{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,11]],"date-time":"2026-09-11T22:55:08Z","timestamp":1789167308537,"version":"build-2803163510"},"reference-count":35,"publisher":"MDPI AG","issue":"12","license":[{"start":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T00:00:00Z","timestamp":1765929600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Veterinary Sciences"],"abstract":"<jats:p>Avian Influenza (AI) remains a critical threat to livestock production in Oceania, with recent outbreaks of Highly Pathogenic Avian Influenza (HPAI) H7 subtypes in Australia and New Zealand. Historically, AI detections in these countries were largely confined to wild birds. However, since 2024, multiple outbreaks in commercial poultry populations have been reported, with the emergence of HPAI H7N3, H7N8, and H7N9 in Australia and H7N6 in New Zealand. To investigate the epidemiological links of these outbreaks, we retrieved all publicly available H7 hemagglutinin (HA) gene sequences from animals in Oceania between 2014 and 2025 that were deposited in GISAID and NCBI databases. Phylogenetic reconstruction using maximum likelihood methods revealed distinct Australian and New Zealand clades, suggesting local viral evolution rather than recent transboundary introductions. The absence of phylogenetic clustering between Oceanian and Asian H7 sequences suggests limited recent gene flow between regions, particularly in the HA gene segment. These local viral mutations can pose a threat to the poultry industry; therefore, continuous genomic surveillance in commercial farms and wild bird reservoirs is crucial. Such efforts support the One Health framework by enabling early detection of pathogenic variants and reducing zoonotic spillover risks for animal and public health.<\/jats:p>","DOI":"10.3390\/vetsci12121208","type":"journal-article","created":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T08:32:27Z","timestamp":1765960347000},"page":"1208","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Phylogenetic Analysis of Highly Pathogenic Avian Influenza H7 Viruses in Australia and New Zealand Suggests Local Viral Evolution"],"prefix":"10.3390","volume":"12","author":[{"given":"Jesiaman","family":"Silaban","sequence":"first","affiliation":[{"name":"School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8292-7085","authenticated-orcid":false,"given":"Stephen","family":"Ogada","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7133-4575","authenticated-orcid":false,"given":"Muhammad Noman","family":"Naseem","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD 4072, Australia"},{"name":"School of Veterinary Science, The University of Queensland, Gatton, QLD 4343, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8453-4880","authenticated-orcid":false,"given":"Yun Hee","family":"Baek","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Chungbuk, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6073-0783","authenticated-orcid":false,"given":"Min-Suk","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Microbiology, College of Medicine and Medical Research Institute, Chungbuk National University, Cheongju 28644, Chungbuk, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0780-0399","authenticated-orcid":false,"given":"Sheila Cecily","family":"Ommeh","sequence":"additional","affiliation":[{"name":"Queensland Alliance for Agriculture & Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD 4072, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1001\/jama.2023.1317","article-title":"Bird Flu Has Begun to Spread in Mammals\u2014Here\u2019s What\u2019s Important to Know","volume":"329","author":"Abbasi","year":"2023","journal-title":"JAMA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"173692","DOI":"10.1016\/j.scitotenv.2024.173692","article-title":"Avian Influenza outbreaks: Human infection risks for beach users\u2014One health concern and environmental surveillance implications","volume":"943","author":"Tiwari","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Simancas-Racines, A., Cadena-Ullauri, S., Guevara-Ram\u00edrez, P., Zambrano, A.K., and Simancas-Racines, D. (2023). Avian Influenza: Strategies to Manage an Outbreak. Pathogens, 12.","DOI":"10.3390\/pathogens12040610"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.59454\/whn-2407-224","article-title":"Avian Flu Outbreaks: Understanding the Impact and Taking Precautions","volume":"5","author":"Bilodeau","year":"2024","journal-title":"WHN Sci. Commun."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1186\/s13567-023-01219-0","article-title":"A systematic review of mechanistic models used to study avian influenza virus transmission and control","volume":"54","author":"Lambert","year":"2023","journal-title":"Vet. Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"105548","DOI":"10.1016\/j.prevetmed.2021.105548","article-title":"Unravelling direct and indirect contact patterns between duck farms in France and their association with the 2016\u20132017 epidemic of highly pathogenic avian influenza (H5N8)","volume":"198","author":"Bauzile","year":"2022","journal-title":"Prev. Vet. Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1016\/j.vetmic.2011.08.002","article-title":"Isolation and characterization of influenza A virus (subtype H5N1) that caused the first highly pathogenic avian influenza outbreak in chicken in Bhutan","volume":"155","author":"Dubey","year":"2012","journal-title":"Vet. Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1111\/zph.12879","article-title":"Surveillance on respiratory diseases reveals enzootic circulation of both H5 and H9 avian influenza viruses in small-scale commercial layer farms of Bangladesh","volume":"68","author":"Rahman","year":"2021","journal-title":"Zoonoses Public Health"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Abdelwhab, E.M., and Mettenleiter, T.C. (2023). Zoonotic Animal Influenza Virus and Potential Mixing Vessel Hosts. Viruses, 15.","DOI":"10.3390\/v15040980"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.coviro.2013.07.007","article-title":"Influenza virus hemagglutinin stalk-based antibodies and vaccines","volume":"3","author":"Krammer","year":"2013","journal-title":"Curr. Opin. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.micinf.2011.01.013","article-title":"Influenza genome diversity and evolution","volume":"13","author":"Tsai","year":"2011","journal-title":"Microbes Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"veae064","DOI":"10.1093\/ve\/veae064","article-title":"Prospects for a sequence-based taxonomy of influenza A virus subtypes","volume":"10","author":"Poon","year":"2024","journal-title":"Virus Evol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2155072","DOI":"10.1080\/22221751.2022.2155072","article-title":"Alarming situation of emerging H5 and H7 avian influenza and effective control strategies","volume":"12","author":"Shi","year":"2023","journal-title":"Emerg. Microbes Infect."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"a038679","DOI":"10.1101\/cshperspect.a038679","article-title":"Pathobiological origins and evolutionary history of highly pathogenic avian influenza viruses","volume":"11","author":"Lee","year":"2021","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"102638","DOI":"10.1016\/j.tmaid.2023.102638","article-title":"A comprehensive review of highly pathogenic avian influenza (HPAI) H5N1: An imminent threat at doorstep","volume":"55","author":"Charostad","year":"2023","journal-title":"Travel Med. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e70055","DOI":"10.1111\/irv.70055","article-title":"Potential Arrival Pathway for Highly Pathogenic Avian Influenza H5N1 to Oceania","volume":"18","author":"Plaza","year":"2024","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"100139","DOI":"10.1016\/j.onehlt.2020.100139","article-title":"An overview of avian influenza in the context of the Australian commercial poultry industry","volume":"10","author":"Scott","year":"2020","journal-title":"One Health"},{"key":"ref_18","unstructured":"Queensland Department of Primary Industries (2025, May 20). Outbreaks of Avian Influenza (Bird Flu), Available online: https:\/\/www.dpi.qld.gov.au\/business-priorities\/biosecurity\/animal-biosecurity-welfare\/animal-health-pests-diseases\/reportable\/avian-influenza-bird-flu."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e13281","DOI":"10.1111\/irv.13281","article-title":"Long-Distance Avian Migrants Fail to Bring 2.3.4.4b HPAI H5N1 Into Australia for a Second Year in a Row","volume":"18","author":"Wille","year":"2024","journal-title":"Influenza Other Respir. Viruses"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"e00088-25","DOI":"10.1128\/mra.00088-25","article-title":"High pathogenicity avian influenza (HPAI) H7N6 virus detected in New Zealand poultry","volume":"14","author":"McCulley","year":"2025","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Stanislawek, W.L., Tana, T., Rawdon, T.G., Cork, S.C., Chen, K., Fatoyinbo, H., Cogger, N., Webby, R.J., Webster, R.G., and Joyce, M. (2024). Avian influenza viruses in New Zealand wild birds, with an emphasis on subtypes H5 and H7: Their distinctive epidemiology and genomic properties. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0303756"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","article-title":"AliView: A Fast and Lightweight Alignment Viewer and Editor for Large Datasets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_24","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":"ref_25","unstructured":"Rambaut, A. (2025, July 10). FigTree, v1.4.4, Available online: https:\/\/tree.bio.ed.ac.uk\/software\/figtree\/."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_27","unstructured":"World Organisation for Animal Health (2023). Avian Disease Surveillance in the Asia and Pacific Region, Regional Representation for Asia and the Pacific. Available online: https:\/\/rr-asia.woah.org\/app\/uploads\/2023\/08\/avian_disease_surveillance_asia_pacific_final_clean.pdf."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Wille, M., Grillo, V., Ban De Gouvea Pedroso, S., Burgess, G.W., Crawley, A., Dickason, C., Hansbro, P.M., Hoque, M.A., Horwood, P.F., and Kirkland, P.D. (2022). Australia as a global sink for the genetic diversity of avian influenza A virus. PLoS Pathog., 18.","DOI":"10.1371\/journal.ppat.1010150"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1126\/science.1122438","article-title":"Global patterns of influenza A virus in wild birds","volume":"312","author":"Olsen","year":"2006","journal-title":"Science"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/nrg2053","article-title":"The evolution of epidemic influenza","volume":"8","author":"Nelson","year":"2007","journal-title":"Nat. Rev. Genet."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e00088-25","DOI":"10.2460\/ajvr.24.01.0018","article-title":"The virus is out of the barn: The emergence of HPAI as a pathogen of avian and mammalian wildlife around the globe","volume":"85","author":"Runstadler","year":"2024","journal-title":"Am. J. Vet. Res."},{"key":"ref_32","unstructured":"Department of Agriculture, Fisheries and Forestry, Australian Government (2025, August 18). Australia Declared Free from H7 Avian Influenza, Available online: https:\/\/www.agriculture.gov.au\/about\/news\/h7-eradication-successful."},{"key":"ref_33","unstructured":"World Organisation for Animal Health (2025, November 10). Australia\u2014Highly Pathogenic Avian Influenza H7 Eradication. Available online: https:\/\/www.woah.org\/app\/uploads\/2025\/09\/2025-07-australia-hpai.pdf."},{"key":"ref_34","unstructured":"Ministry for Primary Industries, New Zealand Government (2025, August 18). A Strain of Bird Flu (H7N6) in Otago\u2014Situation Update, Available online: https:\/\/www.mpi.govt.nz\/biosecurity\/exotic-pests-and-diseases-in-new-zealand\/active-biosecurity-responses-to-pests-and-diseases\/a-strain-of-bird-flu-h7n6-in-otago."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.prevetmed.2019.02.002","article-title":"Modelling the impact of biosecurity practices on the risk of highly pathogenic avian influenza outbreaks in Australian commercial chicken farms","volume":"165","author":"Glass","year":"2019","journal-title":"Prev. Vet. Med."}],"container-title":["Veterinary Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/12\/1208\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,17]],"date-time":"2025-12-17T09:08:35Z","timestamp":1765962515000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-7381\/12\/12\/1208"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,17]]},"references-count":35,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["vetsci12121208"],"URL":"https:\/\/doi.org\/10.3390\/vetsci12121208","relation":{},"ISSN":["2306-7381"],"issn-type":[{"value":"2306-7381","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,17]]}}}