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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">On the origin and continuing evolution of SARS-CoV-2</title><author><name sortKey="Tang, Xiaolu" sort="Tang, Xiaolu" uniqKey="Tang X" first="Xiaolu" last="Tang">Xiaolu Tang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wu, Changcheng" sort="Wu, Changcheng" uniqKey="Wu C" first="Changcheng" last="Wu">Changcheng Wu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Li, Xiang" sort="Li, Xiang" uniqKey="Li X" first="Xiang" last="Li">Xiang Li</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Song, Yuhe" sort="Song, Yuhe" uniqKey="Song Y" first="Yuhe" last="Song">Yuhe Song</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Yao, Xinmin" sort="Yao, Xinmin" uniqKey="Yao X" first="Xinmin" last="Yao">Xinmin Yao</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wu, Xinkai" sort="Wu, Xinkai" uniqKey="Wu X" first="Xinkai" last="Wu">Xinkai Wu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Duan, Yuange" sort="Duan, Yuange" uniqKey="Duan Y" first="Yuange" last="Duan">Yuange Duan</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Zhang, Hong" sort="Zhang, Hong" uniqKey="Zhang H" first="Hong" last="Zhang">Hong Zhang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wang, Yirong" sort="Wang, Yirong" uniqKey="Wang Y" first="Yirong" last="Wang">Yirong Wang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Qian, Zhaohui" sort="Qian, Zhaohui" uniqKey="Qian Z" first="Zhaohui" last="Qian">Zhaohui Qian</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Cui, Jie" sort="Cui, Jie" uniqKey="Cui J" first="Jie" last="Cui">Jie Cui</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Lu, Jian" sort="Lu, Jian" uniqKey="Lu J" first="Jian" last="Lu">Jian Lu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmc">7107875</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7107875</idno><idno type="RBID">PMC:7107875</idno><idno type="doi">10.1093/nsr/nwaa036</idno><idno type="pmid">NONE</idno><date when="2020">2020</date><idno type="wicri:Area/Pmc/Corpus">001302</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001302</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">On the origin and continuing evolution of SARS-CoV-2</title><author><name sortKey="Tang, Xiaolu" sort="Tang, Xiaolu" uniqKey="Tang X" first="Xiaolu" last="Tang">Xiaolu Tang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wu, Changcheng" sort="Wu, Changcheng" uniqKey="Wu C" first="Changcheng" last="Wu">Changcheng Wu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Li, Xiang" sort="Li, Xiang" uniqKey="Li X" first="Xiang" last="Li">Xiang Li</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Song, Yuhe" sort="Song, Yuhe" uniqKey="Song Y" first="Yuhe" last="Song">Yuhe Song</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Yao, Xinmin" sort="Yao, Xinmin" uniqKey="Yao X" first="Xinmin" last="Yao">Xinmin Yao</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wu, Xinkai" sort="Wu, Xinkai" uniqKey="Wu X" first="Xinkai" last="Wu">Xinkai Wu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Duan, Yuange" sort="Duan, Yuange" uniqKey="Duan Y" first="Yuange" last="Duan">Yuange Duan</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Zhang, Hong" sort="Zhang, Hong" uniqKey="Zhang H" first="Hong" last="Zhang">Hong Zhang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Wang, Yirong" sort="Wang, Yirong" uniqKey="Wang Y" first="Yirong" last="Wang">Yirong Wang</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Qian, Zhaohui" sort="Qian, Zhaohui" uniqKey="Qian Z" first="Zhaohui" last="Qian">Zhaohui Qian</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Cui, Jie" sort="Cui, Jie" uniqKey="Cui J" first="Jie" last="Cui">Jie Cui</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Lu, Jian" sort="Lu, Jian" uniqKey="Lu J" first="Jian" last="Lu">Jian Lu</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author></analytic><series><title level="j">National Science Review</title><idno type="ISSN">2095-5138</idno><idno type="eISSN">2053-714X</idno><imprint><date when="2020">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure. These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (COVID-19).</p></div></front></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Natl Sci Rev</journal-id><journal-id journal-id-type="iso-abbrev">Natl Sci Rev</journal-id><journal-id journal-id-type="publisher-id">nsr</journal-id><journal-title-group><journal-title>National Science Review</journal-title></journal-title-group><issn pub-type="ppub">2095-5138</issn><issn pub-type="epub">2053-714X</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmc">7107875</article-id><article-id pub-id-type="doi">10.1093/nsr/nwaa036</article-id><article-id pub-id-type="publisher-id">nwaa036</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>On the origin and continuing evolution of SARS-CoV-2</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Tang</surname><given-names>Xiaolu</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="author-notes" rid="afn1"></xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Changcheng</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="author-notes" rid="afn1"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Xiang</given-names></name><xref ref-type="aff" rid="aff2"></xref><xref ref-type="aff" rid="aff3"></xref><xref ref-type="aff" rid="aff4"></xref><xref ref-type="author-notes" rid="afn1"></xref></contrib><contrib contrib-type="author"><name><surname>Song</surname><given-names>Yuhe</given-names></name><xref ref-type="aff" rid="aff2"></xref><xref ref-type="aff" rid="aff5"></xref><xref ref-type="author-notes" rid="afn1"></xref></contrib><contrib contrib-type="author"><name><surname>Yao</surname><given-names>Xinmin</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Wu</surname><given-names>Xinkai</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Duan</surname><given-names>Yuange</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Hong</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Yirong</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Qian</surname><given-names>Zhaohui</given-names></name><xref ref-type="aff" rid="aff6"></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0001-8176-9951</contrib-id><name><surname>Cui</surname><given-names>Jie</given-names></name><email>jcui@ips.ac.cn</email><xref ref-type="aff" rid="aff2"></xref><xref ref-type="aff" rid="aff3"></xref><xref ref-type="corresp" rid="cor2"></xref></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid" authenticated="false">http://orcid.org/0000-0002-4409-1667</contrib-id><name><surname>Lu</surname><given-names>Jian</given-names></name><email>LUJ@pku.edu.cn</email><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"></xref></contrib></contrib-group><aff id="aff1"><label>1</label><institution>State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University</institution>, Beijing, 100871,<country country="CN">China</country></aff><aff id="aff2"><label>2</label><institution>CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences</institution>,<country country="CN">China</country></aff><aff id="aff3"><label>3</label><institution>Center for Biosafety Mega-Science, Chinese Academy of Sciences</institution>,<country country="CN">China</country></aff><aff id="aff4"><label>4</label><institution>University of Chinese Academy of Sciences</institution>,<country country="CN">China</country></aff><aff id="aff5"><label>5</label><institution>School of Life Sciences, Shanghai University</institution>,<country country="CN">China</country></aff><aff id="aff6"><label>6</label><institution>NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College</institution>, Beijing</aff><author-notes><corresp id="cor1"><bold>Corresponding author.</bold> E-mail: <email>LUJ@pku.edu.cn</email></corresp><corresp id="cor2"><bold>Corresponding author.</bold> E-mail: <email>jcui@ips.ac.cn</email></corresp><fn id="afn1"><p>These authors contributed equally to this work.</p></fn></author-notes><pub-date pub-type="epub" iso-8601-date="2020-03-03"><day>03</day><month>3</month><year>2020</year></pub-date><pub-date pub-type="pmc-release"><day>03</day><month>3</month><year>2020</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<elocation-id>nwaa036</elocation-id><permissions><copyright-statement>© The Author(s) 2020. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.</copyright-statement><copyright-year>2020</copyright-year><license license-type="cc-by" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="nwaa036.pdf"></self-uri><abstract><title>ABSTRACT</title><p>The SARS-CoV-2 epidemic started in late December 2019 in Wuhan, China, and has since impacted a large portion of China and raised major global concern. Herein, we investigated the extent of molecular divergence between SARS-CoV-2 and other related coronaviruses. Although we found only 4% variability in genomic nucleotides between SARS-CoV-2 and a bat SARS-related coronavirus (SARSr-CoV; RaTG13), the difference at neutral sites was 17%, suggesting the divergence between the two viruses is much larger than previously estimated. Our results suggest that the development of new variations in functional sites in the receptor-binding domain (RBD) of the spike seen in SARS-CoV-2 and viruses from pangolin SARSr-CoVs are likely caused by mutations and natural selection besides recombination. Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (∼70%) is more prevalent than the S type (∼30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure. These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (COVID-19).</p></abstract><kwd-group kwd-group-type="keywords"><kwd>SARS-CoV-2</kwd><kwd>virus</kwd><kwd>molecular evolution</kwd><kwd>population genetics</kwd></kwd-group><custom-meta-group><custom-meta><meta-name>edited-state</meta-name><meta-value>accepted-manuscript</meta-value></custom-meta><custom-meta><meta-name>article-lifecycle</meta-name><meta-value>PAP</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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