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King J, Pohlmann A, Bange A, Horn E, Hälterlein B, Breithaupt A, Globig A, Günther A, Kelm A, Wiedemann C, Grund C, Haecker K, Garthe S, Harder T, Beer M, Schwemmer P. Red knots in Europe: a dead end host species or a new niche for highly pathogenic avian influenza? J Gen Virol 2024; 105:002003. [PMID: 38975739 PMCID: PMC11316594 DOI: 10.1099/jgv.0.002003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/09/2024] Open
Abstract
The 2020/2021 epidemic in Europe of highly pathogenic avian influenza virus (HPAIV) of subtype H5 surpassed all previously recorded European outbreaks in size, genotype constellations and reassortment frequency and continued into 2022 and 2023. The causative 2.3.4.4b viral lineage proved to be highly proficient with respect to reassortment with cocirculating low pathogenic avian influenza viruses and seems to establish an endemic status in northern Europe. A specific HPAIV reassortant of the subtype H5N3 was detected almost exclusively in red knots (Calidris canutus islandica) in December 2020. It caused systemic and rapidly fatal disease leading to a singular and self-limiting mass mortality affecting about 3500 birds in the German Wadden Sea, roughly 1 % of the entire flyway population of islandica red knots. Phylogenetic analyses revealed that the H5N3 reassortant very likely had formed in red knots and remained confined to this species. While mechanisms of virus circulation in potential reservoir species, dynamics of spill-over and reassortment events and the roles of environmental virus sources remain to be identified, the year-round infection pressure poses severe threats to endangered avian species and prompts adaptation of habitat and species conservation practices.
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Affiliation(s)
- Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Andreas Bange
- Research and Technology Centre (FTZ), University of Kiel, Hafentörn 1, 25761 Büsum, Germany
| | - Elisabeth Horn
- Research and Technology Centre (FTZ), University of Kiel, Hafentörn 1, 25761 Büsum, Germany
| | - Bernd Hälterlein
- National Park Authority Schleswig-Holstein Wadden Sea, Schlossgarten 1, 25832 Tönning, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Anja Globig
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Anne Günther
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Angie Kelm
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Christian Wiedemann
- National Park Authority Schleswig-Holstein Wadden Sea, Schlossgarten 1, 25832 Tönning, Germany
| | - Christian Grund
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Karena Haecker
- Research and Technology Centre (FTZ), University of Kiel, Hafentörn 1, 25761 Büsum, Germany
| | - Stefan Garthe
- Research and Technology Centre (FTZ), University of Kiel, Hafentörn 1, 25761 Büsum, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald – Insel Riems, Germany
| | - Philipp Schwemmer
- Research and Technology Centre (FTZ), University of Kiel, Hafentörn 1, 25761 Büsum, Germany
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Graziosi G, Lupini C, Catelli E, Carnaccini S. Highly Pathogenic Avian Influenza (HPAI) H5 Clade 2.3.4.4b Virus Infection in Birds and Mammals. Animals (Basel) 2024; 14:1372. [PMID: 38731377 PMCID: PMC11083745 DOI: 10.3390/ani14091372] [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: 04/02/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Avian influenza viruses (AIVs) are highly contagious respiratory viruses of birds, leading to significant morbidity and mortality globally and causing substantial economic losses to the poultry industry and agriculture. Since their first isolation in 2013-2014, the Asian-origin H5 highly pathogenic avian influenza viruses (HPAI) of clade 2.3.4.4b have undergone unprecedented evolution and reassortment of internal gene segments. In just a few years, it supplanted other AIV clades, and now it is widespread in the wild migratory waterfowl, spreading to Asia, Europe, Africa, and the Americas. Wild waterfowl, the natural reservoir of LPAIVs and generally more resistant to the disease, also manifested high morbidity and mortality with HPAIV clade 2.3.4.4b. This clade also caused overt clinical signs and mass mortality in a variety of avian and mammalian species never reported before, such as raptors, seabirds, sealions, foxes, and others. Most notably, the recent outbreaks in dairy cattle were associated with the emergence of a few critical mutations related to mammalian adaptation, raising concerns about the possibility of jumping species and acquisition of sustained human-to-human transmission. The main clinical signs and anatomopathological findings associated with clade 2.3.4.4b virus infection in birds and non-human mammals are hereby summarized.
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Affiliation(s)
- Giulia Graziosi
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Caterina Lupini
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Elena Catelli
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell’Emilia, 40064 Bologna, Italy; (G.G.); (C.L.); (E.C.)
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
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3
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Zeng J, Du F, Xiao L, Sun H, Lu L, Lei W, Zheng J, Wang L, Shu S, Li Y, Zhang Q, Tang K, Sun Q, Zhang C, Long H, Qiu Z, Zhai K, Li Z, Zhang G, Sun Y, Wang D, Zhang Z, Lycett SJ, Gao GF, Shu Y, Liu J, Du X, Pu J. Spatiotemporal genotype replacement of H5N8 avian influenza viruses contributed to H5N1 emergence in 2021/2022 panzootic. J Virol 2024; 98:e0140123. [PMID: 38358287 PMCID: PMC10949427 DOI: 10.1128/jvi.01401-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Since 2020, clade 2.3.4.4b highly pathogenic avian influenza H5N8 and H5N1 viruses have swept through continents, posing serious threats to the world. Through comprehensive analyses of epidemiological, genetic, and bird migration data, we found that the dominant genotype replacement of the H5N8 viruses in 2020 contributed to the H5N1 outbreak in the 2021/2022 wave. The 2020 outbreak of the H5N8 G1 genotype instead of the G0 genotype produced reassortment opportunities and led to the emergence of a new H5N1 virus with G1's HA and MP genes. Despite extensive reassortments in the 2021/2022 wave, the H5N1 virus retained the HA and MP genes, causing a significant outbreak in Europe and North America. Furtherly, through the wild bird migration flyways investigation, we found that the temporal-spatial coincidence between the outbreak of the H5N8 G1 virus and the bird autumn migration may have expanded the H5 viral spread, which may be one of the main drivers of the emergence of the 2020-2022 H5 panzootic.IMPORTANCESince 2020, highly pathogenic avian influenza (HPAI) H5 subtype variants of clade 2.3.4.4b have spread across continents, posing unprecedented threats globally. However, the factors promoting the genesis and spread of H5 HPAI viruses remain unclear. Here, we found that the spatiotemporal genotype replacement of H5N8 HPAI viruses contributed to the emergence of the H5N1 variant that caused the 2021/2022 panzootic, and the viral evolution in poultry of Egypt and surrounding area and autumn bird migration from the Russia-Kazakhstan region to Europe are important drivers of the emergence of the 2020-2022 H5 panzootic. These findings provide important targets for early warning and could help control the current and future HPAI epidemics.
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Affiliation(s)
- Jinfeng Zeng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Fanshu Du
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Linna Xiao
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Honglei Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lu Lu
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Weipan Lei
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jialu Zheng
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Lu Wang
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Sicheng Shu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yudong Li
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiang Zhang
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Kang Tang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Qianru Sun
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Chi Zhang
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Haoyu Long
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zekai Qiu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Ke Zhai
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zhichao Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, China
| | - Geli Zhang
- College of Land Science and Technology, China Agricultural University, Beijing, China
| | - Yipeng Sun
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Dayan Wang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhengwang Zhang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Demonstration Center for Experimental Life Sciences & Biotechnology Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Samantha J. Lycett
- The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- National Health Commission Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology of Chinese Academy of Medical Science (CAMS)/Peking Union Medical College (PUMC), Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Juan Pu
- National Key Laboratory of Veterinary Public Health and Safety, Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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4
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Abolnik C, Phiri T, Peyrot B, de Beer R, Snyman A, Roberts D, Ludynia K, Jordaan F, Maartens M, Ismail Z, Strydom C, van der Zel G, Anthony J, Daniell N, De Boni L, Grewar J, Olivier A, Roberts L. The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021-2022. Viruses 2023; 15:1383. [PMID: 37376682 DOI: 10.3390/v15061383] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
In southern Africa, clade 2.3.4.4B H5N1 high pathogenicity avian influenza (HPAI) was first detected in South African (SA) poultry in April 2021, followed by outbreaks in poultry or wild birds in Lesotho and Botswana. In this study, the complete or partial genomes of 117 viruses from the SA outbreaks in 2021-2022 were analyzed to decipher the sub-regional spread of the disease. Our analysis showed that seven H5N1 sub-genotypes were associated with the initial outbreaks, but by late 2022 only two sub-genotypes still circulated. Furthermore, SA poultry was not the source of Lesotho's outbreaks, and the latter was most likely an introduction from wild birds. Similarly, SA and Botswana's outbreaks in 2021 were unrelated, but viruses of Botswana's unique sub-genotype were introduced into SA later in 2022 causing an outbreak in ostriches. At least 83% of SA's commercial poultry cases in 2021-2022 were point introductions from wild birds. Like H5N8 HPAI in 2017-2018, a coastal seabird-restricted sub-lineage of H5N1 viruses emerged in the Western Cape province in 2021 and spread to Namibia, causing mortalities in Cape Cormorants. In SA ~24,000 of this endangered species died, and the loss of >300 endangered African penguins further threatens biodiversity.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - Thandeka Phiri
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - Belinda Peyrot
- Provincial Veterinary Laboratory, Western Cape Department of Agriculture, Stellenbosch 7600, South Africa
| | - Renee de Beer
- Provincial Veterinary Laboratory, Western Cape Department of Agriculture, Stellenbosch 7600, South Africa
| | - Albert Snyman
- Southern African Foundation for the Conservation of Coastal Birds (SANCCOB), Cape Town 7441, South Africa
| | - David Roberts
- Southern African Foundation for the Conservation of Coastal Birds (SANCCOB), Cape Town 7441, South Africa
| | - Katrin Ludynia
- Southern African Foundation for the Conservation of Coastal Birds (SANCCOB), Cape Town 7441, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville 7535, South Africa
| | | | | | - Zehaad Ismail
- SMT Veterinary Laboratory, Irene, Pretoria 0178, South Africa
| | - Christine Strydom
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- SMT Veterinary Laboratory, Irene, Pretoria 0178, South Africa
| | - Gerbrand van der Zel
- Gauteng Department of Agriculture and Rural Development, Johannesburg 2000, South Africa
| | - Jade Anthony
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - Nadine Daniell
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
| | - Liesl De Boni
- Gauteng Department of Agriculture and Rural Development, Johannesburg 2000, South Africa
| | - John Grewar
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- jDATA (Pty) Ltd., Sandbaai 7200, South Africa
| | - Adriaan Olivier
- South African Ostrich Business Chamber, Oudtshoorn 6620, South Africa
| | - Laura Roberts
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria 0110, South Africa
- Department of Agriculture, Western Cape Government, Elsenburg 7607, South Africa
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Surveillance and Phylogenetic Characterisation of Avian Influenza Viruses Isolated from Wild Waterfowl in Zambia in 2015, 2020, and 2021. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/4606850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
In recent years, the southern African region has experienced repeated incursions of highly pathogenic avian influenza viruses (HPAIVs), with wild migratory birds being implicated in the spread. To understand the profile of avian influenza viruses (AIVs) circulating in Zambia, we surveyed wild waterfowl for AIVs and phylogenetically characterised the isolates detected in 2015, 2020, and 2021. A total of 2,851 faecal samples of wild waterfowl were collected from Lochinvar National Park in the Southern Province of Zambia. During the study period, 85 (3.0%) low pathogenicity AIVs belonging to various subtypes were isolated, with H2N9, H8N4, and H10N8 being reported for the first time in avian species in Africa. The majority of the isolates were detected from glossy ibis (order Pelecaniformes) making it the first report of AIV from these birds in Zambia. Phylogenetic analysis of all eight gene segments of the 30 full genomes obtained in this study revealed that all the isolates belonged to the Eurasian lineage with their closest relatives being viruses isolated from wild and/or domestic birds in Bangladesh, Belgium, Egypt, Georgia, Mongolia, the Netherlands, and South Africa. Additionally, the Zambian viruses were grouped into distinct clusters based on the year of isolation. While no notifiable AIVs of the H5 or H7 subtypes were detected in wild birds in Zambia, viral internal protein genes of some viruses were closely related to H7 low pathogenicity AIVs. This study shows that periodically, a considerable diversity of AIV subtypes are introduced into the Zambian ecosystem by wild migratory waterfowl. The findings highlight the importance of continuous surveillance and monitoring of AIVs in wild waterfowl, including birds traditionally not considered to be major AIV reservoirs, for a better understanding of the eco-epidemiology and evolutionary dynamics of AIVs in Africa.
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Descriptive Epidemiology of and Response to the High Pathogenicity Avian Influenza (H5N8) Epidemic in South African Coastal Seabirds, 2018. Transbound Emerg Dis 2023. [DOI: 10.1155/2023/2708458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
High pathogenicity avian influenza (HPAI) clade 2.3.4.4b H5N8 virus was detected in coastal seabirds in late 2017 in South Africa, following a devastating epidemic in the commercial poultry and ostrich industries. By May 2018, the infection had been confirmed in fifteen seabird species at 31 sites along the southern coast, with the highest mortality recorded in terns (Family Laridae, Order Charadriiformes). Over 7,500 positive or suspected cases in seabirds were reported. Among those infected were three endangered species: African penguins (Spheniscus demersus Linnaeus, 1758), Cape cormorants (Phalacrocorax capensis Wahlberg, 1855), and Cape gannets (Morus capensis Lichtenstein, 1823). The scale and impact of this outbreak were unprecedented in southern African coastal seabirds and raised logistical challenges in resource allocation, risk mitigation, and outbreak response. It required the collaboration of multiple stakeholder groups, including a variety of government departments and nongovernmental organizations. With another HPAI outbreak in South African seabirds in 2021 and major incursions in seabird species in the northern hemisphere in 2022, it is vital to share and consolidate knowledge on the subject. We describe the epidemic, the lessons learned, and recommendations for developing contingency plans.
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Continued evolution of the Eurasian avian-like H1N1 swine influenza viruses in China. SCIENCE CHINA. LIFE SCIENCES 2023; 66:269-282. [PMID: 36219302 DOI: 10.1007/s11427-022-2208-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 09/26/2022] [Indexed: 12/05/2022]
Abstract
Animal influenza viruses continue to pose a threat to human public health. The Eurasian avian-like H1N1 (EA H1N1) viruses are widespread in pigs throughout Europe and China and have caused human infections in several countries, indicating their pandemic potential. To carefully monitor the evolution of the EA H1N1 viruses in nature, we collected nasal swabs from 103,110 pigs in 22 provinces in China between October 2013 and December 2019, and isolated 855 EA H1N1 viruses. Genomic analysis of 319 representative viruses revealed that these EA H1N1 viruses formed eight different genotypes through reassortment with viruses of other lineages circulating in humans and pigs, and two of these genotypes (G4 and G5) were widely distributed in pigs. Animal studies indicated that some strains have become highly pathogenic in mice and highly transmissible in ferrets via respiratory droplets. Moreover, two-thirds of the EA H1N1 viruses reacted poorly with ferret serum antibodies induced by the currently used H1N1 human influenza vaccine, suggesting that existing immunity may not prevent the transmission of the EA H1N1 viruses in humans. Our study reveals the evolution and pandemic potential of EA H1N1 viruses and provides important insights for future pandemic preparedness.
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8
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Laleye AT, Adeyemi M, Abolnik C. Propagation of avian influenza virus in embryonated ostrich eggs. Onderstepoort J Vet Res 2022; 89:e1-e6. [PMID: 36546513 PMCID: PMC9772752 DOI: 10.4102/ojvr.v89i1.2011] [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: 03/07/2022] [Revised: 06/14/2022] [Accepted: 06/28/2022] [Indexed: 12/30/2022] Open
Abstract
Influenza A viruses (IAVs) are typically isolated and cultured by successive passages using 9- to 11-day-old embryonated chicken eggs (ECEs) and in 14-day old ECEs for virus mutational studies. Real-time reverse transcription-polymerase chain reaction tests (RT-PCRs) are commonly used for IAV diagnosis, but virus isolation remains invaluable in terms of its high sensitivity, providing viable isolates for further studies and the ability to distinguish between viable and nonviable virus. Efforts at isolating ostrich-origin IAVs from RT-PCR positive specimens using ECEs have often been unsuccessful, raising the possibility of a species bottleneck, whereby ostrich-adapted IAVs may not readily infect and replicate in ECEs, yet the capacity of an ostrich embryo to support the replication of influenza viruses has not been previously demonstrated. This study describes an optimised method for H5 and H7 subtype IAV isolation and propagation in 28-day old embryonated ostrich eggs (EOEs), the biological equivalent of 14-day old ECEs. The viability of EOEs transported from breeding sites could be maximised by pre-incubating the eggs for 12 to 14 days prior to long-distance transportation. This method applied to studies for ostrich-adapted virus isolation and in ovo studies will enable better understanding of the virus-host interaction in ostriches and the emergence of potentially zoonotic diseases.
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Affiliation(s)
- Agnes T. Laleye
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa,National Veterinary Research Institute, Vom, Nigeria
| | - Modupeore Adeyemi
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
| | - Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Pretoria, South Africa
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9
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Gu W, Shi J, Cui P, Yan C, Zhang Y, Wang C, Zhang Y, Xing X, Zeng X, Liu L, Tian G, Suzuki Y, Li C, Deng G, Chen H. Novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 virus have been detected in poultry and caused multiple human infections in China. Emerg Microbes Infect 2022; 11:1174-1185. [PMID: 35380505 PMCID: PMC9126593 DOI: 10.1080/22221751.2022.2063076] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The globally circulating H5N8 avian influenza viruses bearing the clade 2.3.4.4b hemagglutinin (HA) gene are responsible for the loss of more than 33 million domestic poultry since January 2020. Moreover, the H5N8 viruses have reassorted with other avian influenza viruses and formed H5N1, H5N2, H5N3, H5N4, and H5N5 viruses in Europe, Africa, and North America. In this study, we analyzed 15 H5N6 viruses isolated from poultry and seven H5N6 viruses isolated from humans, and found these viruses formed seven different genotypes by deriving the clade 2.3.4.4b HA gene of H5N8 viruses, the neuraminidase of domestic duck H5N6 viruses, and internal genes of different viruses that previously circulated in domestic ducks and wild birds in China. Two of these genotypes (genotype 3 and genotype 6) have caused human infections in multiple provinces. The H5N6 viruses isolated from poultry have distinct pathotypes in mice; some of them replicate systemically and are highly lethal in mice. Although these viruses exclusively bind to avian-type receptors, it is worrisome that they may obtain key mutations that would increase their affinity for human-type receptors during replication in humans. Our study indicates that the novel H5N6 reassortants bearing the clade 2.3.4.4b HA gene of H5N8 viruses were generated through reassortment in domestic ducks and may have spread across a wide area of China, thereby posing a new challenge to the poultry industry and human health. Our findings emphasize the importance of careful monitoring, evaluation, and control of the H5N6 viruses circulating in nature.
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Affiliation(s)
- Wenli Gu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Pengfei Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Cheng Yan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Congcong Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Yuancheng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Xin Xing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Xianying Zeng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Guobin Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Yasuo Suzuki
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Chengjun Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People's Republic of China
| | - Guohua Deng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, People's Republic of China
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Wild Bird Surveillance in the Gauteng Province of South Africa during the High-Risk Period for Highly Pathogenic Avian Influenza Virus Introduction. Viruses 2022; 14:v14092027. [PMID: 36146838 PMCID: PMC9504564 DOI: 10.3390/v14092027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/16/2022] Open
Abstract
Migratory birds carried clade 2.3.4.4B H5Nx highly pathogenic avian influenza (HPAI) viruses to South Africa in 2017, 2018 and 2021, where the Gauteng Province is a high-risk zone for virus introduction. Here, we combined environmental faecal sampling with sensitive rRT-PCR methods and direct Ion Torrent sequencing to survey wild populations between February and May 2022. An overall IAV incidence of 42.92% (100/231) in water bird faecal swab pools or swabs from moribund or dead European White Storks (Ciconia ciconia) was detected. In total, 7% of the IAV-positive pools tested H5-positive, with clade 2.3.4.4B H5N1 HPAI confirmed in the storks; 10% of the IAV-positive samples were identified as H9N2, and five complete H9N2 genomes were phylogenetically closely related to a local 2021 wild duck H9N2 virus, recent Eurasian LPAI viruses or those detected in commercial ostriches in the Western and Eastern Cape Provinces since 2018. H3N1, H4N2, H5N2 and H8Nx subtypes were also identified. Targeted surveillance of wild birds using environmental faecal sampling can thus be effectively applied under sub-Saharan African conditions, but region-specific studies should first be used to identify peak prevalence times which, in southern Africa, is linked to the peak rainfall period, when ducks are reproductively active.
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11
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Liu H, Wu C, Pang Z, Zhao R, Liao M, Sun H. Phylogenetic and Phylogeographic Analysis of the Highly Pathogenic H5N6 Avian Influenza Virus in China. Viruses 2022; 14:v14081752. [PMID: 36016374 PMCID: PMC9415468 DOI: 10.3390/v14081752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/07/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
The clade 2.3.4.4b H5N8 avian influenza viruses (AIVs) have caused the loss of more than 33 million domestic poultry worldwide since January 2020. Novel H5N6 reassortants with hemagglutinin (HA) from clade 2.3.4.4b H5N8 AIVs are responsible for multiple human infections in China. Therefore, we conducted an epidemiological survey on waterfowl farms in Sichuan and Guangxi provinces and performed a comprehensive spatiotemporal analysis of H5N6 AIVs in China. At the nucleotide level, the H5N6 AIVs isolated in the present study exhibited high homology with the H5N6 AIVs that caused human infections. Demographic history indicates that clade 2.3.4.4b seemingly replaced clade 2.3.4.4h to become China’s predominant H5N6 AIV clade. Based on genomic diversity, we classified clade 2.3.4.4b H5N6 AIV into ten genotypes (2.3.4.4bG1–G10), of which the 2.3.4.4bG5 and G10 AIVs can cause human infections. Phylogeographic results suggest that Hong Kong and Jiangxi acted as important epicentres for clades 2.3.4.4b and 2.3.4.4h, respectively. Taken together, our study provides critical insight into the evolution and spread of H5N6 AIVs in China, which indicates that the novel 2.3.4.4b reassortants pose challenges for public health and poultry.
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Affiliation(s)
- Hanlin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China
| | - Changrong Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China
| | - Zifeng Pang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China
| | - Rui Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China
| | - Ming Liao
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Correspondence: (M.L.); (H.S.)
| | - Hailiang Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Zoonosis Control and Prevention of Guangdong Province, South China Agricultural University, Guangzhou 510642, China
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (M.L.); (H.S.)
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12
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Chauhan RP, Gordon ML. A systematic review of influenza A virus prevalence and transmission dynamics in backyard swine populations globally. Porcine Health Manag 2022; 8:10. [PMID: 35287744 PMCID: PMC8919175 DOI: 10.1186/s40813-022-00251-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/25/2022] [Indexed: 01/01/2023] Open
Abstract
Background Backyard swine farming is critical to generating subsistence and food security in rural and peri-urban households in several developing countries. The objective of this systematic review was to analyze the molecular and serological prevalence of influenza A virus (IAV) in backyard swine populations globally. Results We identified 34 full-text research articles in NCBI-PubMed and Google Scholar databases that have reported IAV sero- and/or virological prevalence in backyard swine up to 11 July 2021. The highest number of studies were reported from Asia (n = 11) followed by North America (n = 10), South America (n = 6), Africa (n = 6), and Europe (n = 1). While the maximum number of studies (44.12%) reported human-to-swine transmission of IAV, swine-to-human (5.88%), poultry-to-swine (5.88%), and wild birds-to-swine (2.94%) transmissions were also reported. An overall higher IAV seroprevalence (18.28%) in backyard swine was detected compared to the virological prevalence (1.32%). The human-origin pandemic A(H1N1)pdm09 virus clade 1A.3.3.2 was the more frequently detected IAV subtype in virological studies (27.27%) than serological studies (18.92%). In addition, the avian-origin highly pathogenic H5N1 and H5N8 viruses were also detected, which further substantiated the evidence of avian–swine interactions in the backyards. Conclusion Human–swine and avian–swine interactions in backyards may transmit IAV between species. Monitoring the circulation and evolution of IAV in backyard swine would help stakeholders make informed decisions to ensure sustainable backyard swine farming and public safety.
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13
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Ramey AM, Hill NJ, DeLiberto TJ, Gibbs SEJ, Camille Hopkins M, Lang AS, Poulson RL, Prosser DJ, Sleeman JM, Stallknecht DE, Wan X. Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America. J Wildl Manage 2022. [DOI: 10.1002/jwmg.22171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Andrew M. Ramey
- U.S. Geological Survey Alaska Science Center 4210 University Drive Anchorage AK 99508 USA
| | - Nichola J. Hill
- Department of Infectious Disease & Global Health, Cummings School of Veterinary Medicine Tufts University 200 Westboro Road North Grafton MA 01536 USA
| | - Thomas J. DeLiberto
- National Wildlife Disease Program, Wildlife Services, Animal and Plant Health Inspection Service U.S. Department of Agriculture 4101 LaPorte Avenue Fort Collins CO 80521 USA
| | - Samantha E. J. Gibbs
- Wildlife Health Office Natural Resource Program Center, National Wildlife Refuge System, U.S. Fish and Wildlife Service 16450 NW 31st Place Chiefland FL 32626 USA
| | - M. Camille Hopkins
- U.S. Geological Survey Ecosystems Mission Area 12201 Sunrise Valley Drive, MS 300 (Room 4A100F) Reston VA 20192 USA
| | - Andrew S. Lang
- Department of Biology Memorial University of Newfoundland 232 Elizabeth Avenue St. John's Newfoundland A1B 3X9 Canada
| | - Rebecca L. Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Diann J. Prosser
- U.S. Geological Survey Eastern Ecological Science Center at the Patuxent Research Refuge 12100 Beech Forest Road Laurel MD 20708 USA
| | - Jonathan M. Sleeman
- U.S. Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison WI 53711 USA
| | - David E. Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine University of Georgia 589 D.W. Brooks Drive Athens GA 30602 USA
| | - Xiu‐Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), Department of Molecular Microbiology and Immunology, Bond Life Sciences Center, Department of Electronic Engineering and Computer Science University of Missouri Columbia MO 65211 USA
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14
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Pieterse R, Strydom C, Abolnik C. Effects of swab pool size and transport medium on the detection and isolation of avian influenza viruses in ostriches. BMC Vet Res 2022; 18:48. [PMID: 35042528 PMCID: PMC8764811 DOI: 10.1186/s12917-022-03150-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 01/05/2022] [Indexed: 12/03/2022] Open
Abstract
Background Rigorous testing is a prerequisite to prove freedom of notifiable influenza A virus infections in commercially farmed ostriches, as is the isolation and identification of circulating strains. Pooling 5 ostrich tracheal swabs in a 50 % v/v phosphate-buffered saline (PBS): glycerol transport medium (without antibiotics) is the current standard practice to increase reverse transcription real time PCR (RT-rtPCR) testing throughput and simultaneously reduce the test costs. In this study we investigated whether doubling ostrich tracheal swabs to 10 per pool would affect the sensitivity of detection of H5N8 high pathogenicity avian influenza virus (HPAIV) and H7N1 low pathogenicity avian influenza virus (LPAIV) by quantitative RT-rtPCR, and we also compared the effect of a protein-rich, brain heart infusion broth (BHI) virus transport media containing broad spectrum antimicrobials (VTM) on the efficacy of isolating the H5N8 and H7N1 viruses from ostrich tracheas, since the historical isolation success rate from these birds has been poor. Results Increasing the ostrich swabs from 5 to 10 per pool in 3 mls of transport medium had no detrimental effect on the sensitivity of the RT-rtPCR assay in detecting H5N8 HPAIV or H7N1 LPAIV; and doubling of the swab pool size even seemed to improve the sensitivity of virus detection at levels that were statistically significant (p less than or equal to 0.05) in medium and low doses of spiked H5N8 HPAIV and at high levels of spiked H7N1 LPAIV. On virus isolation, more samples were positive when swabs were stored in a protein-rich viral transport medium supplemented with antimicrobials in PBS: glycerol (10/18 vs. 7/18 for H5N8 HPAI); although the differences were not statistically significant, overall higher virus titres were detected (106.7 – 103.0 vs. 106.6 - 103.1 EID50 for H5N8 HPAIV and 105.5 - 101.4 vs. 105.1 – 101.3 EID50 for H7N1 LPAIV); and fewer passages were required with less filtration for both H5N8 HPAI and H7N1 LPAI strains. Conclusion Ostrich tracheal swab pool size could be increased from 5 to 10 in 3mls of VTM with no loss in sensitivity of the RT-rtPCR assay in detecting HPAI or LPAI viruses, and HPAI virus could be isolated from a greater proportion of swabs stored in VTM compared to PBS: glycerol without antibiotics.
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15
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Ramey AM, Reeves AB, Lagassé BJ, Patil V, Hubbard LE, Kolpin DW, McCleskey RB, Repert DA, Stallknecht DE, Poulson RL. Evidence for interannual persistence of infectious influenza A viruses in Alaska wetlands. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:150078. [PMID: 34525758 PMCID: PMC9277558 DOI: 10.1016/j.scitotenv.2021.150078] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
Influenza A viruses (IAVs) deposited by wild birds into the environment may lead to sporadic mortality events and economically costly outbreaks among domestic birds. There is a paucity of information, however, regarding the persistence of infectious IAVs within the environment following deposition. In this investigation, we assessed the persistence of 12 IAVs that were present in cloacal and/or oropharyngeal swabs of naturally infected ducks. Infectivity of these IAVs was monitored over approximately one year with each virus tested in five water types: (1) distilled water held in the lab at 4 °C and (2-5) filtered surface water from each of four Alaska sites and maintained in the field at ambient temperature. By evaluating infectivity of IAVs in ovo following sample retrieval at four successive time points, we observed declines in IAV infectivity through time. Many viruses persisted for extended periods, as evidenced by ≥25% of IAVs remaining infectious in replicate samples for each treatment type through three sampling time points (144-155 days post-sample collection) and two viruses remaining viable in a single replicate sample each when tested upon collection at a fourth time point (361-377 days post-sample collection). The estimated probability of persistence of infectious IAVs in all five water types was estimated to be between 0.25 and 0.75 during days 50-200 post-sample collection as inferred through Kaplan-Meier survival analysis. Our results provide evidence that IAVs may remain infectious for extended periods, up to or even exceeding one year, when maintained in surface waters under ambient temperatures. Therefore, wetlands may represent an important medium in which infectious IAVs may reside outside of a biotic reservoir.
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Affiliation(s)
- Andrew M Ramey
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Andrew B Reeves
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Benjamin J Lagassé
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA; Department of Biology and Wildlife, University of Alaska Fairbanks, P.O. Box 756100, Fairbanks, AK 99775, USA
| | - Vijay Patil
- U. S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA.
| | - Laura E Hubbard
- U. S. Geological Survey, Upper Midwest Water Science Center, 8505 Research Way, Middleton, WI 53562, USA.
| | - Dana W Kolpin
- U. S. Geological Survey, Central Midwest Water Science Center, 400 S. Clinton Street, Iowa City, IA 52244, USA.
| | - R Blaine McCleskey
- U. S. Geological Survey, Water Resources Mission Area, 3215 Marine Street, Building 6, Boulder, CO 80309, USA.
| | - Deborah A Repert
- U. S. Geological Survey, Water Resources Mission Area, 3215 Marine Street, Building 6, Boulder, CO 80309, USA.
| | - David E Stallknecht
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Rebecca L Poulson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
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16
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Genetic and biological characteristics of the globally circulating H5N8 avian influenza viruses and the protective efficacy offered by the poultry vaccine currently used in China. SCIENCE CHINA-LIFE SCIENCES 2021; 65:795-808. [PMID: 34757542 DOI: 10.1007/s11427-021-2025-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/02/2021] [Indexed: 12/20/2022]
Abstract
The H5N8 avian influenza viruses have been widely circulating in wild birds and are responsible for the loss of over 33 million domestic poultry in Europe, Russia, Middle East, and Asia since January 2020. To monitor the invasion and spread of the H5N8 virus in China, we performed active surveillance by analyzing 317 wild bird samples and swab samples collected from 41,172 poultry all over the country. We isolated 22 H5N8 viruses from wild birds and 14 H5N8 viruses from waterfowls. Genetic analysis indicated that the 36 viruses formed two different genotypes: one genotype viruses were widely detected from different wild birds and domestic waterfowls; the other genotype was isolated from a whopper swan. We further revealed the origin and spatiotemporal spread of these two distinct H5N8 virus genotypes in 2020 and 2021. Animal studies indicated that the H5N8 isolates are highly pathogenic to chickens, mildly pathogenic in ducks, but have distinct pathotypes in mice. Moreover, we found that vaccinated poultry in China could be completely protected against H5N8 virus challenge. Given that the H5N8 viruses are likely to continue to spread in wild birds, vaccination of poultry is highly recommended in high-risk countries to prevent H5N8 avian influenza.
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17
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Marimwe MC, Fosgate GT, Roberts LC, Tavornpanich S, Olivier AJ, Abolnik C. The spatiotemporal epidemiology of high pathogenicity avian influenza outbreaks in key ostrich producing areas of South Africa. Prev Vet Med 2021; 196:105474. [PMID: 34564052 DOI: 10.1016/j.prevetmed.2021.105474] [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: 02/23/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 10/20/2022]
Abstract
High pathogenicity avian influenza (HPAI) has become a major focus point worldwide due to its zoonotic potential and economic effects resulting from trade restrictions and high mortality rates in poultry. Key ostrich producing provinces of South Africa have experienced three H5N2 HPAI outbreaks (2004, 2006 and 2011) and one H5N8 HPAI (2017) outbreak over the past two decades. The Klein Karoo region in the Western Cape Province, a province with a largely Mediterranean climate, is the predominant ostrich producing region in the country. Understanding the epidemiology of HPAI in ostrich producing areas is an essential first step in developing effective and efficient control measures. This study investigated the spatiotemporal patterns associated with the 2011 (H5N2) and 2017 (H5N8) HPAI outbreaks in the key ostrich producing areas of South Africa. Six hundred and nine and 340 active ostrich farms/holdings were subjected to surveillance during 2011 and 2017 respectively, with over 70 % of these farms located within five local municipalities of the study area. Forty-two and fifty-one farms were affected in the 2011 and 2017 outbreaks respectively. Both HPAI outbreaks occurred predominantly in areas of high ostrich farm density. However, the temporal occurrence, spatial and directional distributions of the outbreaks were different. The 2011 outbreak occurred earlier in the South African autumn months with a predominantly contiguous and stationary distribution, whilst the 2017 outbreak onset was during the winter with a more expansive multidirectional spatial distribution. Results suggest potential dissimilarities in the important risk factors for introduction and possible mode of spread. The 2011 outbreak pattern resembled an outbreak characterised by point introductions with the risk of introduction possibly being linked to high ostrich farm density and common management and husbandry practices in the ostrich industry. In contrast, the 2017 outbreak appeared to have a more propagating mode of transmission. The findings highlight epidemiological features of HPAI outbreak occurrence within ostrich populations that could be used to inform surveillance and control measures including targeted surveillance within high-risk spatial clusters. The study emphasizes the importance of both; implementation of a multi-pronged approach to HPAI control and the need for constant evaluation of the interaction of the host, environment and agent with each outbreak, in order to strengthen disease control.
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Affiliation(s)
- Miriam C Marimwe
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa; Western Cape Department of Agriculture, Elsenburg, 7607, South Africa.
| | - Geoffrey T Fosgate
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa
| | - Laura C Roberts
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa; Western Cape Department of Agriculture, Elsenburg, 7607, South Africa
| | - Saraya Tavornpanich
- Department of Epidemiology, Norwegian Veterinary Institute, Oslo, 0160, Norway
| | - Adriaan J Olivier
- South African Ostrich Business Chamber, Oudtshoorn, 6620, South Africa
| | - Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa
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18
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Hubálek Z. Pathogenic microorganisms associated with gulls and terns (Laridae). JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zdeněk Hubálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; e-mail:
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19
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Abolnik C, Strydom C, Landman D, Pieterse R. Identification of bacteria in the tracheal swabs of farmed ostriches and their effect on the viability of influenza A virus. J Vet Diagn Invest 2021; 33:1089-1095. [PMID: 34293996 DOI: 10.1177/10406387211034483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Avian influenza surveillance is a requirement for commercial trade in ostrich products, but influenza A viruses (IAVs) have proven difficult to isolate from ostrich tracheal swabs that test positive using molecular methods. We hypothesized that microbes unique to the ostrich trachea propagate in the transport medium after sampling and affect viral viability. We cultured tracheal swabs from 50 ostriches on 4 farms in South Africa, and recovered and identified 13 bacterial, 1 yeast, and 2 fungal species. Dietzia sp. had not been identified previously in the oropharyngeal tract of a bird, to our knowledge. The bacteria were tested for antimicrobial susceptibility, and most aerobic species, except for Streptococcus sp. and Pseudomonas sp., were sensitive to enrofloxacin; all were susceptible to sulfonamide. Virus inhibition experiments determined that ostrich-source Streptococcus sp., Pantoea sp., and Citrobacter freundii produced extracellular metabolites that caused a substantial reduction in the IAV titers of 99.9%. Streptomyces, Corynebacterium, Staphylococcus, Arthrobacter gandavensis, Pseudomonas putida, and Acinetobacter spp. similarly reduced the viability of IAV from 77.6% to 24.1%. Dietzia appeared to have no effect, but Rothia dentocariosa, Rhodotorula spp., and Clostridium spp. slightly increased the viability of IAV by 25.9, 34.9, and 58.5%, respectively.
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Affiliation(s)
- Celia Abolnik
- Departments of Production Animal Studies, University of Pretoria Faculty of Veterinary Science, Onderstepoort, South Africa
| | | | - Debbie Landman
- Veterinary Tropical Diseases, University of Pretoria Faculty of Veterinary Science, Onderstepoort, South Africa
| | - Reneé Pieterse
- Veterinary Tropical Diseases, University of Pretoria Faculty of Veterinary Science, Onderstepoort, South Africa.,Provincial Veterinary Laboratory, Western Cape Department of Agriculture, Stellenbosch, South Africa
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20
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Zhang J, Chen Y, Shan N, Wang X, Lin S, Ma K, Li B, Li H, Liao M, Qi W. Genetic diversity, phylogeography, and evolutionary dynamics of highly pathogenic avian influenza A (H5N6) viruses. Virus Evol 2020; 6:veaa079. [PMID: 33324491 PMCID: PMC7724252 DOI: 10.1093/ve/veaa079] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
From 2013 onwards, the spread of novel H5N6 highly pathogenic avian influenza (HPAI) viruses in China has posed great threats to not only poultry industry but also human health. Since late-2016 in particular, frequent outbreaks of clade 2.3.4.4 H5N6 HPAI viruses among wild birds have promoted viral dissemination in South Korea, Japan, and European countries. In response to those trends, we conducted molecular genetic analysis of global clade 2.3.4.4 H5N6 viruses in order to characterize spatio-temporal patterns of viral diffusion and genetic diversity among wild birds and poultry. The clade 2.3.4.4 H5N6 viruses were classified into three groups (Group B, C, and D). During the cocirculation of Group C/D H5N6 viruses from 2013 to 2017, viral movements occurred between close or adjacent regions of China, Vietnam, South Korea, and Japan. In addition, viral migration rates from Guangdong and Hunan to multiple adjacent provinces seemed to have been highly supported by transmission routes (Bayes factors >100), suggesting that southern China was an epicenter for the spread of H5N6 viruses in poultry during that period. Since the introduction of H5N6 viruses originating in wild birds in late-2016, evolving H5N6 viruses have lost most previous genotypes (e.g. G1, G2, and G1.2), whereas some prevailing genotypes (e.g. G1.1, G1.1.b, and G3) in aquatic birds have been dominated, and in particular, the effective population size of H5N6 originating in wild birds dramatically increased; however, the population size of poultry-origin H5N6 viruses declined during the same period, indicating that wild bird migration might accelerate the genetic diversity of H5N6 viruses. Phylogeographic approaches revealed that two independent paths of H5N6 viruses into South Korea and Japan from 2016 to 2018 and provided evidence of Group B and Group C H5N6 viruses were originated from Europe and China, respectively, as regions located in the East Asia-Australian migration flyway, which accelerated the genetic variability and dissemination. Altogether, our study provides insights to examine time of origin, evolutionary rate, diversification patterns, and phylogeographical approach of global clade 2.3.4.4 H5N6 HPAI viruses for assessing their evolutionary process and dissemination pathways.
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Affiliation(s)
- Jiahao Zhang
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission.,Ministry of Agricultural and Rural Affairs, Key Laboratory of Zoonoses.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China
| | - Yiqun Chen
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Nan Shan
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China.,Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, Jiangsu 210023, P.R. China
| | - Xiaomin Wang
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Shuxia Lin
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Kaixiong Ma
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Bo Li
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Huanan Li
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission.,Ministry of Agricultural and Rural Affairs, Key Laboratory of Zoonoses.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China
| | - Wenbao Qi
- College of Veterinary Medicine, South China Agricultural University.,National Avian Influenza Para-Reference Laboratory.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, National Development and Reform Commission.,Ministry of Agricultural and Rural Affairs, Key Laboratory of Zoonoses.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China.,Guangdong Laboratory for Lingnan Modern Agriculture, Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China
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21
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King J, Harder T, Conraths FJ, Beer M, Pohlmann A. The genetics of highly pathogenic avian influenza viruses of subtype H5 in Germany, 2006-2020. Transbound Emerg Dis 2020; 68:1136-1150. [PMID: 32964686 DOI: 10.1111/tbed.13843] [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] [Received: 06/18/2020] [Revised: 09/03/2020] [Accepted: 09/12/2020] [Indexed: 12/22/2022]
Abstract
The H5 A/Goose/Guangdong/1/1996 (gs/GD) lineage emerged in China in 1996. Rooted in the respective gs/GD lineage, the hemagglutinin (HA) gene of highly pathogenic avian influenza viruses (HPAIV) has genetically diversified into a plethora of clades and subclades and evolved into an assortment of sub- and genotypes. Some caused substantial losses in the poultry industry and had a major impact on wild bird populations alongside public health implications due to a zoonotic potential of certain clades. After the primary introduction of the HPAI H5N1 gs/GD lineage into Europe in autumn 2005 and winter 2005/2006, Germany has seen recurring incursions of four varying H5Nx subtypes (H5N1, H5N8, H5N5, H5N6) carrying multiple distinct reassortants, all descendants of the gs/GD virus. The first HPAIV H5 epidemic in Germany during 2006/2007 was caused by a clade 2.2 subtype H5N1 virus. Phylogenetic analysis confirmed three distinct clusters belonging to clades 2.2.1, 2.2.2 and 2.2, concurring with geographic and temporal structures. From 2014 onwards, HPAIV clade 2.3.4.4 has dominated the epidemiological situation in Germany. The initial clade 2.3.4.4a HPAIV H5N8, reaching Germany in November 2014, caused a limited epidemic affecting five poultry holdings, one zoo in Northern Germany and few wild birds. After November 2016, HPAIV of clade 2.3.4.4b have dominated the situation to date. The most extensive HPAIV H5 epidemic on record reached Germany in winter 2016/2017, encompassing multiple incursion events with two subtypes (H5N8, H5N5) and entailing five reassortants. A novel H5N6 clade 2.3.4.4b strain affected Germany from December 2017 onwards, instigating low-level infection in smallholdings and wild birds. Recently, in spring 2020, a novel incursion of a genetically distinct HPAI clade 2.3.4.4b H5N8 virus caused another epidemic in Europe, which affected a small number of poultry holdings, one zoo and two wild birds throughout Germany.
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Affiliation(s)
- Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | - Franz J Conraths
- Institute of Epidemiology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
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22
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Kalonda A, Saasa N, Nkhoma P, Kajihara M, Sawa H, Takada A, Simulundu E. Avian Influenza Viruses Detected in Birds in Sub-Saharan Africa: A Systematic Review. Viruses 2020; 12:v12090993. [PMID: 32906666 PMCID: PMC7552061 DOI: 10.3390/v12090993] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
In the recent past, sub-Saharan Africa has not escaped the devastating effects of avian influenza virus (AIV) in poultry and wild birds. This systematic review describes the prevalence, spatiotemporal distribution, and virus subtypes detected in domestic and wild birds for the past two decades (2000–2019). We collected data from three electronic databases, PubMed, SpringerLink electronic journals and African Journals Online, using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol. A total of 1656 articles were reviewed, from which 68 were selected. An overall prevalence of 3.0% AIV in birds was observed. The prevalence varied between regions and ranged from 1.1% to 7.1%. The Kruskal–Wallis and Wilcoxon signed-rank sum test showed no significant difference in the prevalence of AIV across regions, χ2(3) = 5.237, p = 0.1553 and seasons, T = 820, z = −1.244, p = 0.2136. Nineteen hemagglutinin/neuraminidase subtype combinations were detected during the reviewed period, with southern Africa recording more diverse AIV subtypes than other regions. The most detected subtype was H5N1, followed by H9N2, H5N2, H5N8 and H6N2. Whilst these predominant subtypes were mostly detected in domestic poultry, H1N6, H3N6, H4N6, H4N8, H9N1 and H11N9 were exclusively detected in wild birds. Meanwhile, H5N1, H5N2 and H5N8 were detected in both wild and domestic birds suggesting circulation of these subtypes among wild and domestic birds. Our findings provide critical information on the eco-epidemiology of AIVs that can be used to improve surveillance strategies for the prevention and control of avian influenza in sub-Saharan Africa.
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Affiliation(s)
- Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Disease of Humans and Animals, School of Veterinary Medicine, Lusaka 10101, Zambia
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
| | - Masahiro Kajihara
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Macha Research Trust, Choma 20100, Zambia
- Correspondence: ; Tel.: +260-977469479
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23
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Systematic Review of Important Viral Diseases in Africa in Light of the 'One Health' Concept. Pathogens 2020; 9:pathogens9040301. [PMID: 32325980 PMCID: PMC7238228 DOI: 10.3390/pathogens9040301] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/03/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022] Open
Abstract
Emerging and re-emerging viral diseases are of great public health concern. The recent emergence of Severe Acute Respiratory Syndrome (SARS) related coronavirus (SARS-CoV-2) in December 2019 in China, which causes COVID-19 disease in humans, and its current spread to several countries, leading to the first pandemic in history to be caused by a coronavirus, highlights the significance of zoonotic viral diseases. Rift Valley fever, rabies, West Nile, chikungunya, dengue, yellow fever, Crimean-Congo hemorrhagic fever, Ebola, and influenza viruses among many other viruses have been reported from different African countries. The paucity of information, lack of knowledge, limited resources, and climate change, coupled with cultural traditions make the African continent a hotspot for vector-borne and zoonotic viral diseases, which may spread globally. Currently, there is no information available on the status of virus diseases in Africa. This systematic review highlights the available information about viral diseases, including zoonotic and vector-borne diseases, reported in Africa. The findings will help us understand the trend of emerging and re-emerging virus diseases within the African continent. The findings recommend active surveillance of viral diseases and strict implementation of One Health measures in Africa to improve human public health and reduce the possibility of potential pandemics due to zoonotic viruses.
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24
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Valley-Omar Z, Cloete A, Pieterse R, Walaza S, Salie-Bassier Y, Smith M, Govender N, Seleka M, Hellferscee O, Mtshali PS, Allam M, Ismail A, Anthony T, Seutloali M, McCarthy K, van Helden L, Cohen C, Treurnicht FK. Human surveillance and phylogeny of highly pathogenic avian influenza A(H5N8) during an outbreak in poultry in South Africa, 2017. Influenza Other Respir Viruses 2020; 14:266-273. [PMID: 32058677 PMCID: PMC7182598 DOI: 10.1111/irv.12724] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/19/2019] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Background In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. Methods Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations. Results Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.
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Affiliation(s)
- Ziyaad Valley-Omar
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Department of Pathology, Division of Medical Virology, University of Cape Town, South Africa
| | - Alicia Cloete
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Reneé Pieterse
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Sibongile Walaza
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Yusrah Salie-Bassier
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mikhail Smith
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mpho Seleka
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Orienka Hellferscee
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Phillip Senzo Mtshali
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Tasneem Anthony
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Michelle Seutloali
- Department of Agriculture, Western Cape Provincial Veterinary Laboratory, Stellenbosch, South Africa
| | - Kerrigan McCarthy
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Lesley van Helden
- Veterinary Services, Western Cape Department of Agriculture, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette Kathleen Treurnicht
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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25
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Avian Influenza H5N8 Outbreak in African Penguins (Spheniscus demersus), Namibia, 2019. J Wildl Dis 2020. [DOI: 10.7589/2019-03-067] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Abolnik C. Outbreaks of Clade 2.3.4.4 H5N8 highly pathogenic avian influenza in 2018 in the northern regions of South Africa were unrelated to those of 2017. Transbound Emerg Dis 2019; 67:1371-1381. [PMID: 31833671 DOI: 10.1111/tbed.13448] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 11/28/2022]
Abstract
Asian-origin H5N8 highly pathogenic avian influenza (HPAI) viruses of the H5 Goose/Guangdong/96 lineage, clade 2.3.4.4 group B, reached South Africa by June 2017. By the end of that year, 5.4 million layers and broiler chickens died or were culled, with total losses in the poultry industry estimated at US$ 140 million, and thousands of exotic birds in zoological collections, endangered endemic species and backyard poultry and pet birds also perished. The 2017 H5N8 HPAI outbreaks were characterized by two distinct spatial clusters, each associated with specific reassortant viral genotypes. Genotypes 1, 2, 3 and 5 were restricted to the northern regions, spanning the provinces of Limpopo, Gauteng, North West, Mpumalanga, KwaZulu-Natal and Free State. The second, much larger cluster of outbreaks was in the south, in the Western and Eastern Cape provinces, wherein 2017 and 2018 outbreaks were caused solely by genotype 4. The last confirmed case of H5N8 HPAI in the northern region in 2017 was in early October, and the viruses seemed to disappear over the summer. However, starting in mid-February 2018, H5N8 HPAI outbreaks resurged in the north. Viruses from two of the eight outbreaks were sequenced, one from an outbreak in quails (Coturnix japonica) in the North West Province, and another from commercial pullets in the Gauteng province. Phylogenetic analysis identified the viruses as a distinct sixth genotype that was most likely a new introduction to South Africa in early 2018.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
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27
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Abolnik C, Strydom C, Rauff DL, Wandrag DBR, Petty D. Continuing evolution of H6N2 influenza a virus in South African chickens and the implications for diagnosis and control. BMC Vet Res 2019; 15:455. [PMID: 31852473 PMCID: PMC6921544 DOI: 10.1186/s12917-019-2210-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/09/2019] [Indexed: 01/29/2023] Open
Abstract
Background The threat of poultry-origin H6 avian influenza viruses to human health emphasizes the importance of monitoring their evolution. South Africa’s H6N2 epidemic in chickens began in 2001 and two co-circulating antigenic sub-lineages of H6N2 could be distinguished from the outset. The true incidence and prevalence of H6N2 in the country has been difficult to determine, partly due to the continued use of an inactivated whole virus H6N2 vaccine and the inability to distinguish vaccinated from non-vaccinated birds on serology tests. In the present study, the complete genomes of 12 H6N2 viruses isolated from various farming systems between September 2015 and February 2019 in three major chicken-producing regions were analysed and a serological experiment was used to demonstrate the effects of antigenic mismatch in diagnostic tests. Results Genetic drift in H6N2 continued and antigenic diversity in sub-lineage I is increasing; no sub-lineage II viruses were detected. Reassortment patterns indicated epidemiological connections between provinces as well as different farming systems, but there was no reassortment with wild bird or ostrich influenza viruses. The sequence mismatch between the official antigens used for routine hemagglutination inhibition (HI) testing and circulating field strains has increased steadily, and we demonstrated that H6N2 field infections are likely to be missed. More concerning, sub-lineage I H6N2 viruses acquired three of the nine HA mutations associated with human receptor-binding preference (A13S, V187D and A193N) since 2002. Most sub-lineage I viruses isolated since 2015 acquired the K702R mutation in PB2 associated with the ability to infect humans, whereas prior to 2015 most viruses in sub-lineages I and II contained the avian lysine marker. All strains had an unusual HA0 motif of PQVETRGIF or PQVGTRGIF. Conclusions The H6N2 viruses in South African chickens are mutating and reassorting amongst themselves but have remained a genetically pure lineage since they emerged more than 18 years ago. Greater efforts must be made by government and industry in the continuous isolation and characterization of field strains for use as HI antigens, new vaccine seed strains and to monitor the zoonotic threat of H6N2 viruses.
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Affiliation(s)
- Celia Abolnik
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa.
| | - Christine Strydom
- Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttleton, Centurion, 0140, South Africa
| | - Dionne Linda Rauff
- Deltamune (Pty) Ltd, 248 Jean Avenue, Lyttleton, Centurion, 0140, South Africa
| | - Daniel Barend Rudolph Wandrag
- Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Old Soutpan Road, Onderstepoort, 0110, South Africa
| | - Deryn Petty
- The Poultry Practice, PO Box 5615, Walmer, Port Elizabeth, 6065, South Africa
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28
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Disentangling the role of Africa in the global spread of H5 highly pathogenic avian influenza. Nat Commun 2019; 10:5310. [PMID: 31757953 PMCID: PMC6874648 DOI: 10.1038/s41467-019-13287-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/08/2019] [Indexed: 12/30/2022] Open
Abstract
The role of Africa in the dynamics of the global spread of a zoonotic and economically-important virus, such as the highly pathogenic avian influenza (HPAI) H5Nx of the Gs/GD lineage, remains unexplored. Here we characterise the spatiotemporal patterns of virus diffusion during three HPAI H5Nx intercontinental epidemic waves and demonstrate that Africa mainly acted as an ecological sink of the HPAI H5Nx viruses. A joint analysis of host dynamics and continuous spatial diffusion indicates that poultry trade as well as wild bird migrations have contributed to the virus spreading into Africa, with West Africa acting as a crucial hotspot for virus introduction and dissemination into the continent. We demonstrate varying paths of avian influenza incursions into Africa as well as virus spread within Africa over time, which reveal that virus expansion is a complex phenomenon, shaped by an intricate interplay between avian host ecology, virus characteristics and environmental variables.
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29
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Evidence of the Presence of Low Pathogenic Avian Influenza A Viruses in Wild Waterfowl in 2018 in South Africa. Pathogens 2019; 8:pathogens8040163. [PMID: 31557802 PMCID: PMC6963398 DOI: 10.3390/pathogens8040163] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/26/2019] [Accepted: 09/11/2019] [Indexed: 11/16/2022] Open
Abstract
Avian influenza viruses are pathogens of global concern to both animal and human health. Wild birds are the natural reservoir of avian influenza viruses and facilitate virus transport over large distances. Surprisingly, limited research has been performed to determine avian influenza host species and virus dynamics in wild birds on the African continent, including South Africa. This study described the first wild bird surveillance efforts for influenza A viruses in KwaZulu-Natal Province in South Africa after the 2017/2018 outbreak with highly pathogenic avian influenza virus H5N8 in poultry. A total of 550 swab samples from 278 migratory waterfowl were tested using real-time RT-PCR methods. Two samples (0.7%) were positive for avian influenza virus based on the matrix gene real-time RT-PCR but were negative for the hemagglutinin subtypes H5 and H7. Unfortunately, no sequence information or viable virus could be retrieved from the samples. This study shows that avian influenza viruses are present in the South African wild bird population, emphasizing the need for more extensive surveillance studies to determine the South African avian influenza gene pool and relevant local host species.
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30
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Complete Genome Sequence of a Class I Avian Orthoavulavirus 1 Isolated from Commercial Ostriches. Microbiol Resour Announc 2019; 8:8/30/e00543-19. [PMID: 31346015 PMCID: PMC6658685 DOI: 10.1128/mra.00543-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A hemagglutinating virus isolated during routine surveillance in ostriches was sequenced, identified as avian orthoavulavirus 1 (AOaV-1), and classified as a class I genotype 1.2 virus, with recent common ancestors in Eurasian wild ducks. This is the first class I AOaV-1 isolate from Africa and the first identified in ostriches. A hemagglutinating virus isolated during routine surveillance in ostriches was sequenced, identified as avian orthoavulavirus 1 (AOaV-1), and classified as a class I genotype 1.2 virus, with recent common ancestors in Eurasian wild ducks. This is the first class I AOaV-1 isolate from Africa and the first identified in ostriches.
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Experimental infection of racing pigeons (Columba livia domestica) with highly pathogenic Clade 2.3.4.4 sub-group B H5N8 avian influenza virus. Vet Microbiol 2018; 227:127-132. [PMID: 30473343 DOI: 10.1016/j.vetmic.2018.10.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/25/2018] [Accepted: 10/28/2018] [Indexed: 12/19/2022]
Abstract
Reported mass mortalities in wild pigeons and doves during the 2017/2018 Clade 2.3.4.4 HPAI H5N8 outbreaks in South Africa necessitated an investigation of healthy racing pigeons for their susceptibility and ability to transmit a Clade 2.3.4.4 sub-group B virus of South African origin. Pigeons challenged with medium (104.5 EID50) and high doses (106 EID50) but not a low dose (103 EID50) of virus, shed virus in low levels of <103 EID50/ml from the oropharynx and cloaca for up to eight days, with peak shedding around 4 days post challenge. Challenged pigeons were able to transmit the virus to contact pigeons, but not contact chickens. Neither pigeons nor chickens presented clinical disease, and only two pigeons in the group that received the high challenge dose developed influenza A-virus specific antibodies. The levels of virus shed by the racing pigeons were well below the published bird infectious dose 50 values for most poultry, especially chickens, therefore the risk that racing pigeons could act as propagators and disseminators through excretion of Clade 2.3.4.4 HPAI H5N8 strains remains negligible.
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