Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
Identifieur interne : 001631 ( Pmc/Curation ); précédent : 001630; suivant : 001632Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans
Auteurs : Sander Van Boheemen ; Miranda De Graaf ; Chris Lauber ; Theo M. Bestebroer ; V. Stalin Raj ; Ali Moh Zaki ; Albert D. M. E. Osterhaus ; Bart L. Haagmans ; Alexander E. Gorbalenya ; Eric J. Snijder ; Ron A. M. FouchierSource :
- mBio [ 2150-7511 ] ; 2012.
Abstract
A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to
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DOI: 10.1128/mBio.00473-12
PubMed: 23170002
PubMed Central: 3509437
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans</title><author><name sortKey="Van Boheemen, Sander" sort="Van Boheemen, Sander" uniqKey="Van Boheemen S" first="Sander" last="Van Boheemen">Sander Van Boheemen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="De Graaf, Miranda" sort="De Graaf, Miranda" uniqKey="De Graaf M" first="Miranda" last="De Graaf">Miranda De Graaf</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Lauber, Chris" sort="Lauber, Chris" uniqKey="Lauber C" first="Chris" last="Lauber">Chris Lauber</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Bestebroer, Theo M" sort="Bestebroer, Theo M" uniqKey="Bestebroer T" first="Theo M." last="Bestebroer">Theo M. Bestebroer</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Raj, V Stalin" sort="Raj, V Stalin" uniqKey="Raj V" first="V. Stalin" last="Raj">V. Stalin Raj</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zaki, Ali Moh" sort="Zaki, Ali Moh" uniqKey="Zaki A" first="Ali Moh" last="Zaki">Ali Moh Zaki</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Osterhaus, Albert D M E" sort="Osterhaus, Albert D M E" uniqKey="Osterhaus A" first="Albert D. M. E." last="Osterhaus">Albert D. M. E. Osterhaus</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Haagmans, Bart L" sort="Haagmans, Bart L" uniqKey="Haagmans B" first="Bart L." last="Haagmans">Bart L. Haagmans</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gorbalenya, Alexander E" sort="Gorbalenya, Alexander E" uniqKey="Gorbalenya A" first="Alexander E." last="Gorbalenya">Alexander E. Gorbalenya</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Snijder, Eric J" sort="Snijder, Eric J" uniqKey="Snijder E" first="Eric J." last="Snijder">Eric J. Snijder</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Fouchier, Ron A M" sort="Fouchier, Ron A M" uniqKey="Fouchier R" first="Ron A. M." last="Fouchier">Ron A. M. Fouchier</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23170002</idno><idno type="pmc">3509437</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509437</idno><idno type="RBID">PMC:3509437</idno><idno type="doi">10.1128/mBio.00473-12</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">001631</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001631</idno><idno type="wicri:Area/Pmc/Curation">001631</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001631</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans</title><author><name sortKey="Van Boheemen, Sander" sort="Van Boheemen, Sander" uniqKey="Van Boheemen S" first="Sander" last="Van Boheemen">Sander Van Boheemen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="De Graaf, Miranda" sort="De Graaf, Miranda" uniqKey="De Graaf M" first="Miranda" last="De Graaf">Miranda De Graaf</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Lauber, Chris" sort="Lauber, Chris" uniqKey="Lauber C" first="Chris" last="Lauber">Chris Lauber</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Bestebroer, Theo M" sort="Bestebroer, Theo M" uniqKey="Bestebroer T" first="Theo M." last="Bestebroer">Theo M. Bestebroer</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Raj, V Stalin" sort="Raj, V Stalin" uniqKey="Raj V" first="V. Stalin" last="Raj">V. Stalin Raj</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zaki, Ali Moh" sort="Zaki, Ali Moh" uniqKey="Zaki A" first="Ali Moh" last="Zaki">Ali Moh Zaki</name><affiliation><nlm:aff id="aff3"></nlm:aff></affiliation></author><author><name sortKey="Osterhaus, Albert D M E" sort="Osterhaus, Albert D M E" uniqKey="Osterhaus A" first="Albert D. M. E." last="Osterhaus">Albert D. M. E. Osterhaus</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Haagmans, Bart L" sort="Haagmans, Bart L" uniqKey="Haagmans B" first="Bart L." last="Haagmans">Bart L. Haagmans</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gorbalenya, Alexander E" sort="Gorbalenya, Alexander E" uniqKey="Gorbalenya A" first="Alexander E." last="Gorbalenya">Alexander E. Gorbalenya</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Snijder, Eric J" sort="Snijder, Eric J" uniqKey="Snijder E" first="Eric J." last="Snijder">Eric J. Snijder</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Fouchier, Ron A M" sort="Fouchier, Ron A M" uniqKey="Fouchier R" first="Ron A. M." last="Fouchier">Ron A. M. Fouchier</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>ABSTRACT</title><p>A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to <italic>Tylonycteris</italic> bat coronavirus HKU4 (BtCoV-HKU4) and <italic>Pipistrellus</italic> bat coronavirus HKU5 (BtCoV-HKU5), which prototype two species in lineage C of the genus <italic>Betacoronavirus</italic>. In accordance with the guidelines of the International Committee on Taxonomy of Viruses, and in view of the 75% and 77% amino acid sequence identity in 7 conserved replicase domains with BtCoV-HKU4 and BtCoV-HKU5, respectively, we propose that HCoV-EMC/2012 prototypes a novel species in the genus <italic>Betacoronavirus</italic>. HCoV-EMC/2012 may be most closely related to a coronavirus detected in <italic>Pipistrellus pipistrellus</italic> in The Netherlands, but because only a short sequence from the most conserved part of the RNA-dependent RNA polymerase-encoding region of the genome was reported for this bat virus, its genetic distance from HCoV-EMC remains uncertain. HCoV-EMC/2012 is the sixth coronavirus known to infect humans and the first human virus within betacoronavirus lineage C.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="De Groot, Rj" uniqKey="De Groot R">RJ de Groot</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perlman, S" uniqKey="Perlman S">S Perlman</name></author><author><name sortKey="Netland, J" uniqKey="Netland J">J Netland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gloza Rausch, F" uniqKey="Gloza Rausch F">F Gloza-Rausch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lau, Sk" uniqKey="Lau S">SK Lau</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Li, W" uniqKey="Li W">W Li</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pfefferle, S" uniqKey="Pfefferle S">S 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<front><journal-meta><journal-id journal-id-type="nlm-ta">mBio</journal-id><journal-id journal-id-type="iso-abbrev">MBio</journal-id><journal-id journal-id-type="hwp">mbio</journal-id><journal-id journal-id-type="pmc">mbio</journal-id><journal-id journal-id-type="publisher-id">mBio</journal-id><journal-title-group><journal-title>mBio</journal-title></journal-title-group><issn pub-type="epub">2150-7511</issn><publisher><publisher-name>American Society of Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23170002</article-id><article-id pub-id-type="pmc">3509437</article-id><article-id pub-id-type="publisher-id">mBio00473-12</article-id><article-id pub-id-type="doi">10.1128/mBio.00473-12</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans</article-title><alt-title>Genome and Phylogeny of Human Coronavirus EMC/2012</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>van Boheemen</surname><given-names>Sander</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>de Graaf</surname><given-names>Miranda</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lauber</surname><given-names>Chris</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bestebroer</surname><given-names>Theo M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Raj</surname><given-names>V. Stalin</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zaki</surname><given-names>Ali Moh</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Osterhaus</surname><given-names>Albert D. M. E.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Haagmans</surname><given-names>Bart L.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gorbalenya</surname><given-names>Alexander E.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Snijder</surname><given-names>Eric J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Fouchier</surname><given-names>Ron A. M.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><aff id="aff1">Viroscience Lab, Erasmus MC, Rotterdam, The Netherlands<label><sup>a</sup></label>;</aff><aff id="aff2">Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands<label><sup>b</sup></label>;</aff><aff id="aff3">Dr. Soliman Fakeeh Hospital, Jeddah, Saudi Arabia<label><sup>c</sup></label>; and</aff><aff id="aff4">Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia<label><sup>d</sup></label></aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Ron A. M. Fouchier, <email>r.fouchier@erasmusmc.nl</email>.</corresp><fn fn-type="edited-by"><p><bold>Editor</bold> Michael Buchmeier, University of California, Irvine</p></fn></author-notes><pub-date pub-type="epub"><day>20</day><month>11</month><year>2012</year></pub-date><pub-date pub-type="collection"><season>Nov-Dec</season><year>2012</year></pub-date><volume>3</volume><issue>6</issue><elocation-id>e00473-12</elocation-id><history><date date-type="received"><day>24</day><month>10</month><year>2012</year></date><date date-type="accepted"><day>1</day><month>11</month><year>2012</year></date></history><permissions><copyright-statement>Copyright © 2012 van Boheemen et al.</copyright-statement><copyright-year>2012</copyright-year><copyright-holder>van Boheemen et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported</ext-link> license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><title>ABSTRACT</title><p>A novel human coronavirus (HCoV-EMC/2012) was isolated from a man with acute pneumonia and renal failure in June 2012. This report describes the complete genome sequence, genome organization, and expression strategy of HCoV-EMC/2012 and its relation with known coronaviruses. The genome contains 30,119 nucleotides and contains at least 10 predicted open reading frames, 9 of which are predicted to be expressed from a nested set of seven subgenomic mRNAs. Phylogenetic analysis of the replicase gene of coronaviruses with completely sequenced genomes showed that HCoV-EMC/2012 is most closely related to <italic>Tylonycteris</italic> bat coronavirus HKU4 (BtCoV-HKU4) and <italic>Pipistrellus</italic> bat coronavirus HKU5 (BtCoV-HKU5), which prototype two species in lineage C of the genus <italic>Betacoronavirus</italic>. In accordance with the guidelines of the International Committee on Taxonomy of Viruses, and in view of the 75% and 77% amino acid sequence identity in 7 conserved replicase domains with BtCoV-HKU4 and BtCoV-HKU5, respectively, we propose that HCoV-EMC/2012 prototypes a novel species in the genus <italic>Betacoronavirus</italic>. HCoV-EMC/2012 may be most closely related to a coronavirus detected in <italic>Pipistrellus pipistrellus</italic> in The Netherlands, but because only a short sequence from the most conserved part of the RNA-dependent RNA polymerase-encoding region of the genome was reported for this bat virus, its genetic distance from HCoV-EMC remains uncertain. HCoV-EMC/2012 is the sixth coronavirus known to infect humans and the first human virus within betacoronavirus lineage C.</p></abstract><abstract abstract-type="executive-summary"><title>IMPORTANCE</title><p>Coronaviruses are capable of infecting humans and many animal species. Most infections caused by human coronaviruses are relatively mild. However, the outbreak of severe acute respiratory syndrome (SARS) caused by SARS-CoV in 2002 to 2003 and the fatal infection of a human by HCoV-EMC/2012 in 2012 show that coronaviruses are able to cause severe, sometimes fatal disease in humans. We have determined the complete genome of HCoV-EMC/2012 using an unbiased virus discovery approach involving next-generation sequencing techniques, which enabled subsequent state-of-the-art bioinformatics, phylogenetics, and taxonomic analyses. By establishing its complete genome sequence, HCoV-EMC/2012 was characterized as a new genotype which is closely related to bat coronaviruses that are distant from SARS-CoV. We expect that this information will be vital to rapid advancement of both clinical and vital research on this emerging pathogen.</p></abstract><counts><page-count count="9"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>November/December 2012</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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