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Recombination and selection play crucial roles in the evolutionary adaptation of MPXV; however, the evolution of MPXV and its relationship with the recent, ground\u2010breaking monkeypox epidemic remains poorly understood. To gain insights into the evolutionary dynamics of MPXV, comprehensive in silico recombination and selection analyses were conducted based on MPXV whole genome sequence data. Three types of recombination were identified: five ancestor\u2010sharing interspecies recombination events, six specific interspecies recombination events and four intraspecies recombination events. The results highlight the prevalent occurrence of recombination in MPXV, with 73.3% occurring in variable regions of the genome. Selection analysis was performed from three dimensions: proteins around recombination regions, proteins from recombinant ancestors and MPXV branches, and whole\u2010genome gene analysis. Results revealed 2 and 7 proteins under positive selection in the first two dimensions, respectively. These proteins are mainly involved in infection immunity, apoptosis regulation and viral virulence. Whole\u2010genome analysis detected 25 genes under positive selection, mainly associated with immune response and viral regulation. Understanding their evolutionary patterns will help predict and prevent cross\u2010species transmission, zoonotic outbreaks and potential human epidemics.<\/jats:p>","DOI":"10.1002\/jmv.29825","type":"journal-article","created":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T02:38:34Z","timestamp":1721875114000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Recombination and selection trajectory of the monkeypox virus during its adaptation in the human population"],"prefix":"10.1002","volume":"96","author":[{"given":"Jialu","family":"Zheng","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":"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":"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":"Jian","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":"Kaijie","family":"Liu","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":"Yixiong","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Infectious Disease Prevention Bao'an Center for Disease Control and Prevention Shenzhen P.R. 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