Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
Identifieur interne : 000F70 ( Pmc/Checkpoint ); précédent : 000F69; suivant : 000F71Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
Auteurs : Matthew Cotten ; Simon J. Watson ; Alimuddin I. Zumla ; Hatem Q. Makhdoom ; Anne L. Palser ; Swee Hoe Ong ; Abdullah A. Al Rabeeah ; Rafat F. Alhakeem ; Abdullah Assiri ; Jaffar A. Al-Tawfiq ; Ali Albarrak ; Mazin Barry ; Atef Shibl ; Fahad A. Alrabiah ; Sami Hajjar ; Hanan H. Balkhy ; Hesham Flemban ; Andrew Rambaut ; Paul Kellam ; Ziad A. MemishSource :
- mBio [ 2150-7511 ] ; 2014.
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (
Url:
DOI: 10.1128/mBio.01062-13
PubMed: 24549846
PubMed Central: 3944817
Affiliations:
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PMC:3944817Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus</title>
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<author><name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name>
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<author><name sortKey="Makhdoom, Hatem Q" sort="Makhdoom, Hatem Q" uniqKey="Makhdoom H" first="Hatem Q." last="Makhdoom">Hatem Q. Makhdoom</name>
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<front><div type="abstract" xml:lang="en"><title>ABSTRACT</title>
<p>The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10<sup>−3</sup>
substitutions per site per year (95% credible interval [95% CI], 8.76 × 10<sup>−4</sup>
; 1.37 × 10<sup>−3</sup>
) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (<italic>R</italic>
<sub>0</sub>
) for the virus that is less than 1.</p>
</div>
</front>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<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">24549846</article-id>
<article-id pub-id-type="pmc">3944817</article-id>
<article-id pub-id-type="publisher-id">mBio01062-13</article-id>
<article-id pub-id-type="doi">10.1128/mBio.01062-13</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus</article-title>
<alt-title>Spread, Circulation, and Evolution of MERS-CoV</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Cotten</surname>
<given-names>Matthew</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Watson</surname>
<given-names>Simon J.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Zumla</surname>
<given-names>Alimuddin I.</given-names>
</name>
<xref ref-type="aff" rid="aff2 aff3 aff4"><sup>b,c,d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Makhdoom</surname>
<given-names>Hatem Q.</given-names>
</name>
<xref ref-type="aff" rid="aff5"><sup>e</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Palser</surname>
<given-names>Anne L.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ong</surname>
<given-names>Swee Hoe</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>a</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Al Rabeeah</surname>
<given-names>Abdullah A.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Alhakeem</surname>
<given-names>Rafat F.</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Assiri</surname>
<given-names>Abdullah</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>b</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Al-Tawfiq</surname>
<given-names>Jaffar A.</given-names>
</name>
<xref ref-type="aff" rid="aff6"><sup>f</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Albarrak</surname>
<given-names>Ali</given-names>
</name>
<xref ref-type="aff" rid="aff7"><sup>g</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Barry</surname>
<given-names>Mazin</given-names>
</name>
<xref ref-type="aff" rid="aff8"><sup>h</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shibl</surname>
<given-names>Atef</given-names>
</name>
<xref ref-type="aff" rid="aff8"><sup>h</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Alrabiah</surname>
<given-names>Fahad A.</given-names>
</name>
<xref ref-type="aff" rid="aff9"><sup>i</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hajjar</surname>
<given-names>Sami</given-names>
</name>
<xref ref-type="aff" rid="aff9"><sup>i</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Balkhy</surname>
<given-names>Hanan H.</given-names>
</name>
<xref ref-type="aff" rid="aff10"><sup>j</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Flemban</surname>
<given-names>Hesham</given-names>
</name>
<xref ref-type="aff" rid="aff11"><sup>k</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rambaut</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="aff12 aff13"><sup>l,m</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kellam</surname>
<given-names>Paul</given-names>
</name>
<xref ref-type="aff" rid="aff1 aff3 aff4"><sup>a,c,d</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Memish</surname>
<given-names>Ziad A.</given-names>
</name>
<xref ref-type="aff" rid="aff2 aff14"><sup>b,n</sup>
</xref>
</contrib>
<aff id="aff1"><label><sup>a</sup>
</label>
Wellcome Trust Sanger Institute, Hinxton, United Kingdom</aff>
<aff id="aff2"><label><sup>b</sup>
</label>
Global Centre for Mass Gatherings Medicine (GCMGM), Ministry of Health, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff3"><label><sup>c</sup>
</label>
Department of Medical Microbiology, University College London Hospitals NHS Foundation Trust, London, United Kingdom</aff>
<aff id="aff4"><label><sup>d</sup>
</label>
Division of Infection and Immunity, University College London, London, United Kingdom</aff>
<aff id="aff5"><label><sup>e</sup>
</label>
Jeddah Regional Laboratory, Ministry of Health, Jeddah, Kingdom of Saudi Arabia</aff>
<aff id="aff6"><label><sup>f</sup>
</label>
Saudi Aramco Medical Services Organization, Saudi Aramco, Dhahran, Kingdom of Saudi Arabia</aff>
<aff id="aff7"><label><sup>g</sup>
</label>
Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff8"><label><sup>h</sup>
</label>
King Saud University, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff9"><label><sup>i</sup>
</label>
King Faisal Specialist Hospital, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff10"><label><sup>j</sup>
</label>
King Abdulaziz Medical City, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff11"><label><sup>k</sup>
</label>
Alhada Military Hospital, Riyadh, Kingdom of Saudi Arabia</aff>
<aff id="aff12"><label><sup>l</sup>
</label>
Institute of Evolutionary Biology, Ashworth Laboratories, Kings Buildings, West Mains Road, Edinburgh, United Kingdom</aff>
<aff id="aff13"><label><sup>m</sup>
</label>
Fogarty International Center, NIH, Bethesda, Maryland, USA</aff>
<aff id="aff14"><label><sup>n</sup>
</label>
College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia</aff>
</contrib-group>
<author-notes><corresp id="cor1">Address correspondence to Ziad A. Memish, <email>zmemish@yahoo.com</email>
.</corresp>
<fn fn-type="equal"><p>M.C., S.J.W., A.I.Z., P.K., and Z.A.M. contributed equally to this work.</p>
</fn>
<fn fn-type="edited-by"><p><bold>Editor</bold>
Michael Katze, University of Washington</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>18</day>
<month>2</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><season>Jan-Feb</season>
<year>2014</year>
</pub-date>
<volume>5</volume>
<issue>1</issue>
<elocation-id>e01062-13</elocation-id>
<history><date date-type="received"><day>9</day>
<month>12</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>16</day>
<month>1</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Cotten et al.</copyright-statement>
<copyright-year>2014</copyright-year>
<copyright-holder>Cotten 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 license</ext-link>
, 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>The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10<sup>−3</sup>
substitutions per site per year (95% credible interval [95% CI], 8.76 × 10<sup>−4</sup>
; 1.37 × 10<sup>−3</sup>
) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (<italic>R</italic>
<sub>0</sub>
) for the virus that is less than 1.</p>
</abstract>
<abstract abstract-type="executive-summary"><title>IMPORTANCE</title>
<p>MERS-CoV adaptation toward higher rates of sustained human-to-human transmission appears not to have occurred yet. While MERS-CoV transmission currently appears weak, careful monitoring of changes in MERS-CoV genomes and of the MERS epidemic should be maintained. The observation of phylogenetically related MERS-CoV in geographically diverse locations must be taken into account in efforts to identify the animal source and transmission of the virus.</p>
</abstract>
<counts><page-count count="11"></page-count>
</counts>
<custom-meta-group><custom-meta><meta-name>cover-date</meta-name>
<meta-value>January/February 2014</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations><list></list>
<tree><noCountry><name sortKey="Al Rabeeah, Abdullah A" sort="Al Rabeeah, Abdullah A" uniqKey="Al Rabeeah A" first="Abdullah A." last="Al Rabeeah">Abdullah A. Al Rabeeah</name>
<name sortKey="Al Tawfiq, Jaffar A" sort="Al Tawfiq, Jaffar A" uniqKey="Al Tawfiq J" first="Jaffar A." last="Al-Tawfiq">Jaffar A. Al-Tawfiq</name>
<name sortKey="Albarrak, Ali" sort="Albarrak, Ali" uniqKey="Albarrak A" first="Ali" last="Albarrak">Ali Albarrak</name>
<name sortKey="Alhakeem, Rafat F" sort="Alhakeem, Rafat F" uniqKey="Alhakeem R" first="Rafat F." last="Alhakeem">Rafat F. Alhakeem</name>
<name sortKey="Alrabiah, Fahad A" sort="Alrabiah, Fahad A" uniqKey="Alrabiah F" first="Fahad A." last="Alrabiah">Fahad A. Alrabiah</name>
<name sortKey="Assiri, Abdullah" sort="Assiri, Abdullah" uniqKey="Assiri A" first="Abdullah" last="Assiri">Abdullah Assiri</name>
<name sortKey="Balkhy, Hanan H" sort="Balkhy, Hanan H" uniqKey="Balkhy H" first="Hanan H." last="Balkhy">Hanan H. Balkhy</name>
<name sortKey="Barry, Mazin" sort="Barry, Mazin" uniqKey="Barry M" first="Mazin" last="Barry">Mazin Barry</name>
<name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name>
<name sortKey="Flemban, Hesham" sort="Flemban, Hesham" uniqKey="Flemban H" first="Hesham" last="Flemban">Hesham Flemban</name>
<name sortKey="Hajjar, Sami" sort="Hajjar, Sami" uniqKey="Hajjar S" first="Sami" last="Hajjar">Sami Hajjar</name>
<name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name>
<name sortKey="Makhdoom, Hatem Q" sort="Makhdoom, Hatem Q" uniqKey="Makhdoom H" first="Hatem Q." last="Makhdoom">Hatem Q. Makhdoom</name>
<name sortKey="Memish, Ziad A" sort="Memish, Ziad A" uniqKey="Memish Z" first="Ziad A." last="Memish">Ziad A. Memish</name>
<name sortKey="Ong, Swee Hoe" sort="Ong, Swee Hoe" uniqKey="Ong S" first="Swee Hoe" last="Ong">Swee Hoe Ong</name>
<name sortKey="Palser, Anne L" sort="Palser, Anne L" uniqKey="Palser A" first="Anne L." last="Palser">Anne L. Palser</name>
<name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name>
<name sortKey="Shibl, Atef" sort="Shibl, Atef" uniqKey="Shibl A" first="Atef" last="Shibl">Atef Shibl</name>
<name sortKey="Watson, Simon J" sort="Watson, Simon J" uniqKey="Watson S" first="Simon J." last="Watson">Simon J. Watson</name>
<name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name>
</noCountry>
</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Pmc/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000F70 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd -nk 000F70 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Pmc |étape= Checkpoint |type= RBID |clé= PMC:3944817 |texte= Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Checkpoint/RBID.i -Sk "pubmed:24549846" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Checkpoint/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
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