{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:28:33Z","timestamp":1791386913609,"version":"4.3.3"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T00:00:00Z","timestamp":1589414400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Natural Science Foundation of Outstanding Youth Fund in China","award":["No. 31922081"],"award-info":[{"award-number":["No. 31922081"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["No. 2016YFD0500402"],"award-info":[{"award-number":["No. 2016YFD0500402"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Young Top-Notch Talents of National Ten Thousand Talent Program"},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["No. Y0201900459"],"award-info":[{"award-number":["No. Y0201900459"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Six Talent Peaks Project of Jiangsu Province of China","award":["No. NY-045"],"award-info":[{"award-number":["No. NY-045"]}]},{"name":"Fonds National de la Recherche Scientifique"},{"name":"FRS-FNRS"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["No. U19 AI135995"],"award-info":[{"award-number":["No. U19 AI135995"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Interne Fondsen KU Leuven"},{"name":"Internal Funds KU Leuven","award":["No. C14\/18\/094"],"award-info":[{"award-number":["No. C14\/18\/094"]}]},{"name":"Research Foundation\u2014Flanders"},{"name":"European Research Council under the European Union\u2019s Horizon 2020 research and innovation program","award":["No. 725422"],"award-info":[{"award-number":["No. 725422"]}]},{"name":"Research Foundation\u2014Flanders","award":["G066215N"],"award-info":[{"award-number":["G066215N"]}]},{"name":"Research Foundation\u2014Flanders","award":["G0D5117N"],"award-info":[{"award-number":["G0D5117N"]}]},{"name":"Research Foundation\u2014Flanders","award":["75 G0B9317N"],"award-info":[{"award-number":["75 G0B9317N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15\u2009years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.<\/jats:p>","DOI":"10.1093\/molbev\/msaa117","type":"journal-article","created":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T07:08:47Z","timestamp":1588921727000},"page":"2641-2654","source":"Crossref","is-referenced-by-count":135,"title":["Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus"],"prefix":"10.1093","volume":"37","author":[{"given":"Wan-Ting","family":"He","sequence":"first","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7243-0865","authenticated-orcid":false,"given":"Xiang","family":"Ji","sequence":"additional","affiliation":[{"name":"Department of Mathematics, Tulane University, New Orleans, LA"},{"name":"Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA"},{"name":"Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"He","sequence":"additional","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon","family":"Dellicour","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium"},{"name":"Spatial Epidemiology Lab (SpELL), Universit\u00e9 Libre de Bruxelles, Bruxelles, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shilei","family":"Wang","sequence":"additional","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gairu","family":"Li","sequence":"additional","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Letian","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marius","family":"Gilbert","sequence":"additional","affiliation":[{"name":"Spatial Epidemiology Lab (SpELL), Universit\u00e9 Libre de Bruxelles, Bruxelles, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henan","family":"Zhu","sequence":"additional","affiliation":[{"name":"Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA"},{"name":"Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gang","family":"Xing","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Veit","sequence":"additional","affiliation":[{"name":"Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Huang","sequence":"additional","affiliation":[{"name":"Zhengzhou New Channel Agricultural Technology Co., Ltd, Zhengzhou, Henan, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guan-Zhu","family":"Han","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaowei","family":"Huang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc A","family":"Suchard","sequence":"additional","affiliation":[{"name":"Departments of Biomathematics and Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA"},{"name":"Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guy","family":"Baele","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lemey","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Su","sequence":"additional","affiliation":[{"name":"MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,5,14]]},"reference":[{"issue":"6","key":"2020101221245135800_msaa117-B1","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1093\/sysbio\/syz020","article-title":"BEAGLE 3: improved performance, scaling, and usability for a high-performance computing library for statistical phylogenetics","volume":"68","author":"Ayres","year":"2019","journal-title":"Syst Biol"},{"issue":"9","key":"2020101221245135800_msaa117-B2","doi-asserted-by":"crossref","first-page":"2157","DOI":"10.1093\/molbev\/mss084","article-title":"Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty","volume":"29","author":"Baele","year":"2012","journal-title":"Mol Biol Evol"},{"issue":"2","key":"2020101221245135800_msaa117-B3","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate 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