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Aranda AJ, Aguilar-Tipacamú G, Perez DR, Bañuelos-Hernandez B, Girgis G, Hernandez-Velasco X, Escorcia-Martinez SM, Castellanos-Huerta I, Petrone-Garcia VM. Emergence, migration and spreading of the high pathogenicity avian influenza virus H5NX of the Gs/Gd lineage into America. J Gen Virol 2025; 106:002081. [PMID: 40279164 PMCID: PMC12032427 DOI: 10.1099/jgv.0.002081] [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: 10/22/2024] [Accepted: 01/31/2025] [Indexed: 04/26/2025] Open
Abstract
The high pathogenicity avian influenza virus H5N1, which first emerged in the winter of 2021, has resulted in multiple outbreaks across the American continent through the summer of 2023 and they continue based on early 2025 records, presenting significant challenges for global health and food security. The viruses causing the outbreaks belong to clade 2.3.4.4b, which are descendants of the lineage A/Goose/Guangdong/1/1996 (Gs/Gd) through genetic reassortments with several low pathogenicity avian influenza viruses present in populations of Anseriformes and Charadriiformes orders. This review addresses these issues by thoroughly analysing available epidemiological databases and specialized literature reviews. This project explores the mechanisms behind the resurgence of the H5N1 virus. It provides a comprehensive overview of the origin, timeline and factors contributing to its prevalence among wild bird populations on the American continent.
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Affiliation(s)
- Alejandro J. Aranda
- Maestría en Salud y Producción Animal Sustentable, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Mexico
| | - Gabriela Aguilar-Tipacamú
- Maestría en Salud y Producción Animal Sustentable, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, Mexico
- Licenciatura en Medicina Veterinaria y Zootecnia, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Querétaro, México
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Bernardo Bañuelos-Hernandez
- Facultad de Veterinaria, Universidad De La Salle Bajío, Avenida Universidad 602, Lomas del Campestre, León, México
| | - George Girgis
- Nevysta Laboratory, Iowa State University Research Park, Ames, Lowa, USA
| | - Xochitl Hernandez-Velasco
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Universidad Nacional Autónoma de México (UNAM), Cd. de México, México
| | - Socorro M. Escorcia-Martinez
- Departamento de Medicina y Zootecnia de Aves, Facultad de Medicina Veterinaria y Zootecnia (FMVZ), Universidad Nacional Autónoma de México (UNAM), Cd. de México, México
| | | | - Victor M. Petrone-Garcia
- Departamento de Ciencias Pecuarias, Facultad de Estudios Superiores de Cuautitlán (FESC), Universidad Nacional Autónoma de México (UNAM), Cuautitlán, Mexico
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Larbi I, Arbi M, Souiai O, Tougorti H, Butcher GD, Nsiri J, Badr C, Behi IE, Lachhab J, Ghram A. Phylogeographic Dynamics of H9N2 Avian Influenza Viruses in Tunisia. Virus Res 2024; 344:199348. [PMID: 38467378 PMCID: PMC10995884 DOI: 10.1016/j.virusres.2024.199348] [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: 01/09/2024] [Revised: 02/25/2024] [Accepted: 02/27/2024] [Indexed: 03/13/2024]
Abstract
Avian influenza virus subtype H9N2 is endemic in commercial poultry in Tunisia. This subtype affects poultry and wild birds in Tunisia and poses a potential zoonotic risk. Tunisian H9N2 strains carry, in their hemagglutinins, the human-like marker 226 L that is most influential in avian-to-human viral transmission. For a better understanding of how ecological aspects of the H9N2 virus and its circulation in poultry, migratory birds and environment shapes the spread of the dissemination of H9N2 in Tunisia, herein, we investigate the epidemiological, evolutionary and zoonotic potential of seven H9N2 poultry isolates and sequence their whole genome. Phylogeographic and phylodymanic analysis were used to examine viral spread within and among wild birds, poultry and environment at geographical scales. Genetic evolution results showed that the eight gene sequences of Tunisian H9N2 AIV were characterized by molecular markers involved with virulence and mammalian infections. The geographical distribution of avian influenza virus appears as a network interconnecting countries in Europe, Asia, North Africa and West Africa. The spatiotemporal dynamics analysis showed that the H9N2 virus was transmitted from Tunisia to neighboring countries notably Libya and Algeria. Interestingly, this study also revealed, for the first time, that there was a virus transmission between Tunisia and Morocco. Bayesian analysis showed exchanges between H9N2 strains of Tunisia and those of the Middle Eastern countries, analysis of host traits showed that duck, wild birds and environment were ancestry related to chicken. The subtypes phylodynamic showed that PB1 segment was under multiple inter-subtype reassortment events with H10N7, H12N5, H5N2 and H6N1 and that PB2 was also a subject of inter-subtype reassortment with H10N4.
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Affiliation(s)
- Imen Larbi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia.
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Oussama Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Halima Tougorti
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Gary David Butcher
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Jihene Nsiri
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Chaima Badr
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Imen El Behi
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Jihene Lachhab
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
| | - Abdeljelil Ghram
- Laboratory of Epidemiology and Veterinary Microbiology, LR19IPT03, Institut Pasteur de Tunis, University of Tunis El Manar, 13, Place Pasteur-BP74, Tunis, Belvédère 1002, Tunisia
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Flores RA, Cammayo-Fletcher PLT, Nguyen BT, Villavicencio AGM, Lee SY, Son Y, Kim JH, Park KI, Yoo WG, Jin YB, Min W, Kim WH. Genetic Characterization and Phylogeographic Analysis of the First H13N6 Avian Influenza Virus Isolated from Vega Gull in South Korea. Viruses 2024; 16:285. [PMID: 38400060 PMCID: PMC10891532 DOI: 10.3390/v16020285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Avian influenza virus (AIV) is a pathogen with zoonotic and pandemic potential. Migratory birds are natural reservoirs of all known subtypes of AIVs, except for H17N10 and H18N11, and they have been implicated in previous highly pathogenic avian influenza outbreaks worldwide. This study identified and characterized the first isolate of the H13N6 subtype from a Vega gull (Larus vegae mongolicus) in South Korea. The amino acid sequence of hemagglutinin gene showed a low pathogenic AIV subtype and various amino acid substitutions were found in the sequence compared to the reference sequence and known H13 isolates. High sequence homology with other H13N6 isolates was found in HA, NA, PB1, and PA genes, but not for PB2, NP, M, and NS genes. Interestingly, various point amino acid mutations were found on all gene segments, and some are linked to an increased binding to human-type receptors, resistance to antivirals, and virulence. Evolutionary and phylogenetic analyses showed that all gene segments are gull-adapted, with a phylogeographic origin of mostly Eurasian, except for PB2, PA, and M. Findings from this study support the evidence that reassortment of AIVs continuously occurs in nature, and migratory birds are vital in the intercontinental spread of avian influenza viruses.
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Affiliation(s)
- Rochelle A. Flores
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Paula Leona T. Cammayo-Fletcher
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Binh T. Nguyen
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Andrea Gail M. Villavicencio
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Seung Yun Lee
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Yongwoo Son
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Jae-Hoon Kim
- National Park Research Institute, Korean National Park Service, Wonju 26441, Gangwon, Republic of Korea;
| | - Kwang Il Park
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Won Gi Yoo
- Department of Parasitology and Tropical Medicine, College of Medicine, Gyeongsang National University, Jinju 52727, Gyeongnam, Republic of Korea;
| | - Yeung Bae Jin
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Wongi Min
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
| | - Woo H. Kim
- Institute of Animal Medicine, College of Veterinary Medicine, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea; (R.A.F.); (P.L.T.C.-F.); (B.T.N.); (A.G.M.V.); (S.Y.L.); (Y.S.); (K.I.P.); (Y.B.J.); (W.M.)
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Druzyaka AV, Druzyaka OR, Sharshov KA, Kasianov N, Dubovitskiy N, Derko AA, Frolov IG, Torniainen J, Wang W, Minina MA, Shestopalov AM. Stable Isotope Analysis Reveals Common Teal ( Anas crecca) Molting Sites in Western Siberia: Implications for Avian Influenza Virus Spread. Microorganisms 2024; 12:357. [PMID: 38399761 PMCID: PMC10891923 DOI: 10.3390/microorganisms12020357] [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: 12/26/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
The wetlands of southwestern Siberia (SWS) are a crossroads of bird migration routes, bringing avian influenza (AIV) strains that were previously isolated in different regions of the continent to Siberia. It is known that Anseriformes that breed in SWS migrate for the winter to central Hindustan or further west, while their migration routes to southeast Asia (SEA) remain unconfirmed. Here, we mapped the molting sites of the migrating Common Teals (Anas crecca) via analyzing stable hydrogen isotope content in feathers of hunters' prey and supplemented the analysis with the genetic structure of viruses isolated from teals in the same region. Post-breeding molt of autumn teals most likely occurred within the study region, whereas probable pre-breeding molting grounds of spring teals were in the south of Hindustan. This link was supported by viral phylogenetic analysis, which showed a close relationship between SWS isolates and viruses from south and southeast Asia. Most viral segments have the highest genetic similarity and the closest phylogenetic relationships with viruses from teal wintering areas in southeast Asian countries, including India and Korea. We assume that the winter molt of SWS breeding teals on the Hindustan coast suggests contacts with the local avifauna, including species migrating along the coast to SEA. Perhaps this is one of the vectors of AIV transmission within Eurasia.
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Affiliation(s)
- Alexey V. Druzyaka
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
| | - Olga R. Druzyaka
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Kirill A. Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Nikita Kasianov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Anastasiya A. Derko
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
| | - Ivan G. Frolov
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str. 2, 630090 Novosibirsk, Russia
- Institute of Zoology, Ministry of Science and Higher Education of the Republic of Kazakhstan, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan
| | - Jyrki Torniainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
- Open Science Centre, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China;
| | - Mariya A. Minina
- Institute of Systematic and Ecology of Animals, Frunze Str. 11, 630091 Novosibirsk, Russia; (O.R.D.); (I.G.F.); (M.A.M.)
| | - Alexander M. Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630060 Novosibirsk, Russia; (K.A.S.); (N.D.); (A.A.D.); (A.M.S.)
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Yu J, Yao Q, Liu J, Zhou Y, Huo M, Ge Y. Concern regarding H3-subtype avian influenza virus. Front Microbiol 2023; 14:1327470. [PMID: 38143863 PMCID: PMC10740181 DOI: 10.3389/fmicb.2023.1327470] [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: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023] Open
Abstract
The H3-subtype of avian influenza virus (AIV) is one of the most frequently detected low pathogenic avian influenza virus (LPAIV) subtypes in birds and fowls, causing substantial economic loss to the poultry industry. Most importantly, besides poultry, mammals could also be infected with it, such as swines, canines, equines, felines, and humans, posing a serious public health threat. This allows the virus to persist widely in poultry and wild birds for a long time, where it may mix with other subtypes, providing conditions for viral recombination or reassortment. Currently, the monitoring of H3-subtype AIV is inadequate, and there is a lack of effective prevention and control measures for H3-subtype AIV. Here, the epidemiology, phylogeny, and genetic variation of H3-subtype AIV were analyzed, and nonsynonymous and synonymous substitution rates (dN/dS) were calculated. Through these steps, we aimed to clarify the current epidemiological feature and evolutionary characteristics of H3-subtype AIV, and provide an operative reference for future scientific control of H3-subtype AIV.
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Pantin-Jackwood MJ, Spackman E, Leyson C, Youk S, Lee SA, Moon LM, Torchetti MK, Killian ML, Lenoch JB, Kapczynski DR, Swayne DE, Suarez DL. Pathogenicity in Chickens and Turkeys of a 2021 United States H5N1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared to Two Previous H5N8 Clade 2.3.4.4 Viruses. Viruses 2023; 15:2273. [PMID: 38005949 PMCID: PMC10674317 DOI: 10.3390/v15112273] [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: 10/20/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (U.S.) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early U.S. H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the U.S. (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and turkeys. The mean bird infective dose (BID50) of the 2021 H5N1 virus was approximately 2.6 log10 50% embryo infective dose (EID50) in chickens and 2.2 log10 EID50 in turkeys, and the virus transmitted to contact-exposed turkeys but not chickens. The BID50 for the 2016 H5N8 virus was also slightly different in chickens and turkeys (4.2 and 4.7 log10 EID50, respectively); however, the BID50 for the 2014 H5N8 virus was higher for chickens than turkeys (3.9 and ~0.9 log10 EID50, respectively). With all viruses, turkeys took longer to die (MDTs of 2.6-8.2 days for turkeys and 1-4 days for chickens), which increased the virus shedding period and facilitated transmission to contacts.
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Affiliation(s)
- Mary J. Pantin-Jackwood
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Christina Leyson
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Sungsu Youk
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
- Department of Medicine, College of Medicine, Chungbuk National University, Cheongju-si 28644, Chungbuk, Republic of Korea
| | - Scott A. Lee
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Linda M. Moon
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - Mia K. Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Mary L. Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Ames, IA 50010, USA
| | - Julianna B. Lenoch
- Wildlife Services, National Wildlife Disease Program, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, CO 80521, USA
| | - Darrell R. Kapczynski
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David E. Swayne
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
| | - David L. Suarez
- Exotic and Emerging Avian Viral Diseases Unit, Southeast Poultry Research Laboratory, U.S. National Poultry Research Center, Agricultural Research Service, U.S. Department of Agriculture, Athens, GA 30605, USA; (E.S.); (L.M.M.); (D.L.S.)
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Chauhan RP, Fogel R, Limson J. Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa. Microorganisms 2023; 11:2802. [PMID: 38004813 PMCID: PMC10672864 DOI: 10.3390/microorganisms11112802] [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: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
White spot syndrome virus is a highly contagious pathogen affecting shrimp farming worldwide. The host range of this virus is primarily limited to crustaceans, such as shrimps, crabs, prawns, crayfish, and lobsters; however, several species of non-crustaceans, including aquatic insects, piscivorous birds, and molluscs may serve as the vectors for ecological dissemination. The present study was aimed at studying the faecal virome of domestic chickens (Gallus gallus domesticus) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (n = 35) were collected from domestic chickens in December 2022. The cloacal swab specimens were pooled-each pool containing five cloacal swabs-for metagenomic analysis using a sequence-independent single-primer amplification protocol, followed by Nanopore MinION sequencing. While the metagenomic sequencing generated several contigs aligning with reference genomes of animal viruses, one striking observation was the presence of a White spot syndrome virus genome in one pool of cloacal swab specimens. The generated White spot syndrome virus genome was 273,795 bp in size with 88.5% genome coverage and shared 99.94% nucleotide sequence identity with a reference genome reported in China during 2018 (GenBank accession: NC_003225.3). The Neighbour-Joining tree grouped South African White spot syndrome virus genome with other White spot syndrome virus genomes reported from South East Asia. To our knowledge, this is the first report of a White spot syndrome virus genome generated from domestic chickens. The significance of White spot syndrome virus infection in domestic chickens is yet to be determined.
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Affiliation(s)
| | | | - Janice Limson
- Biotechnology Innovation Centre, Rhodes University, Makhanda 6139, Eastern Cape, South Africa; (R.P.C.); (R.F.)
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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: 2] [Impact Index Per Article: 1.0] [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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Youk S, Torchetti MK, Lantz K, Lenoch JB, Killian ML, Leyson C, Bevins SN, Dilione K, Ip HS, Stallknecht DE, Poulson RL, Suarez DL, Swayne DE, Pantin-Jackwood MJ. H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021-April 2022. Virology 2023; 587:109860. [PMID: 37572517 DOI: 10.1016/j.virol.2023.109860] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American wild bird avian influenza viruses. Reassortments of up to five internal genes generated a total of 21 distinct clusters; of these, six genotypes represented 92% of the HPAIVs examined. By phylodynamic analyses, most detections in domestic birds were shown to be point-source transmissions from wild birds, with limited farm-to-farm spread.
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Affiliation(s)
- Sungsu Youk
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA; Microbiology Laboratory, Department of Medicine, College of Medicine, Chungbuk National University, Chungbuk, South Korea
| | - Mia Kim Torchetti
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Kristina Lantz
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Julianna B Lenoch
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Mary Lea Killian
- National Veterinary Services Laboratories, Animal and Plant Health Inspection Service, USDA, Ames, IA, USA
| | - Christina Leyson
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Sarah N Bevins
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Krista Dilione
- Wildlife Services National Wildlife Disease Program, Animal and Plant Health Inspections Service, USDA, Fort Collins, CO, USA
| | - Hon S Ip
- United States Geological Survey, National Wildlife Health Center, Laboratory Services Branch, Madison, WI, USA
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - David L Suarez
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - David E Swayne
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA
| | - Mary J Pantin-Jackwood
- Southeast Poultry Research Laboratory, U.S. National Poultry Research Laboratory, Agricultural Research Service, USDA, Athens, GA, USA.
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Malmberg JL, Miller M, Jennings-Gaines J, Allen SE. Mortality in Wild Turkeys (Meleagris gallopavo) Associated with Natural Infection with H5N1 Highly Pathogenic Avian Influenza Virus (HPAIV) Subclade 2.3.4.4. J Wildl Dis 2023; 59:767-773. [PMID: 37486883 DOI: 10.7589/jwd-d-22-00161] [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: 10/25/2022] [Accepted: 03/27/2023] [Indexed: 07/26/2023]
Abstract
A Eurasian strain of H5N1 highly pathogenic avian influenza virus (HPAIV) was first detected in North America in December 2021 and has since been confirmed in numerous wild and domestic avian species. In April 2022, 41 Wild Turkeys (Meleagris gallopavo) were found dead in Johnson County, Wyoming, USA adjacent to a property with confirmed HPAIV in a backyard poultry flock. Oropharyngeal swabs were collected from 11 of the 41 turkeys and necropsy was performed on seven. Avian influenza virus RNA was detected in all 11 turkeys by real-time reverse-transcription PCR. Acute, multiorgan necrosis was observed grossly and identified in all seven turkeys evaluated by histopathology, most consistently in the lung, spleen, liver, gastrointestinal tract, and gonads. Lesions indicate high virulence of subclade 2.3.4.4b H5N1 HPAIV in Wild Turkeys, with infections presenting as clusters of acute mortality. Although documented cases of HPAIV in Wild Turkeys are rare, these findings signify a risk of spillback from domestic poultry, which may be heightened by the recent rise in backyard poultry ownership and the use of peridomestic habitat by wild birds. Additional research is needed to better understand the risk of disease transmission at the interface of Wild Turkeys and backyard poultry and the potential conservation and management implications of HPAIV in wild gallinaceous birds.
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Affiliation(s)
- Jennifer L Malmberg
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Wyoming State Veterinary Laboratory, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Current affiliation and address: National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, US Department of Agriculture, 4101 LaPorte Avenue, Fort Collins, Colorado 80521, USA
| | - Myrna Miller
- Department of Veterinary Sciences, University of Wyoming, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
- Wyoming State Veterinary Laboratory, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
| | - Jessica Jennings-Gaines
- Veterinary Services, Wildlife Health Laboratory, Wyoming Game and Fish Department, 1174 Snowy Range Road, Laramie, Wyoming 82070, USA
| | - Samantha E Allen
- Veterinary Services, Wyoming Game and Fish Department, 1212 South Adams Street, Laramie, Wyoming 82070, USA
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Petherbridge G, Gadzhiev AA, Shestopalov АМ, Alekseev AY, Sharshov KA, Daudova MG. An early warning system for highly pathogenic viruses borne by waterbird species and related dynamics of climate change in the Caspian Sea region: Outlines of a concept. SOUTH OF RUSSIA: ECOLOGY, DEVELOPMENT 2022. [DOI: 10.18470/1992-1098-2022-2-233-263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aim. Formulation of the outlines of the concept of ViEW (Viral Early Warning) which is intended as a long term system of multidisciplinary transboundary cooperation between specialist institutions of all five Caspian region states to research, regularly monitor and share data about the generation, transmission and epidemiology of avian‐borne pathogens and their vectors in the region, and the ways climate change may affect these processes.Material and Methods. The concept is based on the multidisciplinary experience of the authors in researching the processes incorporated in the ViEW concept and on an in‐depth survey of the literature involved.Results. The outlines of the ViEW concept are presented in this study for review and comment by interested parties and stakeholders.Conclusion. Review of activities and opinions of specialists and organizations with remits relating to the development, establishment and maintenance of ViEW, indicates that such a system is a necessity for global animal and human health because of the role that the Caspian region plays in the mass migration of species of waterbird known as vectors for avian influenza and the already evident impacts of climate change on their phenologies. Waterbirds frequenting the Caspian Sea littorals and their habitats together constitute a major potential global hotspot or High Risk region for the generation and transmission of highly pathogenic avian influenza viruses and other dangerous zoonotic diseases.
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Affiliation(s)
| | | | - А. М. Shestopalov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - A. Yu. Alekseev
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
| | - K. A. Sharshov
- Research Institute of Virology, Federal Research Centre of Fundamental and Translational Medicine, Siberian Branch, Russian Academy of Sciences
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12
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Gass JD, Kellogg HK, Hill NJ, Puryear WB, Nutter FB, Runstadler JA. Epidemiology and Ecology of Influenza A Viruses among Wildlife in the Arctic. Viruses 2022; 14:1531. [PMID: 35891510 PMCID: PMC9315492 DOI: 10.3390/v14071531] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/10/2022] [Indexed: 02/01/2023] Open
Abstract
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host-pathogen-environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
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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; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Hunter K. Kellogg
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Nichola J. Hill
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA;
| | - Wendy B. Puryear
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (H.K.K.); (W.B.P.); (F.B.N.); (J.A.R.)
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Mine J, Tsunekuni R, Tanikawa T, Uchida Y, Dubovitskiy N, Derko A, Sobolev I, Shestopalov A, Sharshov K, Saito T. Genetics of Japanese H5N8 high pathogenicity avian influenza viruses isolated in winter 2020-2021 and their genetic relationship with avian influenza viruses in Siberia. Transbound Emerg Dis 2022; 69:e2195-e2213. [PMID: 35445801 DOI: 10.1111/tbed.14559] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022]
Abstract
In winter 2020-2021, Japan experienced multiple serious outbreaks of H5N8 high pathogenicity avian influenza (HPAI)-52 outbreaks at poultry farms and 58 cases in wild birds or the environment-that occurred simultaneously with outbreaks in Europe. Here, we examined how the H5N8 HPAI viruses (HPAIVs) emerged and spread through Japan and across the Eurasian continent. Phylogenetic and phylogeographic analyses were performed using full genetic sequences of the viruses that caused 52 outbreaks at poultry farms or were isolated from 11 infected wild birds. Genetically, the viruses showed five genotypes (E1, E2, E3, E5, E7) that have already been reported in Korea. The viruses showing the E3 genotype were found to have caused most of the HPAI outbreaks at poultry farms and were detected over the longest period of time. The internal genes of the viruses were genetically related to those of AIVs isolated through avian influenza surveillance activities in regions of Siberia including Buryatia, Yakutia, and Amur regions, suggesting that the Japanese viruses emerged via reassortment events with AIVs genetically related to Siberian AIVs. In addition, H5N2 and H5N8 HPAIVs were isolated from wild birds during surveillance activities conducted in the Novosibirsk region of Siberia in summer 2020. Phylogenetic analyses revealed that these viruses possessed hemagglutinin genes that were related to those of H5N8 HPAIVs that were circulating in Europe in winter 2020-2021. These results suggest that the viruses in wild birds during summer in Siberia most likely spread in both Asia and Europe the following winter. Together, the present results emphasize the importance of continual monitoring of AIVs in Siberia for forecasting outbreaks not only in Asia but also further away in Europe. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Junki Mine
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Ryota Tsunekuni
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Taichiro Tanikawa
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Yuko Uchida
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Anastasiya Derko
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Ivan Sobolev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Takehiko Saito
- National Institute of Animal Health, National Agriculture and Food Research Organization, 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan.,United Graduate School of Veterinary Sciences, Gifu University, 1-1, Yanagito, Gifu, 501-1112, Japan
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Isolation and Identification of a Highly Pathogenic Avian Influenza H5N6 Virus from Migratory Waterfowl in Western Mongolia. J Wildl Dis 2021; 58:211-214. [PMID: 34699593 DOI: 10.7589/jwd-d-21-00032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/25/2021] [Indexed: 11/20/2022]
Abstract
In April 2020, two Whooper Swans (Cygnus cygnus) and one Swan Goose (Anser cygnoides) were found dead at three different locations in western Mongolia. Virus isolation from organs taken from the carcasses and full genome sequencing revealed that all three birds were positive for highly pathogenic H5N6 avian influenza virus (HPAIV) belonging to subclade 2.3.4.4h. Confirming similar reports from central Mongolia and western China, these findings have important implications for the monitoring, control, and management of HPAIVs in wild bird and commercial poultry populations in Mongolia.
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Deciphering transmission dynamics and spillover of avian influenza viruses from avian species to swine populations globally. Virus Genes 2021; 57:541-555. [PMID: 34625868 PMCID: PMC8500266 DOI: 10.1007/s11262-021-01873-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/26/2021] [Indexed: 12/21/2022]
Abstract
Genome sequences of eleven avian influenza virus (AIV) subtypes have been reported in swine populations from seven countries until August 2020. To unravel the transmission dynamics and spillover events of AIVs from avian reservoirs to swine, full-length hemagglutinin (HA) sequences of AIV subtypes (n = 11) reported from various avian species and swine were retrieved from the ‘Influenza Research Database’. Phylogenetic analysis identified closely related avian and swine AIV sequences suggesting potential spillover events from multiple domestic and wild avian species, including chicken, duck, pigeon, goose, quail, and aquatic birds to swine. Furthermore, N-linked glycosylation analysis of these closely related AIV sequences supported the possibility of multiple spillover events of highly pathogenic H5N1 and low pathogenic H9N2 viruses from various avian species to swine. The principal coordinate analysis further validated these findings for H5N1 and H9N2 viruses; however, spillover events of the other nine AIV subtypes were limited. Interestingly, the presence of potential mammalian adaptation markers, particularly in some of the swine H5N1, H7N9, and H9N2 viruses, suggested that these viruses may have already adapted in swine. The occurrence and circulation of these AIVs in swine, especially the H5N1 and H9N2 viruses with numerous spillover events from the avian reservoirs to swine, pose a significant threat in terms of their reassortment with endemic swine viruses or circulating human influenza viruses within the swine which may facilitate the emergence of a novel influenza virus strain with pandemic potential.
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Multiple Gene Segments Are Associated with Enhanced Virulence of Clade 2.3.4.4 H5N8 Highly Pathogenic Avian Influenza Virus in Mallards. J Virol 2021; 95:e0095521. [PMID: 34232725 DOI: 10.1128/jvi.00955-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Highly pathogenic avian influenza (HPAI) viruses from the H5Nx Goose/Guangdong/96 lineage continue to cause outbreaks in domestic and wild bird populations. Two distinct genetic groups of H5N8 HPAI viruses, hemagglutinin (HA) clades 2.3.4.4A and 2.3.4.4B, caused intercontinental outbreaks in 2014 to 2015 and 2016 to 2017, respectively. Experimental infections using viruses from these outbreaks demonstrated a marked difference in virulence in mallards, with the H5N8 virus from 2014 causing mild clinical disease and the 2016 H5N8 virus causing high mortality. To assess which gene segments are associated with enhanced virulence of H5N8 HPAI viruses in mallards, we generated reassortant viruses with 2014 and 2016 viruses. For single-segment reassortants in the genetic backbone of the 2016 virus, pathogenesis experiments in mallards revealed that morbidity and mortality were reduced for all eight single-segment reassortants compared to the parental 2016 virus, with significant reductions in mortality observed with the polymerase basic protein 2 (PB2), nucleoprotein (NP), and matrix (M) reassortants. No differences in morbidity and mortality were observed with reassortants that either have the polymerase complex segments or the HA and neuraminidase (NA) segments of the 2016 virus in the genetic backbone of the 2014 virus. In vitro assays showed that the NP and polymerase acidic (PA) segments of the 2014 virus lowered polymerase activity when combined with the polymerase complex segments of the 2016 virus. Furthermore, the M segment of the 2016 H5N8 virus was linked to filamentous virion morphology. Phylogenetic analyses demonstrated that gene segments related to the more virulent 2016 H5N8 virus have persisted in the contemporary H5Nx HPAI gene pool until 2020. IMPORTANCE Outbreaks of H5Nx HPAI viruses from the goose/Guangdong/96 lineage continue to occur in many countries and have resulted in substantial impact on wild birds and poultry. Epidemiological evidence has shown that wild waterfowl play a major role in the spread of these viruses. While HPAI virus infection in gallinaceous species causes high mortality, a wide range of disease outcomes has been observed in waterfowl species. In this study, we examined which gene segments contribute to severe disease in mallards infected with H5N8 HPAI viruses. No virus gene was solely responsible for attenuating the high virulence of a 2016 H5N8 virus, but the PB2, NP, and M segments significantly reduced mortality. The findings herein advance our knowledge on the pathobiology of avian influenza viruses in waterfowl and have potential implications on the ecology and epidemiology of H5Nx HPAI in wild bird populations.
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Hirschinger J, Vergne T, Corre T, Hingrat Y, Guerin JL, Le Loc'h G. Exposure assessment for avian influenza and Newcastle disease viruses from peridomestic wild birds in a conservation breeding site in the United Arab Emirates. Transbound Emerg Dis 2021; 69:2361-2372. [PMID: 34333870 DOI: 10.1111/tbed.14253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 02/16/2021] [Accepted: 07/20/2021] [Indexed: 11/29/2022]
Abstract
Worldwide, wild birds are frequently suspected to be involved in the occurrence of outbreaks of different diseases in captive-bred birds although proofs are lacking and most of the dedicated studies are insufficiently conclusive to confirm or characterize the roles of wild birds in such outbreaks. The aim of this study was to assess and compare, for the most abundant peridomestic wild birds, the different exposure routes for avian influenza and Newcastle disease viruses in conservation breeding sites of Houbara bustards in the United Arab Emirates. To do so, we considered all of the potential pathways by which captive bustards could be exposed to avian influenza and Newcastle disease viruses by wild birds, and ran a comparative study of the likelihood of exposure via each of the pathways considered. We merged data from an ecological study dedicated to local wild bird communities with an analysis of the contacts between wild birds and captive bustards and with a prevalence survey of avian influenza and Newcastle disease viruses in wild bird populations. We also extracted data from an extensive review of the scientific literature and by the elicitation of expert opinion. Overall, this analysis highlighted those captive bustards had a high risk of being exposed to pathogens by wild birds. This risk was higher for Newcastle disease virus than avian influenza virus, and House sparrows represented the riskiest species for the transmission of both viruses through direct exposure from direct contact with an infectious bird that got inside the aviary and indirect exposure from consumption of water contaminated from the faeces of an infected bird that got inside the aviary for Newcastle disease virus and avian influenza virus, respectively. These results also reaffirm the need to implement biosecurity measures to limit contacts between wild and captive birds and highlight priority targets for a thoughtful and efficient sanitary management strategy.
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Affiliation(s)
- Julien Hirschinger
- Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Hôtes Agents Pathogènes, Toulouse, France.,Reneco International Wildlife Consultants LLC, Abu Dhabi, United Arab Emirates
| | - Timothée Vergne
- Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Hôtes Agents Pathogènes, Toulouse, France
| | - Tifenn Corre
- INRAE, US-ODR 0685, Observatoire du Développement Rural, Centre Occitanie-Toulouse, Castanet Tolosan, France
| | - Yves Hingrat
- Reneco International Wildlife Consultants LLC, Abu Dhabi, United Arab Emirates
| | - Jean Luc Guerin
- Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Hôtes Agents Pathogènes, Toulouse, France
| | - Guillaume Le Loc'h
- Université de Toulouse, Ecole Nationale Vétérinaire de Toulouse, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Unité Mixte de Recherche Interactions Hôtes Agents Pathogènes, Toulouse, France
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18
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Liang Y, Krog JS, Ryt-Hansen P, Pedersen AG, Kvisgaard LK, Holm E, Nielsen PD, Hammer AS, Madsen JJ, Thorup K, Larsen LE, Hjulsager CK. Molecular Characterization of Highly Pathogenic Avian Influenza Viruses H5N6 Detected in Denmark in 2018-2019. Viruses 2021; 13:1052. [PMID: 34199456 PMCID: PMC8226499 DOI: 10.3390/v13061052] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
Beginning in late 2017, highly pathogenic avian influenza (HPAI) H5N6 viruses caused outbreaks in wild birds and poultry in several European countries. H5N6 viruses were detected in 43 wild birds found dead throughout Denmark. Most of the Danish virus-positive dead birds were found in the period from February to April 2018. However, unlike the rest of Europe, sporadic HPAI H5N6-positive dead wild birds were detected in Denmark in July, August, September, and December 2018, with the last positive bird being found in January 2019. HPAI viruses were not detected in active surveillance of apparently healthy wild birds. In this study, we use full genome sequencing and phylogenetic analysis to investigate the wild bird HPAI H5N6 viruses found in Denmark. The Danish viruses were found to be closely related to those of contemporary HPAI H5N6 viruses detected in Europe. Their sequences formed two clusters indicating that at least two or more introductions of H5N6 into Denmark occurred. Notably, all viruses detected in the latter half of 2018 and in 2019 grouped into the same cluster. The H5N6 viruses appeared to have been maintained undetected in the autumn 2018.
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Affiliation(s)
- Yuan Liang
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (P.R.-H.); (L.K.K.); (A.S.H.); (L.E.L.)
| | - Jesper Schak Krog
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.S.K.); (E.H.)
| | - Pia Ryt-Hansen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (P.R.-H.); (L.K.K.); (A.S.H.); (L.E.L.)
| | - Anders Gorm Pedersen
- DTU Health Tech, Bioinformatics, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark;
| | - Lise Kirstine Kvisgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (P.R.-H.); (L.K.K.); (A.S.H.); (L.E.L.)
| | - Elisabeth Holm
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.S.K.); (E.H.)
| | - Pernille Dahl Nielsen
- Animal Health Division, Danish Veterinary and Food Administration, 2600 Glostrup, Denmark;
| | - Anne Sofie Hammer
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (P.R.-H.); (L.K.K.); (A.S.H.); (L.E.L.)
| | | | - Kasper Thorup
- GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark;
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (Y.L.); (P.R.-H.); (L.K.K.); (A.S.H.); (L.E.L.)
| | - Charlotte Kristiane Hjulsager
- Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark; (J.S.K.); (E.H.)
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19
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Velkers FC, Manders TTM, Vernooij JCM, Stahl J, Slaterus R, Stegeman JA. Association of wild bird densities around poultry farms with the risk of highly pathogenic avian influenza virus subtype H5N8 outbreaks in the Netherlands, 2016. Transbound Emerg Dis 2020; 68:76-87. [PMID: 32419342 PMCID: PMC8048466 DOI: 10.1111/tbed.13595] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 03/10/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Highly pathogenic (HP) avian influenza viruses (AIV) can spread globally through migratory birds and cause massive outbreaks in commercial poultry. AIV outbreaks have been associated with proximity to waterbodies, presence of waterfowl or wild bird cases near poultry farms. In this study, we compared densities of selected HPAI high‐risk wild bird species around 7 locations (H farms) infected with HPAIV H5N8 in the Netherlands in 2016–2017 to densities around 21 non‐infected reference farms. Nine reference farms were in low‐lying water‐rich areas (R‐W) and 12 in higher non‐water‐rich areas (R‐NW). Average monthly numbers/km2 of Eurasian wigeons, tufted ducks, Anatidae (ducks, geese and swans) and Laridae (gulls) were calculated between September and April in rings of 0–1, 1–3, 3–6 and 6–10 km around the farms. Linear mixed model analyses showed generally higher bird densities for H and R‐W compared to R‐NW farms between October and March. This was most striking for Eurasian wigeons, with in peak month December 105 (95% CI:17–642) and 40 (7–214) times higher densities around H and R‐W farms, respectively, compared to R‐NW farms. Increased densities around H farms for Eurasian wigeons and Anatidae were more pronounced for distances up to 10 km compared to 0–1 km that mostly consists of the farm yard, which is an unattractive habitat for waterfowl. This distance effect was not observed in gulls, nor in tufted ducks that live on large open waterbodies which are unlikely to be within 0–1 km of farms. This study provides insights into spatio‐temporal density dynamics of HPAI high‐risk birds around farms and their associations with poultry outbreaks. The outcomes indicate that knowledge of environmental and ecological drivers for wild bird presence and abundance may facilitate identification of priority areas for surveillance and biosecurity measures and decisions on establishments of poultry farms to reduce risk of HPAI outbreaks.
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Affiliation(s)
- Francisca C Velkers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Thijs T M Manders
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Johannes C M Vernooij
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Julia Stahl
- Sovon, Dutch Center for Field Ornithology, Nijmegen, The Netherlands
| | - Roy Slaterus
- Sovon, Dutch Center for Field Ornithology, Nijmegen, The Netherlands
| | - J Arjan Stegeman
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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20
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Sharshov K, Mine J, Sobolev I, Kurskaya O, Dubovitskiy N, Kabilov M, Alikina T, Nakayama M, Tsunekuni R, Derko A, Prokopyeva E, Alekseev A, Shchelkanov M, Druzyaka A, Gadzhiev A, Uchida Y, Shestopalov A, Saito T. Characterization and Phylodynamics of Reassortant H12Nx Viruses in Northern Eurasia. Microorganisms 2019; 7:microorganisms7120643. [PMID: 31816947 PMCID: PMC6956379 DOI: 10.3390/microorganisms7120643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/19/2019] [Accepted: 11/30/2019] [Indexed: 11/16/2022] Open
Abstract
Wild waterfowl birds are known to be the main reservoir for a variety of avian influenza viruses of different subtypes. Some subtypes, such as H2Nx, H8Nx, H12Nx, and H14Nx, occur relatively rarely in nature. During 10-year long-term surveillance, we isolated five rare H12N5 and one H12N2 viruses in three different distinct geographic regions of Northern Eurasia and studied their characteristics. H12N2 from the Far East region was a double reassortant containing hemagglutinin (HA), non-structural (NS) and nucleoprotein (NP) segments of the American lineage and others from the classical Eurasian avian-like lineage. H12N5 viruses contain Eurasian lineage segments. We suggest a phylogeographical scheme for reassortment events associated with geographical groups of aquatic birds and their migration flyways. The H12N2 virus is of particular interest as this subtype has been found in common teal in the Russian Far East region, and it has a strong relation to North American avian influenza virus lineages, clearly showing that viral exchange of segments between the two continents does occur. Our results emphasize the importance of Avian Influenza Virus (AIV) surveillance in Northern Eurasia for the annual screening of virus characteristics, including the genetic constellation of rare virus subtypes, to understand the evolutionary ecology of AIV.
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Affiliation(s)
- Kirill Sharshov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
- Correspondence: ; Tel.: +7-960-794-2136; Fax: +7-383-333-6456
| | - Junki Mine
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ivan Sobolev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Olga Kurskaya
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Nikita Dubovitskiy
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Marsel Kabilov
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Tatiana Alikina
- Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia; (M.K.); (T.A.)
| | - Momoko Nakayama
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Ryota Tsunekuni
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Anastasiya Derko
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Elena Prokopyeva
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Alexander Alekseev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Michael Shchelkanov
- School of Biomedicine, Far Eastern Federal University, 690091 Vladivostok, Russia;
- Laboratory of Virology, Federal Scientific Center of East Asia Terrestrial Biodiversity, 690022 Vladivostok, Russia
- Laboratory of marine microbiota, National Scientific Center o Marine Biology, 690041 Vladivostok, Russia
| | - Alexey Druzyaka
- Laboratory of behavioral ecology, Institute of Animal Systematics and Ecology, 630091 Novosibirsk, Russia;
| | - Alimurad Gadzhiev
- Department of Ecology, Dagestan State University, 367000 Makhachkala, Russia;
| | - Yuko Uchida
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
| | - Alexander Shestopalov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, 630117 Novosibirsk, Russia; (I.S.); (O.K.); (N.D.); (E.P.); (A.A.); (A.S.)
| | - Takehiko Saito
- Division of Transboundary Animal Disease, National Institute of Animal Health, Tsukuba, Ibaraki 305-0856, Japan; (J.M.); (M.N.); (R.T.); (Y.U.); (T.S.)
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