{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T21:54:49Z","timestamp":1783979689309,"version":"3.55.0"},"reference-count":27,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T00:00:00Z","timestamp":1776729600000},"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>The first influenza A(H5N1) human case associated with the A(H5N1) dairy cattle outbreak in the United States was identified in April 2024. The U.S. CDC response to this outbreak was activated days later and remained active until July 2025. During this time, 70 human cases of influenza A(H5N1) were detected with a range of epidemiological links to sources of exposure. Next-generation sequencing (NGS) of human samples was an effectual mechanism for tracking and analyzing the outbreak evolution throughout the response. Due to the specimens\u2019 importance and their variable physical quality, an assortment of laboratory methods was utilized including influenza segment-specific amplification, enrichment capture, short-read, and long-read sequencing. Combining these methods allowed for high-quality genomic data production with rapid turnaround times\u2014typically 2 days from sample receipt to public database submission. By leveraging replicate sequencing, enrichment capture, and sequencing of diagnostic amplicons, valuable genomic data could be produced directly from human clinical specimens that would have normally been considered too weak for routine virologic surveillance sequencing. The resulting assemblies were characterized and analyzed by CDC and shared with local and state public health authorities to facilitate case investigations and risk assessment. These data were further used for phylogenetic analyses of viruses from human cases to investigate likely animal-to-human transmission events and identify clusters within the outbreak that might indicate trends in the types of exposures. Through the adaptable laboratory workflow and the rapid release of viral genomic data, the public health risk mitigation strategies could be evaluated and adjusted in real time.<\/jats:p>","DOI":"10.3390\/v18040482","type":"journal-article","created":{"date-parts":[[2026,4,22]],"date-time":"2026-04-22T09:01:24Z","timestamp":1776848484000},"page":"482","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Next-Generation Sequencing Strategies During the 2024\u20132025 Avian Influenza A(H5N1) Emergency Response in the U.S"],"prefix":"10.3390","volume":"18","author":[{"given":"Julia C.","family":"Frederick","sequence":"first","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6247-5082","authenticated-orcid":false,"given":"Kristine A.","family":"Lacek","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9973-6410","authenticated-orcid":false,"given":"Matthew J.","family":"Wersebe","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Shu","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8211-659X","authenticated-orcid":false,"given":"Lisa M.","family":"Keong","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juliana","family":"DaSilva","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3486-1725","authenticated-orcid":false,"given":"Malania M.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7481-1207","authenticated-orcid":false,"given":"Sydney R.","family":"Sheffield","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0226-5183","authenticated-orcid":false,"given":"Jimma","family":"Liddell","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Natasha","family":"Burnett","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3012-1404","authenticated-orcid":false,"given":"Reina","family":"Chau","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2007-4210","authenticated-orcid":false,"given":"Amanda H.","family":"Sullivan","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yunho","family":"Jang","sequence":"additional","affiliation":[{"name":"Influenza 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USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Norman","family":"Hassell","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4285-5579","authenticated-orcid":false,"given":"Xiao-Yu","family":"Zheng","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ha T.","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, 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G.","family":"Dugan","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles T.","family":"Davis","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8591-3954","authenticated-orcid":false,"given":"Benjamin L.","family":"Rambo-Martin","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA 30329, 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Gen. Virol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"109860","DOI":"10.1016\/j.virol.2023.109860","article-title":"H5N1 highly pathogenic avian influenza clade 2.3.4.4b in wild and domestic birds: Introductions into the United States and reassortments, December 2021\u2013April 2022","volume":"587","author":"Youk","year":"2023","journal-title":"Virology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"3889","DOI":"10.1038\/s41591-025-03905-2","article-title":"Human infections with highly pathogenic avian influenza A(H5N1) viruses in the United States from March 2024 to May 2025","volume":"31","author":"Rolfes","year":"2025","journal-title":"Nat. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"501","DOI":"10.15585\/mmwr.mm7321e1","article-title":"Outbreak of Highly Pathogenic Avian Influenza A(H5N1) Viruses in U.S. Dairy Cattle and Detection of Two Human Cases\u2014United States, 2024","volume":"73","author":"Garg","year":"2024","journal-title":"MMWR Morb. Mortal. Wkly. Rep."},{"key":"ref_5","unstructured":"Centers for Disease Control and Prevention (2025, August 19). Genetic Sequences of Highly Pathogenic Avian Influenza A(H5N1) Viruses Identified in a Person in Louisiana, CDC, Available online: https:\/\/www.cdc.gov\/bird-flu\/spotlights\/h5n1-response-12232024.html."},{"key":"ref_6","unstructured":"Centers for Disease Control and Prevention (2025, August 01). H5 Bird Flu: Current Situation. 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