{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T15:50:21Z","timestamp":1790783421295,"version":"4.1.0"},"reference-count":40,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T00:00:00Z","timestamp":1715299200000},"content-version":"vor","delay-in-days":9,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81961128002"],"award-info":[{"award-number":["81961128002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Journal of Medical Virology"],"published-print":{"date-parts":[[2024,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The H1N1pdm09 virus has been a persistent threat to public health since the 2009 pandemic. Particularly, since the relaxation of COVID\u201019 pandemic mitigation measures, the influenza virus and SARS\u2010CoV\u20102 have been concurrently prevalent worldwide. To determine the antigenic evolution pattern of H1N1pdm09 and develop preventive countermeasures, we collected influenza sequence data and immunological data to establish a new antigenic evolution analysis framework. A machine learning model (XGBoost, accuracy\u2009=\u20090.86, area under the receiver operating characteristic curve\u2009=\u20090.89) was constructed using epitopes, physicochemical properties, receptor binding sites, and glycosylation sites as features to predict the antigenic similarity relationships between influenza strains. An antigenic correlation network was constructed, and the Markov clustering algorithm was used to identify antigenic clusters. Subsequently, the antigenic evolution pattern of H1N1pdm09 was analyzed at the global and regional scales across three continents. We found that H1N1pdm09 evolved into around five antigenic clusters between 2009 and 2023 and that their antigenic evolution trajectories were characterized by cocirculation of multiple clusters, low\u2010level persistence of former dominant clusters, and local heterogeneity of cluster circulations. Furthermore, compared with the seasonal H1N1 virus, the potential cluster\u2010transition determining sites of H1N1pdm09 were restricted to epitopes Sa and Sb. This study demonstrated the effectiveness of machine learning methods for characterizing antigenic evolution of viruses, developed a specific model to rapidly identify H1N1pdm09 antigenic variants, and elucidated their evolutionary patterns. Our findings may provide valuable support for the implementation of effective surveillance strategies and targeted prevention efforts to mitigate the impact of H1N1pdm09.<\/jats:p>","DOI":"10.1002\/jmv.29657","type":"journal-article","created":{"date-parts":[[2024,5,10]],"date-time":"2024-05-10T07:39:18Z","timestamp":1715326758000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Characterizing the antigenic evolution of pandemic influenza A (H1N1) pdm09 from 2009 to 2023"],"prefix":"10.1002","volume":"96","author":[{"given":"Peiwen","family":"Cheng","sequence":"first","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ke","family":"Zhai","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjie","family":"Han","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinfeng","family":"Zeng","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zekai","family":"Qiu","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yilin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kang","family":"Tang","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Health Statistics, School of Public Health Guangdong Medical University  Dongguan China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Tang","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haoyu","family":"Long","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory  Guangzhou China"},{"name":"State Key Laboratory of Respiratory Disease, The Key Laboratory of Advanced Interdisciplinary Studies Center the First Affiliated Hospital of Guangzhou Medical University  Guangzhou China"},{"name":"Suzhou Institute of Systems Medicine Chinese Academy of Medical Sciences &amp; Peking Union Medical College  Suzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8184-8430","authenticated-orcid":false,"given":"Xiangjun","family":"Du","sequence":"additional","affiliation":[{"name":"School of Public Health (Shenzhen) Sun Yat\u2010sen University  Guangzhou China"},{"name":"School of Public Health (Shenzhen) Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"},{"name":"Shenzhen Key Laboratory of Pathogenic Microbes and Biosecurity Shenzhen Campus of Sun Yat\u2010sen University  Shenzhen China"},{"name":"Key Laboratory of Tropical Disease Control, Ministry of Education Sun Yat\u2010sen University  Guangzhou China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2024,5,10]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(17)33293-2"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(22)00503-5"},{"issue":"2","key":"e_1_2_8_4_1","first-page":"135","article-title":"Risk assessment of public health emergencies concerned in China, February 2023","volume":"38","author":"Mengxue D","year":"2023","journal-title":"Dis Surveill"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/289373a0"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2053"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1097211"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a038489"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms1710"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1007683"},{"key":"e_1_2_8_11_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2021\/9997669","article-title":"A deep learning approach for predicting antigenic variation of influenza A H3N2","volume":"2021","author":"Xia YL","year":"2021","journal-title":"Comput Math Methods Med"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1244730"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0207777"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep14171"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.virs.2023.05.008"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msz050"},{"issue":"1","key":"e_1_2_8_17_1","first-page":"19","article-title":"The new pandemic influenza A\/(H1N1)pdm09 virus: is it really \u201cnew\u201d?","volume":"57","author":"Baldo V","year":"2016","journal-title":"J Prev Med Hyg"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41572-018-0002-y"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008553"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkf436"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature14460"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1038\/s42256-019-0138-9"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.14492"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.7.1575"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.1239303"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-S1-S41"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp077"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkab301"},{"issue":"11","key":"e_1_2_8_29_1","first-page":"117","article-title":"Organisation mondiale de la sant\u00e9. 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