{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T14:53:44Z","timestamp":1789052024722,"version":"build-2803163510"},"reference-count":92,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T00:00:00Z","timestamp":1779408000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["101084171"],"award-info":[{"award-number":["101084171"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"award":["101084171"],"award-info":[{"award-number":["101084171"]}],"id":[{"id":"https:\/\/ror.org\/019w4f821","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The global emergence of the avian influenza virus (AIV) H5N1 clade 2.3.4.4b since 2016 has caused substantial losses in wild bird and poultry populations, along with heightened risks of transmission to humans and other mammals. Vaccination of poultry has been a key strategy to curb the virus\u2019s spread and mitigate its socioeconomic impact. This report describes an outbreak of high pathogenicity avian influenza virus (HPAIV) H5N1 clade 2.3.4.4b in a flock of 15,000 brown layer chickens (170 days old), all of which had received a four-dose vaccination regimen with H5N1\/H5N8 commercial vaccines at 17, 50, 100, and 125 days of age. Despite this vaccination history, H5N1 infection was confirmed approximately seven weeks post-vaccination. H5N1 infection was confirmed by RT-qPCR, virus isolation, and full genome sequencing covering all eight gene segments, followed by phylogenetic and molecular analyses. Clinical signs included reduced feed intake, decreased egg production, and a cumulative mortality rate of 35% over 52 days. Hemagglutination inhibition (HI) testing with various H5 antigens revealed inconsistent antibody titers (geometric mean: 4.0 to 9.1 log2). Genetic analysis of the full-length HA and NA gene sequences further revealed strong similarity to contemporaneous H5N1 clade 2.3.4.4b strains circulating in Egypt, with multiple mutations in the HA head domain, particularly near immunogenic epitopes and receptor binding sites. These findings highlight the limitations of current vaccination strategies under conditions of antigenic mismatch and complex immunization schedules, emphasizing the need for improved vaccine matching and continuous molecular surveillance. To improve outbreak management in poultry, enhanced vaccination protocols, stringent biosecurity measures, and rigorous monitoring practices are critical.<\/jats:p>","DOI":"10.3390\/v18060589","type":"journal-article","created":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T12:14:52Z","timestamp":1779452092000},"page":"589","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Molecular Characterization of H5N1 Clade 2.3.4.4b Virus in Vaccinated Layer Chickens"],"prefix":"10.3390","volume":"18","author":[{"given":"Ahmed H.","family":"Salaheldin","sequence":"first","affiliation":[{"name":"Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0096-6297","authenticated-orcid":false,"given":"Mustafa Ozan","family":"Atasoy","sequence":"additional","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Cumhuriyet University, Sivas 58040, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4864-7837","authenticated-orcid":false,"given":"Juliane","family":"Lang","sequence":"additional","affiliation":[{"name":"Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3635-423X","authenticated-orcid":false,"given":"Ann Kathrin","family":"Ahrens","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5318-665X","authenticated-orcid":false,"given":"Anne","family":"Pohlmann","sequence":"additional","affiliation":[{"name":"Institute of Diagnostic Virology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1798-7086","authenticated-orcid":false,"given":"Mohammed A.","family":"Rohaim","sequence":"additional","affiliation":[{"name":"Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hatem S.","family":"Abd El-Hamid","sequence":"additional","affiliation":[{"name":"Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2103-0922","authenticated-orcid":false,"given":"Elsayed M.","family":"Abdelwhab","sequence":"additional","affiliation":[{"name":"Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, 17493 Greifswald-Insel Riems, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"26","DOI":"10.3382\/ps.2011-01635","article-title":"Predicting the environmental impacts of chicken systems in the United Kingdom through a life cycle assessment: Egg production systems","volume":"91","author":"Leinonen","year":"2012","journal-title":"Poult. 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