{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T19:50:14Z","timestamp":1774381814838,"version":"3.50.1"},"reference-count":61,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T00:00:00Z","timestamp":1702339200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I &amp;gt; IIa and IIb-A &amp;gt; IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzad003","type":"journal-article","created":{"date-parts":[[2024,1,9]],"date-time":"2024-01-09T19:12:57Z","timestamp":1704827577000},"source":"Crossref","is-referenced-by-count":16,"title":["Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3377-8439","authenticated-orcid":false,"given":"Ke-Jia","family":"Shan","sequence":"first","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University , Beijing 100871,","place":["China"]},{"name":"Sinovac Biotech Ltd. , Beijing 100085,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2428-8630","authenticated-orcid":false,"given":"Changcheng","family":"Wu","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing 100052,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7737-5092","authenticated-orcid":false,"given":"Xiaolu","family":"Tang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University , Beijing 100871,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3362-662X","authenticated-orcid":false,"given":"Roujian","family":"Lu","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing 100052,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6976-459X","authenticated-orcid":false,"given":"Yaling","family":"Hu","sequence":"additional","affiliation":[{"name":"Sinovac Biotech Ltd. , Beijing 100085,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5963-1136","authenticated-orcid":false,"given":"Wenjie","family":"Tan","sequence":"additional","affiliation":[{"name":"NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing 100052,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4409-1667","authenticated-orcid":false,"given":"Jian","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University , Beijing 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