{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,8]],"date-time":"2026-10-08T17:02:45Z","timestamp":1791478965424,"version":"4.3.4"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T00:00:00Z","timestamp":1754265600000},"content-version":"vor","delay-in-days":215,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Innovation and Technology Commission of the Hong Kong SAR Government and Seed Funding for Strategic Interdisciplinary Research Scheme from the University Research Committee","award":["102010190"],"award-info":[{"award-number":["102010190"]}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["75N93021C00015"],"award-info":[{"award-number":["75N93021C00015"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Allergy and Infectious Diseases at the National Institutes of Health","award":["75N93021C00015"],"award-info":[{"award-number":["75N93021C00015"]}]},{"name":"National Institute of Allergy and Infectious Diseases at the National Institutes of Health","award":["R00-AI147029-05"],"award-info":[{"award-number":["R00-AI147029-05"]}]},{"name":"Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services","award":["75N93021C00015"],"award-info":[{"award-number":["75N93021C00015"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The 2022 panzootic of highly pathogenic avian influenza (HPAI) A(H5) viruses has led to unprecedented transmission to multiple mammalian species. Avian influenza A viruses of the H5 subtype circulate globally among birds and are classified into distinct clades based on their haemagglutinin (HA) genetic sequences. Thus, the ability to accurately and rapidly assign clades to newly sequenced isolates is key to surveillance and outbreak response. Cocirculation of endemic, low-pathogenicity avian influenza (LPAI) A(H5) lineages in North American and European wild birds necessitates the ability to rapidly and accurately distinguish between infections arising from these lineages and epizootic HPAI A(H5) viruses. However, currently available clade assignment tools are limited and often require command-line expertise, hindering their utility for public health surveillance labs. To address this gap, we have developed datasets to enable A(H5) clade assignments with Nextclade, a drag-and-drop tool originally developed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic clade classification. Using annotated reference datasets for all historical A(H5) clades, clade 2.3.2.1 descendants, and clade 2.3.4.4 descendants provided by the Food and Agriculture Organization\/World Health Organization\/World Organisation for Animal Health H5 Working Group, we identified clade-defining mutations for every established clade to enable tree-based clade assignment. We then created three Nextclade datasets which can be used to assign clades to A(H5) HA sequences and call mutations relative to reference strains through a drag-and-drop interface. Nextclade assignments were benchmarked with 19\u2009834 unique sequences not in the reference set using a prereleased version of LABEL, a well-validated and widely used command-line software. Prospective assignment of new sequences with Nextclade and LABEL produced very well-matched assignments (match rates of 97.8% and 99.1% for the 2.3.2.1 and 2.3.4.4 datasets, respectively). The all-clades dataset\u00a0also performed well (94.8% match rate) and correctly distinguished between all HPAI and LPAI strains. This tool additionally allows for the identification of polybasic cleavage site sequences and potential N-linked glycosylation sites. These datasets therefore provide an alternative, rapid method to accurately assign clades to new A(H5) HA sequences, with the benefit of an easy-to-use browser interface.<\/jats:p>","DOI":"10.1093\/ve\/veaf058","type":"journal-article","created":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T10:57:47Z","timestamp":1754305067000},"source":"Crossref","is-referenced-by-count":5,"title":["Development of avian influenza A(H5) virus datasets for Nextclade enables rapid and accurate clade assignment"],"prefix":"10.1093","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6977-4168","authenticated-orcid":false,"given":"Jordan T","family":"Ort","sequence":"first","affiliation":[{"name":"Department of Microbiology, Perelman School of Medicine, University of Pennsylvania , 3610 Hamilton Walk, Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel S","family":"Shepard","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention , 1600 Clifton Road, Atlanta, GA 30333 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonja A","family":"Zolnoski","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Perelman School of Medicine, University of Pennsylvania , 3610 Hamilton Walk, Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9769-1527","authenticated-orcid":false,"given":"Tommy T-Y","family":"Lam","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Emerging Infectious Diseases, HKU-Pasteur Research Pole, School of Public Health, the University of Hong Kong , 21 Sassoon Road, Pokfulam, Hong Kong SAR ,","place":["China"]},{"name":"Centre for Immunology and Infection, Hong Kong Science and Technology Park , 17 Science Park West Avenue, Shatin, Hong Kong SAR ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C Todd","family":"Davis","sequence":"additional","affiliation":[{"name":"Influenza Division, National Center for Immunizations and Respiratory Disease, Centers for Disease Control and Prevention , 1600 Clifton Road, Atlanta, GA 30333 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2525-1407","authenticated-orcid":false,"given":"Richard A","family":"Neher","sequence":"additional","affiliation":[{"name":"Biozentrum, University of Basel , Klingelbergstrasse 50, 4056 Basel ,","place":["Switzerland"]},{"name":"Swiss Institute of Bioinformatics , Klingelbergstrasse 50, 4056 Basel ,","place":["Switzerland"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5722-1988","authenticated-orcid":false,"given":"Louise H","family":"Moncla","sequence":"additional","affiliation":[{"name":"Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania , 3800 Spruce Street, Philadelphia, PA 19104 ,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,8,4]]},"reference":[{"key":"2025082206313540400_ref1","doi-asserted-by":"crossref","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J Open Source Softw"},{"key":"2025082206313540400_ref2","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.1080\/22221751.2022.2088407","article-title":"Global dissemination of H5N1 influenza viruses bearing the clade 2.3.4.4b HA gene and biologic analysis of the ones detected in China","volume":"11","author":"Cui","year":"2022","journal-title":"Emerg Microbes Infect"},{"key":"2025082206313540400_ref3","doi-asserted-by":"crossref","first-page":"e3002916","DOI":"10.1371\/journal.pbio.3002916","article-title":"Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance","volume":"22","author":"Dadonaite","year":"2024","journal-title":"PLoS Biol"},{"key":"2025082206313540400_ref4","doi-asserted-by":"crossref","first-page":"e01141-20","DOI":"10.1128\/JVI.01141-20","article-title":"Continued evolution of H5Nx avian influenza viruses in Bangladeshi live poultry markets: pathogenic potential in poultry and mammalian models","volume":"94","author":"El-Shesheny","year":"2020","journal-title":"J Virol"},{"key":"2025082206313540400_ref5","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2025082206313540400_ref6","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1126\/science.1213362","article-title":"Airborne transmission of influenza a\/H5N1 virus between ferrets","volume":"336","author":"Herfst","year":"2012","journal-title":"Science"},{"key":"2025082206313540400_ref7","doi-asserted-by":"crossref","first-page":"2906","DOI":"10.21105\/joss.02906","article-title":"Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens","volume":"6","author":"Huddleston","year":"2021","journal-title":"J Open Source Softw"},{"key":"2025082206313540400_ref8","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1038\/nature10831","article-title":"Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA\/H1N1 virus in ferrets","volume":"486","author":"Imai","year":"2012","journal-title":"Nature"},{"key":"2025082206313540400_ref9","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"Katoh","year":"2002","journal-title":"Nucleic Acids Res"},{"key":"2025082206313540400_ref10","doi-asserted-by":"crossref","first-page":"e03324-20","DOI":"10.1128\/mBio.03324-20","article-title":"Plasticity of the influenza virus H5 HA protein","volume":"12","author":"Kong","year":"2021","journal-title":"mBio"},{"key":"2025082206313540400_ref11","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/s41577-023-00868-8","article-title":"We need to keep an eye on avian influenza","volume":"23","author":"Krammer","year":"2023","journal-title":"Nat Rev Immunol"},{"key":"2025082206313540400_ref12","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1002\/rmv.1846","article-title":"Molecular pathogenesis of H5 highly pathogenic avian influenza: the role of the haemagglutinin cleavage site motif","volume":"25","author":"Luczo","year":"2015","journal-title":"Rev Med Virol"},{"key":"2025082206313540400_ref13","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"2025082206313540400_ref14","doi-asserted-by":"crossref","first-page":"e22171","DOI":"10.1002\/jwmg.22171","article-title":"Highly pathogenic avian influenza is an emerging disease threat to wild birds in North America","volume":"86","author":"Ramey","year":"2022","journal-title":"J Wildl Manag"},{"key":"2025082206313540400_ref15","doi-asserted-by":"crossref","first-page":"vex042","DOI":"10.1093\/ve\/vex042","article-title":"TreeTime: maximum-likelihood phylodynamic analysis","volume":"4","author":"Sagulenko","year":"2018","journal-title":"Virus Evol"},{"key":"2025082206313540400_ref16","doi-asserted-by":"crossref","first-page":"e86921","DOI":"10.1371\/journal.pone.0086921","article-title":"LABEL: fast and accurate lineage assignment with assessment of H5N1 and H9N2 influenza A hemagglutinins","volume":"9","author":"Shepard","year":"2014","journal-title":"PLoS One"},{"key":"2025082206313540400_ref17","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1126\/science.aaf8852","article-title":"Role for migratory wild birds in the global spread of avian influenza H5N8","volume":"354","author":"The Global Consortium for H5N8 and Related Influenza Viruses","year":"2016","journal-title":"Science"},{"key":"2025082206313540400_ref18","author":"WHO\/OEI\/FAO H5 Evolution Working Group","year":"2015"},{"key":"2025082206313540400_ref19","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.3201\/eid1407.071681","article-title":"Toward a unified nomenclature system for highly pathogenic avian influenza virus (H5N1)","volume":"14","author":"WHO\/OIE\/FAO H5N1 Evolution Working Group","year":"2008","journal-title":"Emerg Infect Dis"},{"key":"2025082206313540400_ref20","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1111\/j.1750-2659.2009.00078.x","article-title":"Continuing progress towards a unified nomenclature for the highly pathogenic H5N1 avian influenza viruses: divergence of clade 2\u00b72 viruses","volume":"3","author":"WHO\/OIE\/FAO H5N1 Evolution Working Group","year":"2009","journal-title":"Influenza Resp Viruses"},{"key":"2025082206313540400_ref21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1750-2659.2011.00298.x","article-title":"Continued evolution of highly pathogenic avian influenza a (H5N1): updated nomenclature","volume":"6","author":"WHO\/OIE\/FAO H5N1 Evolution Working Group","year":"2012","journal-title":"Influenza Resp Viruses"},{"key":"2025082206313540400_ref22","author":"World Health Organization","year":"2023"},{"key":"2025082206313540400_ref23","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1111\/irv.12230","article-title":"Revised and updated nomenclature for highly pathogenic avian influenza A (H5N1) viruses","volume":"8","author":"World Health Organization\/World Organisation for Animal Health\/Food and Agriculture Organization (WHO\/OIE\/FAO) H5N1 Evolution Working Group","year":"2014","journal-title":"Influenza Resp Viruses"},{"key":"2025082206313540400_ref24","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1006\/viro.1999.9820","article-title":"Genetic characterization of the pathogenic influenza A\/Goose\/Guangdong\/1\/96 (H5N1) virus: similarity of its hemagglutinin gene to those of H5N1 viruses from the 1997 outbreaks in Hong Kong","volume":"261","author":"Xu","year":"1999","journal-title":"Virology"},{"key":"2025082206313540400_ref25","doi-asserted-by":"crossref","first-page":"e1011871","DOI":"10.1371\/journal.pcbi.1011871","article-title":"Robust expansion of phylogeny for fast-growing genome sequence data","volume":"20","author":"Ye","year":"2024","journal-title":"PLoS Comput Biol"}],"container-title":["Virus Evolution"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ve\/advance-article-pdf\/doi\/10.1093\/ve\/veaf058\/63927392\/veaf058.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf058\/63927392\/veaf058.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ve\/article-pdf\/11\/1\/veaf058\/63927392\/veaf058.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T10:31:45Z","timestamp":1755858705000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ve\/article\/doi\/10.1093\/ve\/veaf058\/8221740"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,9]]}},"URL":"https:\/\/doi.org\/10.1093\/ve\/veaf058","relation":{},"ISSN":["2057-1577"],"issn-type":[{"value":"2057-1577","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"veaf058"}}