{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T20:56:59Z","timestamp":1775163419450,"version":"3.50.1"},"reference-count":35,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T00:00:00Z","timestamp":1759104000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Chengdu Agricultural Science and Technology Center Local Finance Special Funds Project","award":["NASC2019AT01"],"award-info":[{"award-number":["NASC2019AT01"]}]},{"name":"The Postdoctoral Science Foundation 72nd Grant of China","award":["2022M723906"],"award-info":[{"award-number":["2022M723906"]}]},{"name":"Chinese Academy of Agricultural Sciences (CASA) Urban Agricultural Research Institute (UARI) Coordinated Program at the Institute Level","award":["S2024007"],"award-info":[{"award-number":["S2024007"]}]},{"name":"Sichuan Province Youth Fund Program","award":["2025ZNSFSC1074"],"award-info":[{"award-number":["2025ZNSFSC1074"]}]}],"content-domain":{"domain":["www.mdpi.com"],"crossmark-restriction":true},"short-container-title":["Genes"],"abstract":"<jats:p>Background: Pseudorabies virus (PRV), a critical porcine herpesvirus, induces severe diseases in both livestock and wildlife, imposing an incalculable burden and economic losses in livestock production. In this study, we investigated the evolutionary mechanisms and host adaptation strategies of the PRV gB gene through genomic alignment. The gB gene is highly conserved in PRV, and its encoded gB protein exhibits functional interchangeability across different herpesvirus species. Notably, the gB protein elicits the production of both complement-dependent and complement-independent neutralizing antibodies in animals, while also being closely associated with syncytium formation. Methods: Phylogenetic analysis and codon usage pattern analysis were performed in this study. A total of 110 gB gene sequences were analyzed, which were collected from [2011 to 2024] across the following regions: [Fujian, Shanxi, Guangxi, Guangdong, Chongqing, Henan, Shaanxi, Heilongjiang, Sichuan, Jiangsu, Jilin, Huzhou, Shandong, Hubei, Jiangxi, Beijing, Shanghai, Chengdu (China)], [Budapest, Szeged (Hungary)], [Tokyo (Japan)], [London (United Kingdom)], [Athens (Greece)], [Berlin (Germany)], and [New Jersey (United States)]. Results: The gB gene of PRV employs an evolutionary \u201cselective optimization\u201d strategy to maintain a dynamic balance between ensuring functional expression and evading host immune pressure, with this core trend strongly supported by its codon usage bias and mutation characteristics. First, the gene exhibits significant codon usage bias [Effective Number of Codons (ENC) = 27.94 \u00b1 0.1528], driven primarily by natural selection rather than mere mutational pressure. Second, phylogenetic analysis shows that the second codon position of gB has the highest mutation rate (1.0586)\u2014a feature closely linked to its antigenic variation and immune escape capabilities, further reflecting adaptive evolution against host immune pressure. Additionally, ENC-GC3 plot analysis reveals the complex regulatory mechanisms underlying codon bias formation, providing molecular evidence for the \u201cselective optimization\u201d strategy and clarifying PRV\u2019s core evolutionary path to balance functional needs and immune pressure over time. Conclusions: Our study findings deepen our understanding of the evolutionary mechanisms of PRV and provide theoretical support for designing vaccines and assessing the risk of cross-species transmission.<\/jats:p>","DOI":"10.3390\/genes16101155","type":"journal-article","created":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T08:00:32Z","timestamp":1759132832000},"page":"1155","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Codon Usage Preference and Evolutionary Analysis of Pseudorabies Virus"],"prefix":"10.3390","volume":"16","author":[{"given":"Aolong","family":"Xiong","sequence":"first","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Li","sequence":"additional","affiliation":[{"name":"Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science & Technology Center, Chengdu 610213, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaodong","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7505-990X","authenticated-orcid":false,"given":"Yunxin","family":"Ren","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fuchao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqi","family":"Li","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziqing","family":"Yuan","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junhong","family":"Bie","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinxiang","family":"Li","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Chengyang Campus, Qingdao Agricultural University, Qingdao 266109, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1454-8969","authenticated-orcid":false,"given":"Changzhan","family":"Xie","sequence":"additional","affiliation":[{"name":"Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science & Technology Center, Chengdu 610213, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1128\/MMBR.69.3.462-500.2005","article-title":"Molecular biology of pseudorabies virus: Impact on neurovirology and veterinary medicine","volume":"69","author":"Pomeranz","year":"2005","journal-title":"Microbiol. 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