{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T22:28:22Z","timestamp":1783117702430,"version":"3.54.6"},"reference-count":96,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:00:00Z","timestamp":1761609600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Scientific and Technological Program of China","award":["2022YFC2303700"],"award-info":[{"award-number":["2022YFC2303700"]}]},{"name":"Key Scientific and Technological Program of China","award":["2021YFC2301300"],"award-info":[{"award-number":["2021YFC2301300"]}]},{"name":"Key Scientific and Technological Program of China","award":["2021YFC2300900"],"award-info":[{"award-number":["2021YFC2300900"]}]},{"name":"Key Scientific and Technological Program of Yunnan","award":["202303AC100026"],"award-info":[{"award-number":["202303AC100026"]}]},{"name":"Yunnan Fundamental Research Projects","award":["202301AT070311"],"award-info":[{"award-number":["202301AT070311"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82151214"],"award-info":[{"award-number":["82151214"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32200137"],"award-info":[{"award-number":["32200137"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the virus's remarkable ability to evolve and adapt in diverse hosts. Despite the observation of recurrent mutations and convergent evolution in the viral genome, the mechanisms driving these processes remain poorly understood, particularly in the context of diverse host environments and limited genomic surveillance. We established a rigorously controlled in vitro cellular system within a Biosafety Level 3 Laboratory, ensuring strict adherence to biosafety protocols while passaging the virus in seven cell lines derived from four tissues across five mammalian species. High-throughput sequencing revealed consistent positive selection on the Spike (S) protein, highlighting its adaptability in the absence of adaptive immune responses or therapeutic pressures. Type I interferons (IFN-I) and APOBEC-mediated editing may emerge as key modulators of viral evolution. Notably, IFN-I activation is inversely correlated with the accumulation of S protein mutations (E484D, P812R\/L, L1186R). Our findings uncover host-specific selective forces in shaping SARS-CoV-2 evolution and highlight the need for systematic approaches to mitigate viral transmission and emerging variants.<\/jats:p>","DOI":"10.1093\/molbev\/msaf274","type":"journal-article","created":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T12:41:46Z","timestamp":1761568906000},"source":"Crossref","is-referenced-by-count":5,"title":["Convergent Evolution and Host-Limiting Impacts of SARS-CoV-2 Revealed by Cellular Experiments"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9650-6089","authenticated-orcid":false,"given":"Ting","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650201 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0364-7216","authenticated-orcid":false,"given":"Ren-Rong","family":"Tian","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650201 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-1976-8099","authenticated-orcid":false,"given":"Fengyi","family":"Li","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan 650223 ,","place":["China"]},{"name":"Savaid Medical School and Future Technology School, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7737-5092","authenticated-orcid":false,"given":"Xiaolu","family":"Tang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Gene Function and Modulation Research, Center for Bioinformatics, School of Life Sciences, Peking University , Beijing 100871 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8680-0996","authenticated-orcid":false,"given":"Wenbin","family":"He","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan 650223 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-7394-3848","authenticated-orcid":false,"given":"Zhen-Ping","family":"Hao","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650201 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-7073-5763","authenticated-orcid":false,"given":"Lin","family":"Zhuo","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650201 ,","place":["China"]},{"name":"Savaid Medical School and Future Technology School, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4409-1667","authenticated-orcid":false,"given":"Jian","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Gene Function and Modulation Research, Center for Bioinformatics, School of Life Sciences, Peking University , Beijing 100871 ,","place":["China"]},{"name":"Beijing Advanced Center of RNA Biology (BEACON), Peking University , Beijing 100871 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6044-6002","authenticated-orcid":false,"given":"Xuemei","family":"Lu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming, Yunnan 650223 ,","place":["China"]},{"name":"Savaid Medical School and Future Technology School, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5469-0324","authenticated-orcid":false,"given":"Yong-Tang","family":"Zheng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genetic Evolution & Animal Models, Key Laboratory of Bioactive Peptides of Yunnan Province, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy of Sciences , Kunming 650201 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