The molecular epidemiology of clade 2.3.4.4B H5N1 high pathogenicity avian influenza in Southern Africa, 2021–2022

dc.contributor.authorAbolnik, Celia
dc.contributor.authorPhiri, Thandeka Precious
dc.contributor.authorPeyrot, Belinda
dc.contributor.authorDe Beer, Renee
dc.contributor.authorSnyman, Albert
dc.contributor.authorRoberts, David
dc.contributor.authorLudynia, Katrin
dc.contributor.authorJordaan, Frances
dc.contributor.authorMaartens, Michele
dc.contributor.authorIsmail, Zehaad
dc.contributor.authorStrydom, Christine
dc.contributor.authorVan der Zel, Gerbrand
dc.contributor.authorAnthony, Jade
dc.contributor.authorDaniell, Nadine
dc.contributor.authorDe Boni, Liesl
dc.contributor.authorGrewar, John Duncan
dc.contributor.authorOlivier, Adriaan
dc.contributor.authorRoberts, Laura C.
dc.contributor.emailcelia.abolnik@up.ac.zaen_US
dc.date.accessioned2024-04-16T08:01:38Z
dc.date.available2024-04-16T08:01:38Z
dc.date.issued2023-06-16
dc.descriptionDATA AVAILABILITY STATEMENT : All the data needed to generate the conclusions made in the article itself are present and/or in the Supplementary data.en_US
dc.description.abstractIn 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.en_US
dc.description.departmentProduction Animal Studiesen_US
dc.description.librarianam2024en_US
dc.description.sdgSDG-15:Life on landen_US
dc.description.sponsorshipThe South African Department of Science and Innovation (DSI)/National Research Foundation (NRF), the Hans Hoheisen Charitable Trust, MeerWissen—African–German Partners for Ocean Knowledge under the Marine Conservation Support Project and the Rupert Nature Foundation for disease surveillance.en_US
dc.description.urihttps://www.mdpi.com/journal/virusesen_US
dc.identifier.citationAbolnik, C.; Phiri, T.; Peyrot, B.; de Beer, R.; Snyman, A.; Roberts, D.; Ludynia, K.; Jordaan, F.; Maartens, M.; Ismail, Z.; et al. The Molecular Epidemiology of Clade 2.3.4.4B H5N1 High Pathogenicity Avian Influenza in Southern Africa, 2021–2022. Viruses 2023, 15, 1383. https://DOI.org/10.3390/v15061383.en_US
dc.identifier.issn1999-4915 (online)
dc.identifier.other10.3390/v15061383
dc.identifier.urihttp://hdl.handle.net/2263/95562
dc.language.isoenen_US
dc.publisherMDPIen_US
dc.rights© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license.en_US
dc.subjectClade 2.3.4.4 H5N1en_US
dc.subjectEvolutionen_US
dc.subjectPhylogenetic analysisen_US
dc.subjectSouthern Africaen_US
dc.subjectCoastal seabirdsen_US
dc.subjectHigh pathogenicity avian influenza (HPAI)en_US
dc.subjectAvian influenza virusen_US
dc.subjectSDG-15: Life on landen_US
dc.titleThe molecular epidemiology of clade 2.3.4.4B H5N1 high pathogenicity avian influenza in Southern Africa, 2021–2022en_US
dc.typeArticleen_US

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