{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T23:55:17Z","timestamp":1778975717913,"version":"3.51.4"},"reference-count":28,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2024,9,28]],"date-time":"2024-09-28T00:00:00Z","timestamp":1727481600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006143","name":"Department of Science and Technology\u2019s Science for Change Program (S4CP) Business Innovation through S&amp;T for Industry (BIST)","doi-asserted-by":"publisher","award":["8738"],"award-info":[{"award-number":["8738"]}],"id":[{"id":"10.13039\/501100006143","id-type":"DOI","asserted-by":"publisher"}]},{"name":"internal BioAssets funds","award":["8738"],"award-info":[{"award-number":["8738"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>H5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, H5 HPAI outbreaks have been reported in 2020, 2022, and 2023. Here, we report the first publicly available complete whole-genome sequence of an H5N1 high-pathogenicity avian influenza virus from a case in Central Luzon. Samples were collected from a flock of layer chickens exhibiting signs of lethargy, droopy wings, and ecchymotic hemorrhages in trachea with excessive mucus exudates. A high mortality rate of 96\u2013100% was observed within the week. Days prior to the high mortality event, migratory birds were observed around the chicken farm. Lungs, spleen, cloacal swabs, and oropharyngeal\u2013tracheal swabs were taken from two chickens from this flock. These samples were positive in quantitative RT-PCR assays for influenza matrix and H5 hemagglutinin (HA) genes. To further characterize the virus, the same samples were subjected to whole-virus-genome amplification and sequencing using the Oxford Nanopore method with mean coverages of 19,190 and 2984, respectively. A phylogenetic analysis of the HA genes revealed that the H5N1 HPAI virus from Central Luzon belongs to the Goose\/Guangdong lineage clade 2.3.4.4b viruses. Other segments also have high sequence identity and the same genetic lineages as other clade 2.3.4.4b viruses from Asia. Collectively, these data indicate that wild migratory birds are the likely source of H5N1 viruses from the 2022 outbreaks in the Philippines. Thus, biosecurity practices and surveillance for HPAI viruses in both domestic and wild birds should be increased to prevent and mitigate HPAI outbreaks.<\/jats:p>","DOI":"10.3390\/pathogens13100844","type":"journal-article","created":{"date-parts":[[2024,9,30]],"date-time":"2024-09-30T07:19:37Z","timestamp":1727680777000},"page":"844","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Molecular Characterization of a Clade 2.3.4.4b H5N1 High Pathogenicity Avian Influenza Virus from a 2022 Outbreak in Layer Chickens in the Philippines"],"prefix":"10.3390","volume":"13","author":[{"given":"Zyne","family":"Baybay","sequence":"first","affiliation":[{"name":"BioAssets Corporation, Santo Tomas 4234, Batangas, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0627-1920","authenticated-orcid":false,"given":"Andrew","family":"Montecillo","sequence":"additional","affiliation":[{"name":"BioAssets Corporation, Santo Tomas 4234, Batangas, Philippines"},{"name":"Institute of Biological Sciences, University of the Philippines Los Ba\u00f1os, Los Ba\u00f1os 4031, Laguna, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Airish","family":"Pantua","sequence":"additional","affiliation":[{"name":"BioAssets Corporation, Santo Tomas 4234, Batangas, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Milagros","family":"Mananggit","sequence":"additional","affiliation":[{"name":"Department of Agriculture Regional Field Office III, San Fernando 2000, Pampanga, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"suffix":"Jr.","given":"Generoso Rene","family":"Romo","sequence":"additional","affiliation":[{"name":"Philippine College of Poultry Practitioners, Tanay 1980, Rizal, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Esmeraldo","family":"San Pedro","sequence":"additional","affiliation":[{"name":"Philippine College of Poultry Practitioners, Tanay 1980, Rizal, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6460-2623","authenticated-orcid":false,"given":"Homer","family":"Pantua","sequence":"additional","affiliation":[{"name":"BioAssets Corporation, Santo Tomas 4234, Batangas, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0016-4334","authenticated-orcid":false,"given":"Christina Lora","family":"Leyson","sequence":"additional","affiliation":[{"name":"BioAssets Corporation, Santo Tomas 4234, Batangas, Philippines"},{"name":"Balik Scientist Program, Department of Science and Technology, Bicutan 1631, Taguig, Philippines"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,9,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s41579-018-0115-z","article-title":"Host and viral determinants of influenza A virus species specificity","volume":"17","author":"Long","year":"2019","journal-title":"Nat. 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