Questions about comparative genomics of SARS coronavirus isolates
Identifieur interne : 000B21 ( Pmc/Corpus ); précédent : 000B20; suivant : 000B22Questions about comparative genomics of SARS coronavirus isolates
Auteurs : Lowell WoodSource :
- Lancet (London, England) [ 0140-6736 ] ; 2003.
Url:
DOI: 10.1016/S0140-6736(03)14130-X
PubMed: 12932399
PubMed Central: 7134733
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Questions about comparative genomics of SARS coronavirus isolates</title><author><name sortKey="Wood, Lowell" sort="Wood, Lowell" uniqKey="Wood L" first="Lowell" last="Wood">Lowell Wood</name><affiliation><nlm:aff id="aff1">Hoover Institution, Stanford University, Stanford, CA 94305, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">12932399</idno><idno type="pmc">7134733</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7134733</idno><idno type="RBID">PMC:7134733</idno><idno type="doi">10.1016/S0140-6736(03)14130-X</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">000B21</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B21</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Questions about comparative genomics of SARS coronavirus isolates</title><author><name sortKey="Wood, Lowell" sort="Wood, Lowell" uniqKey="Wood L" first="Lowell" last="Wood">Lowell Wood</name><affiliation><nlm:aff id="aff1">Hoover Institution, Stanford University, Stanford, CA 94305, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Lancet (London, England)</title><idno type="ISSN">0140-6736</idno><idno type="eISSN">1474-547X</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ruan, Yj" uniqKey="Ruan Y">YJ Ruan</name></author><author><name sortKey="Wei, Cl" uniqKey="Wei C">CL Wei</name></author><author><name sortKey="Ee, La" uniqKey="Ee L">LA Ee</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="letter"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Lancet</journal-id><journal-id journal-id-type="iso-abbrev">Lancet</journal-id><journal-title-group><journal-title>Lancet (London, England)</journal-title></journal-title-group><issn pub-type="ppub">0140-6736</issn><issn pub-type="epub">1474-547X</issn><publisher><publisher-name>Elsevier Ltd.</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">12932399</article-id><article-id pub-id-type="pmc">7134733</article-id><article-id pub-id-type="publisher-id">S0140-6736(03)14130-X</article-id><article-id pub-id-type="doi">10.1016/S0140-6736(03)14130-X</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Questions about comparative genomics of SARS coronavirus isolates</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Wood</surname><given-names>Lowell</given-names></name><email>lowellwood@attbi.com</email><xref rid="aff1" ref-type="aff">a</xref></contrib></contrib-group><aff id="aff1"><label>a</label>Hoover Institution, Stanford University, Stanford, CA 94305, USA</aff><pub-date pub-type="pmc-release"><day>14</day><month>8</month><year>2003</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on .</pmc-comment>
<pub-date pub-type="ppub"><day>16</day><month>8</month><year>2003</year></pub-date><pub-date pub-type="epub"><day>14</day><month>8</month><year>2003</year></pub-date><volume>362</volume><issue>9383</issue><fpage>578</fpage><lpage>578</lpage><permissions><copyright-statement>Copyright © 2003 Elsevier Ltd. All rights reserved.</copyright-statement><copyright-year>2003</copyright-year><copyright-holder>Elsevier Ltd</copyright-holder><license><license-p>Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.</license-p></license></permissions></article-meta></front><body><p content-type="salutation">Sir</p><p id="para10">YiJun Ruan and colleagues' analysis (May 24, p 1779)<xref rid="bib1" ref-type="bibr"><sup>1</sup></xref> of the comparative genomics of coronavirus isolates from 14 patients with severe acute respiratory syndrome (SARS) is to be welcomed. Two questions, however, are begged by their survey.</p><p id="para20">The first question concerns genomic evolution of the SARS virus. The single-stranded RNA genome of the SARS virus assures genetic lability under moderate selective pressures and high rates of genetic drift. Droplets of respiratory-tract fluids in nasopharyngeal aerosols have volumes of 10<sup>−6</sup>–10<sup>−7</sup> mL, so that the expected SARS virion population in a single droplet is between 0·1 and 10, even for patients with maximum degrees of viraemia. Thus, most infective doses are probably in the range of 10–10<sup>3</sup> virions, whereas a patient's SARS virion-load at peak viraemia is about 10<sup>12</sup>. Considering the 10<sup>3</sup> second effective serum lifetime of a virion, a patient's 10<sup>5</sup> second viraemic-term may see generation of about 10<sup>14</sup> virions, or about 10<sup>12</sup> infective doses. Even with 10<sup>2</sup> successfully infective virions sourced per infected cell—a conservative upper-estimate—there are at least half a dozen viral generations per case history, or about 20 viral generations across the three case-history generations studied by Ruan and colleagues. Since the observed per-base replication error-rate of RNA polymerases is about 310<sup>−5</sup> and the SARS viral genome has about 30 000 bases, the expected genome copying error-rate is about one base per viral generation, or about 20 base errors of aggregate genetic drift after 20 generations, roughly congruent with the 16 “observed twice” single nucleotide polymorphisms reported by Ruan and colleagues.</p><p id="para30">Crucially, however, these 14 case-isolates represent infections during March and early April, 2003, whereas Ruan and colleagues relate that the SARS epidemic began in Guangdong province in November, 2002, so that it has been propagating and mutating at least four—and perhaps as much as five—times longer than is represented by the time-span of all the analysed cases. Where is the four–fold larger genetic drift? Specifically, why is there such close genomic similarity between the Singapore cases and all of the overseas cases? Unless these all trace to the same index case in early March, which seems unlikely, their close genomic similarity is quantitatively inexplicable.</p><p id="para40">The second question concerns the ease with which the SARS virus propagates in vitro, a quite unusual, if not unique, characteristic for known human coronaviruses. This issue is at best thoroughly puzzling and at worst deeply troubling. How do Ruan and colleagues think that this set of viral propagation peculiarities arose?</p></body><back><ref-list id="bibl10"><title>References</title><ref id="bib1"><label>1</label><element-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Ruan</surname><given-names>YJ</given-names></name><name><surname>Wei</surname><given-names>CL</given-names></name><name><surname>Ee</surname><given-names>LA</given-names></name></person-group><article-title>Comparative full-length genome sequence analysis of 14 <bold>SARS</bold> coronavirus isolates and common mutations associated with putative origins of infection</article-title><source>Lancet</source><volume>361</volume><year>2003</year><fpage>1779</fpage><lpage>1785</lpage><pub-id pub-id-type="pmid">12781537</pub-id></element-citation></ref></ref-list></back></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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