{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T17:03:06Z","timestamp":1784653386944,"version":"3.55.0"},"reference-count":31,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T00:00:00Z","timestamp":1784505600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Influenza A virus is a segmented, negative-sense RNA virus. Since the early 2020s, H5 clade 2.3.4.4b viruses have spread widely across Europe, Africa, and Asia, affecting wild birds and poultry. Costa Rica reported its first H5 clade 2.3.4.4b avian influenza virus (AIV) case on 19 January 2023. This study describes an outbreak in backyard chickens and ducks. Initial serum samples collected on 24 January showed three chickens negative for AIV, while one duck tested positive by ELISA and agar gel immunodiffusion (AGID). During a second visit on 27 January, three of four chicken sera collected tested positive by ELISA and AGID. Tissue samples were positive for influenza A by qRT-PCR. Next-generation sequencing recovered five of the eight viral genomic segments, and the hemagglutinin cleavage site sequence (REKRRKR\u2193G) confirmed a highly pathogenic avian influenza virus (HPAIV) H5 strain. The samples were submitted to the National Veterinary Services Laboratories for confirmation. Serological testing showed reactivity to North American low pathogenic H5 antigens, and qRT-PCR amplified influenza A and N1 genes. Virus isolation and next-generation sequencing (NGS) of all eight viral genome segments were successfully performed at the WHO Collaborating Centre at St. Jude Children\u2019s Research Hospital (SJCRH).<\/jats:p>","DOI":"10.3390\/v18070799","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T10:44:02Z","timestamp":1784544242000},"page":"799","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Detection of H5N1 HPAIV Clade 2.3.4.4b Avian Influenza Virus in Backyard Chickens in Costa Rica"],"prefix":"10.3390","volume":"18","author":[{"given":"Bernal","family":"Le\u00f3n","sequence":"first","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hebleen","family":"Brenes","sequence":"additional","affiliation":[{"name":"Centro Nacional de Referencia en Virolog\u00eda (CNRV), Instituto Costarricense de Investigaci\u00f3n y Ense\u00f1anza en Nutrici\u00f3n y Salud (Inciensa), Tres R\u00edos, Cartago 30301, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2106-1166","authenticated-orcid":false,"given":"Nidia S.","family":"Trovao","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, College of Veterinary Medicine, University of Illinois  Urbana-Champaign, Urbana, IL 61802, USA"},{"name":"Carl R. Woese Institute for Genomic Biology, University of Illinois  Urbana-Champaign, Urbana, IL 61802, USA"},{"name":"National Center for Supercomputing Applications, University of Illinois  Urbana-Champaign, Urbana, IL 61802, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Aguilar","sequence":"additional","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fabi\u00e1n","family":"Carvajal","sequence":"additional","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Idania","family":"Chac\u00f3n","sequence":"additional","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guisella","family":"Chaves","sequence":"additional","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0363-7248","authenticated-orcid":false,"given":"M\u00f3nica","family":"Guzm\u00e1n","sequence":"additional","affiliation":[{"name":"Laboratorio LSE-LANASEVE, Servicio Nacional de Salud Animal (SENASA), Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudio","family":"Soto-Garita","sequence":"additional","affiliation":[{"name":"Centro Nacional de Referencia en Virolog\u00eda (CNRV), Instituto Costarricense de Investigaci\u00f3n y Ense\u00f1anza en Nutrici\u00f3n y Salud (Inciensa), Tres R\u00edos, Cartago 30301, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Estela","family":"Cordero","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica y Biolog\u00eda Molecular, Centro Nacional de Referencia en Inocuidad Microbiol\u00f3gica de Alimentos (CNRIMA), Instituto Costarricense de Investigaci\u00f3n y Ense\u00f1anza en Nutrici\u00f3n y Salud (Inciensa), Tres R\u00edos, Cartago 30301, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Francisco","family":"Duarte-Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Laboratorio de Gen\u00f3mica y Biolog\u00eda Molecular, Centro Nacional de Referencia en Inocuidad Microbiol\u00f3gica de Alimentos (CNRIMA), Instituto Costarricense de Investigaci\u00f3n y Ense\u00f1anza en Nutrici\u00f3n y Salud (Inciensa), Tres R\u00edos, Cartago 30301, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Trushar","family":"Jeevan","sequence":"additional","affiliation":[{"name":"Department of Host-Microbe Interactions, St. Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4397-7132","authenticated-orcid":false,"given":"Richard","family":"Webby","sequence":"additional","affiliation":[{"name":"Department of Host-Microbe Interactions, St. Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam","family":"Rubrum","sequence":"additional","affiliation":[{"name":"Department of Host-Microbe Interactions, St. Jude Children\u2019s Research Hospital, Memphis, TN 38105, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Randall","family":"Arguedas","sequence":"additional","affiliation":[{"name":"DRM-Di-Ochomogo Costa Rica, Servicio Nacional de Salud Animal (SENASA), San Nicolas, Cartago 30104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronaldo","family":"Chaves","sequence":"additional","affiliation":[{"name":"Programa Nacional de Salud Aviar, Departamento de Epidemiolog\u00eda, Servicio Nacional de Salud Animal (SENASA), Ulloa, Heredia 40104, Costa Rica"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1080\/22221751.2021.1872355","article-title":"Emergence and Spread of Novel H5N8, H5N5 and H5N1 Clade 2.3.4.4 Highly Pathogenic Avian Influenza in 2020","volume":"10","author":"Lewis","year":"2021","journal-title":"Emerg. 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