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The primary target of neutralizing antibodies is the surface antigen hemagglutinin (HA). However, ongoing mutations in the HA sequence result in antigenic drift. The success of a vaccine is contingent on its antigenic congruence with circulating strains. Thus, predicting antigenic variants and deducing antigenic clusters of influenza viruses are pivotal for recommendation of vaccine strains. The antigenicity of influenza A viruses is determined by the interplay of amino acids in the HA1 sequence. In this study, we exploit the ability of convolutional neural networks (CNNs) to extract spatial feature representations in the convolutional layers, which can discern interactions between amino acid sites. We introduce PREDAC-CNN, a model designed to track antigenic evolution of seasonal influenza A viruses. Accessible at http:\/\/predac-cnn.cloudna.cn, PREDAC-CNN formulates a spatially oriented representation of the HA1 sequence, optimized for the convolutional framework. It effectively probes interactions among amino acid sites in the HA1 sequence. Also, PREDAC-CNN focuses exclusively on physicochemical attributes crucial for the antigenicity of influenza viruses, thereby eliminating unnecessary amino acid embeddings. Together, PREDAC-CNN is adept at capturing interactions of amino acid sites within the HA1 sequence and examining the collective impact of point mutations on antigenic variation. Through 5-fold cross-validation and retrospective testing, PREDAC-CNN has shown superior performance in predicting antigenic variants compared to its counterparts. Additionally, PREDAC-CNN has been instrumental in identifying predominant antigenic clusters for A\/H3N2 (1968\u20132023) and A\/H1N1 (1977\u20132023) viruses, significantly aiding in vaccine strain recommendation.<\/jats:p>","DOI":"10.1093\/bib\/bbae033","type":"journal-article","created":{"date-parts":[[2024,2,12]],"date-time":"2024-02-12T07:09:41Z","timestamp":1707721781000},"source":"Crossref","is-referenced-by-count":12,"title":["PREDAC-CNN: predicting antigenic clusters of seasonal influenza A viruses with convolutional neural network"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9594-8483","authenticated-orcid":false,"given":"Jing","family":"Meng","sequence":"first","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123, Jiangsu , China"}]},{"given":"Jingze","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123, Jiangsu , China"}]},{"given":"Wenkai","family":"Song","sequence":"additional","affiliation":[{"name":"College of Computer Science, Sichuan University , Chengdu 610065 , China"}]},{"given":"Honglei","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Cloudna Technology Company , Limited, Beijing 100029 , China"}]},{"given":"Jiangyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory , Guangzhou 510005 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3708-1727","authenticated-orcid":false,"given":"Le","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Computer Science, Sichuan University , Chengdu 610065 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5482-9506","authenticated-orcid":false,"given":"Yousong","family":"Peng","sequence":"additional","affiliation":[{"name":"College of Biology, Hunan University , Changsha 410082 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5869-651X","authenticated-orcid":false,"given":"Aiping","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123, Jiangsu , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6280-6347","authenticated-orcid":false,"given":"Taijiao","family":"Jiang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College , Suzhou 215123, Jiangsu , China"},{"name":"Guangzhou National Laboratory , Guangzhou 510005 , China"},{"name":"State Key Laboratory of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University , Guangzhou, 510120 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,2,10]]},"reference":[{"key":"2024021207093280400_ref1","volume-title":"Influenza Fact Sheet WHO"},{"key":"2024021207093280400_ref2","doi-asserted-by":"crossref","first-page":"434","DOI":"10.4049\/jimmunol.115.2.434","article-title":"Host defenses against influenza virus: the role of anti-hemagglutinin antibody","volume":"115","author":"Virelizier","year":"1975","journal-title":"J Immunol"},{"key":"2024021207093280400_ref3","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1007\/BF01719678","article-title":"Influenza: global surveillance for epidemic and pandemic variants","volume":"10","author":"Cox","year":"1994","journal-title":"Eur J 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