{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,13]],"date-time":"2025-12-13T06:55:41Z","timestamp":1765608941989,"version":"build-2065373602"},"reference-count":46,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2022,10,8]],"date-time":"2022-10-08T00:00:00Z","timestamp":1665187200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Royal Netherlands Academy of Art and Sciences (KNAW)","award":["SPIN3-JRP-61"],"award-info":[{"award-number":["SPIN3-JRP-61"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>After its first detection in 1996, the highly pathogenic avian influenza A(H5Nx) virus has spread extensively worldwide. HPAIv A(H5N1) was first detected in Indonesia in 2003 and has been endemic in poultry in this country ever since. However, Indonesia has limited information related to the phylodynamics of HPAIv A(H5N1) in poultry. The present study aimed to increase the understanding of the evolution and temporal dynamics of HPAIv H5N1 in Indonesian poultry between 2003 and 2016. To this end, HPAIv A(H5N1) hemagglutinin sequences of viruses collected from 2003 to 2016 were analyzed using Bayesian evolutionary analysis sampling trees. Results indicated that the common ancestor of Indonesian poultry HPAIv H5N1 arose approximately five years after the common ancestor worldwide of HPAI A(H5Nx). In addition, this study indicated that only two introductions of HPAIv A(H5N1) occurred, after which these viruses continued to evolve due to extensive spread among poultry. Furthermore, this study revealed the divergence of H5N1 clade 2.3.2.1c from H5N1 clade 2.3.2.1b. Both clades 2.3.2.1c and 2.3.2.1b share a common ancestor, clade 1, suggesting that clade 2.3.2.1 originated and diverged from China and other Asian countries. Since there was limited sequence and surveillance data for the HPAIv A(H5N1) from wild birds in Indonesia, the exact role of wild birds in the spread of HPAIv in Indonesia is currently unknown. The evolutionary dynamics of the Indonesian HPAIv A(H5N1) highlight the importance of continuing and improved genomic surveillance and adequate control measures in the different regions of both the poultry and wild birds. Spatial genomic surveillance is useful to take adequate control measures. Therefore, it will help to prevent the future evolution of HPAI A(H5N1) and pandemic threats.<\/jats:p>","DOI":"10.3390\/v14102216","type":"journal-article","created":{"date-parts":[[2022,10,12]],"date-time":"2022-10-12T02:10:27Z","timestamp":1665540627000},"page":"2216","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Phylodynamics of Highly Pathogenic Avian Influenza A(H5N1) Virus Circulating in Indonesian Poultry"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7683-4832","authenticated-orcid":false,"given":"Desniwaty","family":"Karo-karo","sequence":"first","affiliation":[{"name":"Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands"},{"name":"Centre of Diagnostic Standard Indonesian Agricultural Quarantine Agency, Ministry of Agriculture, Jakarta 13220, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0689-7889","authenticated-orcid":false,"given":"Rogier","family":"Bodewes","sequence":"additional","affiliation":[{"name":"National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8434-4465","authenticated-orcid":false,"given":"Restuadi","family":"Restuadi","sequence":"additional","affiliation":[{"name":"Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6586-717X","authenticated-orcid":false,"given":"Alex","family":"Bossers","sequence":"additional","affiliation":[{"name":"Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands"},{"name":"Institute for Risk Assessment Sciences (IRAS), Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7664-1571","authenticated-orcid":false,"given":"Agustiningsih","family":"Agustiningsih","sequence":"additional","affiliation":[{"name":"National Agency for Research and Innovation of The Republic of Indonesia, Jakarta 10340, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4361-3846","authenticated-orcid":false,"given":"Jan Arend","family":"Stegeman","sequence":"additional","affiliation":[{"name":"Department Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guus","family":"Koch","sequence":"additional","affiliation":[{"name":"Wageningen Bioveterinary Research, 8221 RA Lelystad, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5542-106X","authenticated-orcid":false,"given":"David Handojo","family":"Muljono","sequence":"additional","affiliation":[{"name":"Faculty of Medicine, Universitas Hasanuddin, Makassar 90245, Indonesia"},{"name":"Faculty of Medicine and Health, University of Sydney, Camperdown, NSW 2006, Australia"},{"name":"Eijkman Institute for Molecular Biology, Jakarta 10430, Indonesia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,10,8]]},"reference":[{"key":"ref_1","unstructured":"WHO (2022). 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