across the Atlantic Ocean is relatively rare. An increase in mean ambient temperature over time was predictive of reduced H5Nx virus spread, which may reflect the effect of climate change on declines in host species abundance, decreased persistence of the virus in the environment, or changes in migratory patterns due to ecological alterations. Our data provide new knowledge about the spread and directionality of H5Nx virus dispersal in Europe and the US during an actively evolving intercontinental outbreak, including predictors of virus movement between regions, which will contribute to surveillance and mitigation strategies as the outbreak unfolds, and in future instances of uncontained avian spread of HPAI viruses.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, Boston, MA 02125, USA
| | | | - Elena N. Naumova
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02155, USA
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA
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32
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De Marco MA, Delogu M, Cotti C. Special Issue "Ecology of Influenza A Viruses": Editorial. Microorganisms 2023; 11:1287. [PMID: 37317261 DOI: 10.3390/microorganisms11051287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Wild aquatic birds constitute the main natural reservoir of the influenza A virus (IAV) gene pool, from which novel IAVs can emerge to infect other animals including avian and mammalian species [...].
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Affiliation(s)
- Maria Alessandra De Marco
- Italian Institute for Environmental Protection and Research (ISPRA), 40064 Ozzano dell'Emilia, Italy
| | - Mauro Delogu
- Wildlife and Exotic Animal Service, Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell'Emilia, Italy
| | - Claudia Cotti
- Wildlife and Exotic Animal Service, Department of Veterinary Medical Sciences, University of Bologna, 40064 Ozzano dell'Emilia, Italy
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33
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Rasmussen EA, Czaja A, Cuthbert FJ, Tan GS, Lemey P, Nelson MI, Culhane MR. Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States. Front Genet 2023; 14:1172048. [PMID: 37229191 PMCID: PMC10203411 DOI: 10.3389/fgene.2023.1172048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: The unpredictable evolution of avian influenza viruses (AIVs) presents an ongoing threat to agricultural production and public and wildlife health. Severe outbreaks of highly pathogenic H5N1 viruses in US poultry and wild birds since 2022 highlight the urgent need to understand the changing ecology of AIV. Surveillance of gulls in marine coastal environments has intensified in recent years to learn how their long-range pelagic movements potentially facilitate inter-hemispheric AIV movements. In contrast, little is known about inland gulls and their role in AIV spillover, maintenance, and long-range dissemination. Methods: To address this gap, we conducted active AIV surveillance in ring-billed gulls (Larus delawarensis) and Franklin's gulls (Leucophaeus pipixcan) in Minnesota's natural freshwater lakes during the summer breeding season and in landfills during fall migration (1,686 samples). Results: Whole-genome AIV sequences obtained from 40 individuals revealed three-lineage reassortants with a mix of genome segments from the avian Americas lineage, avian Eurasian lineage, and a global "Gull" lineage that diverged more than 50 years ago from the rest of the AIV global gene pool. No poultry viruses contained gull-adapted H13, NP, or NS genes, pointing to limited spillover. Geolocators traced gull migration routes across multiple North American flyways, explaining how inland gulls imported diverse AIV lineages from distant locations. Migration patterns were highly varied and deviated far from assumed "textbook" routes. Discussion: Viruses circulating in Minnesota gulls during the summer breeding season in freshwater environments reappeared in autumn landfills, evidence of AIV persistence in gulls between seasons and transmission between habitats. Going forward, wider adoption of technological advances in animal tracking devices and genetic sequencing is needed to expand AIV surveillance in understudied hosts and habitats.
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Affiliation(s)
- Elizabeth A. Rasmussen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Agata Czaja
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Francesca J. Cuthbert
- Department of Fisheries, Wildlife and Conservation Biology, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Martha I. Nelson
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Marie R. Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
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34
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Emergence of Highly Pathogenic Avian Influenza A Virus (H5N1) of Clade 2.3.4.4b in Egypt, 2021-2022. Pathogens 2023; 12:pathogens12010090. [PMID: 36678438 PMCID: PMC9863303 DOI: 10.3390/pathogens12010090] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Wild migratory birds have the capability to spread avian influenza virus (AIV) over long distances as well as transmit the virus to domestic birds. In this study, swab and tissue samples were obtained from 190 migratory birds during close surveillance in Egypt in response to the recent outbreaks of the highly pathogenic avian influenza (HPAI) H5N1 virus. The collected samples were tested for a variety of AIV subtypes (H5N1, H9N2, H5N8, and H6N2) as well as other pathogens such as NDV, IBV, ILT, IBDV, and WNV. Among all of the tested samples, the HPAI H5N1 virus was found in six samples; the other samples were found to be negative for all of the tested pathogens. The Egyptian HPAI H5N1 strains shared genetic traits with the HPAI H5N1 strains that are currently being reported in Europe, North America, Asia, and Africa in 2021-2022. Whole genome sequencing revealed markers associated with mammalian adaption and virulence traits among different gene segments, similar to those found in HPAI H5N1 strains detected in Europe and Africa. The detection of the HPAI H5N1 strain of clade 2.3.4.4b in wild birds in Egypt underlines the risk of the introduction of this strain into the local poultry population. Hence, there is reason to be vigilant and continue epidemiological and molecular monitoring of the AIV in close proximity to the domestic-wild bird interface.
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Genetic Analysis of a Novel H16N3 Virus Isolated from a Migratory Gull in China in 2021 and Animal Studies of Infection. Microbiol Spectr 2022; 10:e0248422. [PMID: 36314919 PMCID: PMC9769943 DOI: 10.1128/spectrum.02484-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
H16 avian influenza viruses mainly circulate in wild migratory gulls worldwide, and the infection risks in poultry and mammals remain largely unknown. In this study, we isolated a novel H16N3 virus from migratory gulls in eastern China in 2021. Genetic analysis indicated that the H16N3 virus originated from the H16 and H13 viruses that circulated in wild birds. This H16N3 virus has not adapted to replicate in chickens, ducks, or mice, although it can be transmitted between inoculated and contacted birds. The circulation of H16Nx viruses in the Northern Hemisphere indicates that we should strengthen active surveillance to monitor their prevalence and evolution in migratory gulls and their introduction into other migratory and domestic waterfowl. IMPORTANCE Migratory wild birds are natural reservoirs of H16 viruses and play a key role in the global prevalence of these viruses. Here, we found that H16 viruses predominantly circulate in migratory gulls and that the gull H16N3 virus cannot replicate efficiently in chickens, ducks, or mice without prior adaptation. These findings contribute to our understanding of the ecology, evolution, and biological properties of H16 viruses and will guide avian influenza surveillance in birds.
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36
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Günther A, Krone O, Svansson V, Pohlmann A, King J, Hallgrimsson GT, Skarphéðinsson KH, Sigurðardóttir H, Jónsson SR, Beer M, Brugger B, Harder T. Iceland as Stepping Stone for Spread of Highly Pathogenic Avian Influenza Virus between Europe and North America. Emerg Infect Dis 2022; 28:2383-2388. [PMID: 36261139 PMCID: PMC9707596 DOI: 10.3201/eid2812.221086] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of hemagglutinin type H5 and clade 2.3.4.4b have widely spread within the northern hemisphere since 2020 and threaten wild bird populations, as well as poultry production. We present phylogeographic evidence that Iceland has been used as a stepping stone for HPAIV translocation from northern Europe to North America by infected but mobile wild birds. At least 2 independent incursions of HPAIV H5N1 clade 2.3.4.4b assigned to 2 hemagglutinin clusters, B1 and B2, are documented for summer‒autumn 2021 and spring 2022. Spread of HPAIV H5N1 to and among colony-breeding pelagic avian species in Iceland is ongoing. Potentially devastating effects (i.e., local losses >25%) on these species caused by extended HPAIV circulation in space and time are being observed at several affected breeding sites throughout the North Atlantic.
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