Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study
Identifieur interne : 002171 ( Main/Exploration ); précédent : 002170; suivant : 002172Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study
Auteurs : Matthew Cotten [Royaume-Uni] ; Simon J. Watson [Royaume-Uni] ; Paul Kellam [Royaume-Uni] ; Abdullah A. Al-Rabeeah [Arabie saoudite] ; Hatem Q. Makhdoom [Arabie saoudite] ; Abdullah Assiri [Arabie saoudite] ; Jaffar A. Al-Tawfiq [Arabie saoudite] ; Rafat F. Alhakeem [Arabie saoudite] ; Hossam Madani [Arabie saoudite] ; Fahad A. Alrabiah [Arabie saoudite] ; SAMI AL HAJJAR [Arabie saoudite] ; Wafa N. Al-Nassir [Arabie saoudite] ; Ali Albarrak [Arabie saoudite] ; Hesham Flemban [Arabie saoudite] ; Hanan H. Balkhy [Arabie saoudite] ; Sarah Alsubaie [Arabie saoudite] ; Anne L. Palser [Royaume-Uni] ; Astrid Gall [Royaume-Uni] ; Rachael Bashford-Rogers [Royaume-Uni] ; Andrew Rambaut [Royaume-Uni, États-Unis] ; Alimuddin I. Zumla [Arabie saoudite, Royaume-Uni] ; Ziad A. Memish [Arabie saoudite]Source :
- Lancet : (British edition) [ 0140-6736 ] ; 2013.
Descripteurs français
- KwdFr :
- Amplification de gène, Arabie saoudite (épidémiologie), Coronavirus (génétique), Flambées de maladies, Génome viral, Humains, Infections de l'appareil respiratoire (génétique), Infections de l'appareil respiratoire (transmission), Infections de l'appareil respiratoire (épidémiologie), Infections à coronavirus (génétique), Infections à coronavirus (transmission), Infections à coronavirus (épidémiologie), Syndrome, Séquence nucléotidique, Évolution moléculaire.
- MESH :
- génétique : Coronavirus, Infections de l'appareil respiratoire, Infections à coronavirus.
- épidémiologie : Arabie saoudite, Infections de l'appareil respiratoire, Infections à coronavirus.
- Pascal (Inist)
- Wicri :
- geographic : Arabie saoudite.
- topic : Médecine.
English descriptors
- KwdEn :
- Base Sequence, Coronavirus, Coronavirus (genetics), Coronavirus Infections (epidemiology), Coronavirus Infections (genetics), Coronavirus Infections (transmission), Disease Outbreaks, Evolution, Evolution, Molecular, Gene Amplification, Genome, Genome, Viral, Genomics, Humans, Medicine, Middle East respiratory syndrome, Respiratory Tract Infections (epidemiology), Respiratory Tract Infections (genetics), Respiratory Tract Infections (transmission), Saudi Arabia, Saudi Arabia (epidemiology), Syndrome, Transmission.
- MESH :
- geographic , epidemiology : Saudi Arabia.
- epidemiology : Coronavirus Infections, Respiratory Tract Infections.
- genetics : Coronavirus, Coronavirus Infections, Respiratory Tract Infections.
- transmission : Coronavirus Infections, Respiratory Tract Infections.
- Base Sequence, Disease Outbreaks, Evolution, Molecular, Gene Amplification, Genome, Viral, Humans, Syndrome.
Abstract
Background Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. Methods Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85-95%, and four 30-50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. Findings Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. Interpretation We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R0 values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. Funding Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.
Url:
Affiliations:
- Arabie saoudite, Royaume-Uni, États-Unis
- Angleterre, Grand Londres, Maryland, Écosse
- Londres, Édimbourg
- University College de Londres
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Le document en format XML
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Memish</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">INIST</idno><idno type="inist">14-0014092</idno><date when="2013">2013</date><idno type="stanalyst">PASCAL 14-0014092 INIST</idno><idno type="RBID">Pascal:14-0014092</idno><idno type="wicri:Area/PascalFrancis/Corpus">000036</idno><idno type="wicri:Area/PascalFrancis/Curation">000058</idno><idno type="wicri:Area/PascalFrancis/Checkpoint">000034</idno><idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000034</idno><idno type="wicri:doubleKey">0140-6736:2013:Cotten M:transmission:and:evolution</idno><idno type="wicri:Area/Main/Merge">002195</idno><idno type="wicri:source">PMC</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898949</idno><idno type="RBID">PMC:3898949</idno><idno type="wicri:Area/Pmc/Corpus">000F07</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F07</idno><idno type="wicri:Area/Pmc/Curation">000F07</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F07</idno><idno type="wicri:Area/Pmc/Checkpoint">001161</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001161</idno><idno type="wicri:source">PubMed</idno><idno type="RBID">pubmed:24055451</idno><idno type="wicri:Area/PubMed/Corpus">001B82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001B82</idno><idno type="wicri:Area/PubMed/Curation">001B82</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001B82</idno><idno type="wicri:Area/PubMed/Checkpoint">001A39</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001A39</idno><idno type="wicri:Area/Ncbi/Merge">000B57</idno><idno type="wicri:Area/Ncbi/Curation">000B57</idno><idno type="wicri:Area/Ncbi/Checkpoint">000B57</idno><idno type="wicri:doubleKey">0140-6736:2013:Cotten M:transmission:and:evolution</idno><idno type="wicri:Area/Main/Merge">001E95</idno><idno type="wicri:Area/Main/Curation">002171</idno><idno type="wicri:Area/Main/Exploration">002171</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study</title><author><name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation></author><author><name sortKey="Watson, Simon J" sort="Watson, Simon J" uniqKey="Watson S" first="Simon J." last="Watson">Simon J. Watson</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation></author><author><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation><affiliation wicri:level="4"><inist:fA14 i1="13"><s1>Division of Infection and Immunity, University College London</s1><s2>London</s2><s3>GBR</s3><sZ>3 aut.</sZ><sZ>21 aut.</sZ></inist:fA14><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">University College de Londres</orgName></affiliation></author><author><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><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation></author><author><name sortKey="Makhdoom, Hatem Q" sort="Makhdoom, Hatem Q" uniqKey="Makhdoom H" first="Hatem Q." last="Makhdoom">Hatem Q. Makhdoom</name><affiliation wicri:level="1"><inist:fA14 i1="03"><s1>Jeddah Regional Laboratory, Ministry of Health</s1><s2>Jeddah</s2><s3>SAU</s3><sZ>5 aut.</sZ><sZ>9 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Jeddah</wicri:noRegion></affiliation></author><author><name sortKey="Assiri, Abdullah" sort="Assiri, Abdullah" uniqKey="Assiri A" first="Abdullah" last="Assiri">Abdullah Assiri</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation></author><author><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><affiliation wicri:level="1"><inist:fA14 i1="04"><s1>Saudi Aramco Medical Services Organisation</s1><s2>Saudi Aramco, Dhahran</s2><s3>SAU</s3><sZ>7 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Saudi Aramco Medical Services Organisation</wicri:noRegion></affiliation></author><author><name sortKey="Alhakeem, Rafat F" sort="Alhakeem, Rafat F" uniqKey="Alhakeem R" first="Rafat F." last="Alhakeem">Rafat F. Alhakeem</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation></author><author><name sortKey="Madani, Hossam" sort="Madani, Hossam" uniqKey="Madani H" first="Hossam" last="Madani">Hossam Madani</name><affiliation wicri:level="1"><inist:fA14 i1="03"><s1>Jeddah Regional Laboratory, Ministry of Health</s1><s2>Jeddah</s2><s3>SAU</s3><sZ>5 aut.</sZ><sZ>9 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Jeddah</wicri:noRegion></affiliation></author><author><name sortKey="Alrabiah, Fahad A" sort="Alrabiah, Fahad A" uniqKey="Alrabiah F" first="Fahad A." last="Alrabiah">Fahad A. Alrabiah</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation><affiliation wicri:level="1"><inist:fA14 i1="07"><s1>King Faisal Specialist Hospital</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>10 aut.</sZ><sZ>11 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>King Faisal Specialist Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Sami Al Hajjar" sort="Sami Al Hajjar" uniqKey="Sami Al Hajjar" last="Sami Al Hajjar">SAMI AL HAJJAR</name><affiliation wicri:level="1"><inist:fA14 i1="07"><s1>King Faisal Specialist Hospital</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>10 aut.</sZ><sZ>11 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>King Faisal Specialist Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Al Nassir, Wafa N" sort="Al Nassir, Wafa N" uniqKey="Al Nassir W" first="Wafa N." last="Al-Nassir">Wafa N. Al-Nassir</name><affiliation wicri:level="1"><inist:fA14 i1="08"><s1>Imam Abdulrahman Bin Mohamed Hospital-National Guard Health Affairs-Dammam</s1><s3>SAU</s3><sZ>12 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Imam Abdulrahman Bin Mohamed Hospital-National Guard Health Affairs-Dammam</wicri:noRegion></affiliation></author><author><name sortKey="Albarrak, Ali" sort="Albarrak, Ali" uniqKey="Albarrak A" first="Ali" last="Albarrak">Ali Albarrak</name><affiliation wicri:level="1"><inist:fA14 i1="09"><s1>Prince Sultan Military Medical City</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>13 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Prince Sultan Military Medical City</wicri:noRegion></affiliation></author><author><name sortKey="Flemban, Hesham" sort="Flemban, Hesham" uniqKey="Flemban H" first="Hesham" last="Flemban">Hesham Flemban</name><affiliation wicri:level="1"><inist:fA14 i1="10"><s1>Alhada Military Hospital</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>14 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Alhada Military Hospital</wicri:noRegion></affiliation></author><author><name sortKey="Balkhy, Hanan H" sort="Balkhy, Hanan H" uniqKey="Balkhy H" first="Hanan H." last="Balkhy">Hanan H. Balkhy</name><affiliation wicri:level="1"><inist:fA14 i1="11"><s1>King Abdulaziz Medical City</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>15 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>King Abdulaziz Medical City</wicri:noRegion></affiliation></author><author><name sortKey="Alsubaie, Sarah" sort="Alsubaie, Sarah" uniqKey="Alsubaie S" first="Sarah" last="Alsubaie">Sarah Alsubaie</name><affiliation wicri:level="1"><inist:fA14 i1="12"><s1>Paediatric Infectious Diseases, King Saud University</s1><s3>SAU</s3><sZ>16 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Paediatric Infectious Diseases, King Saud University</wicri:noRegion></affiliation></author><author><name sortKey="Palser, Anne L" sort="Palser, Anne L" uniqKey="Palser A" first="Anne L." last="Palser">Anne L. Palser</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation></author><author><name sortKey="Gall, Astrid" sort="Gall, Astrid" uniqKey="Gall A" first="Astrid" last="Gall">Astrid Gall</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation></author><author><name sortKey="Bashford Rogers, Rachael" sort="Bashford Rogers, Rachael" uniqKey="Bashford Rogers R" first="Rachael" last="Bashford-Rogers">Rachael Bashford-Rogers</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Wellcome Trust Sanger Institute</s1><s2>Hinxton</s2><s3>GBR</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>17 aut.</sZ><sZ>18 aut.</sZ><sZ>19 aut.</sZ></inist:fA14><country>Royaume-Uni</country><wicri:noRegion>Wellcome Trust Sanger Institute</wicri:noRegion></affiliation></author><author><name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name><affiliation wicri:level="3"><inist:fA14 i1="05"><s1>Institute of Evolutionary Biology, Ashworth Laboratories, Kings Buildings, West Mains Road</s1><s2>Edinburgh</s2><s3>GBR</s3><sZ>20 aut.</sZ></inist:fA14><country>Royaume-Uni</country><placeName><settlement type="city">Édimbourg</settlement><region type="country">Écosse</region></placeName></affiliation><affiliation wicri:level="2"><inist:fA14 i1="06"><s1>Fogarty International Center, NIH</s1><s2>Bethesda, MD</s2><s3>USA</s3><sZ>20 aut.</sZ></inist:fA14><country>États-Unis</country><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation><affiliation wicri:level="4"><inist:fA14 i1="13"><s1>Division of Infection and Immunity, University College London</s1><s2>London</s2><s3>GBR</s3><sZ>3 aut.</sZ><sZ>21 aut.</sZ></inist:fA14><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName><orgName type="university">University College de Londres</orgName></affiliation><affiliation wicri:level="3"><inist:fA14 i1="14"><s1>UCL Hospitals NHS Foundation Trust</s1><s2>London</s2><s3>GBR</s3><sZ>21 aut.</sZ></inist:fA14><country>Royaume-Uni</country><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Memish, Ziad A" sort="Memish, Ziad A" uniqKey="Memish Z" first="Ziad A." last="Memish">Ziad A. Memish</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Global Centre for Mass Gatherings Medicine, Ministry of Health</s1><s2>Riyadh</s2><s3>SAU</s3><sZ>4 aut.</sZ><sZ>6 aut.</sZ><sZ>8 aut.</sZ><sZ>10 aut.</sZ><sZ>21 aut.</sZ><sZ>22 aut.</sZ></inist:fA14><country>Arabie saoudite</country><wicri:noRegion>Riyadh</wicri:noRegion></affiliation></author></analytic><series><title level="j" type="main">Lancet : (British edition)</title><title level="j" type="abbreviated">Lancet : (Br. ed.)</title><idno type="ISSN">0140-6736</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc><seriesStmt><title level="j" type="main">Lancet : (British edition)</title><title level="j" type="abbreviated">Lancet : (Br. ed.)</title><idno type="ISSN">0140-6736</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Coronavirus</term><term>Coronavirus (genetics)</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (genetics)</term><term>Coronavirus Infections (transmission)</term><term>Disease Outbreaks</term><term>Evolution</term><term>Evolution, Molecular</term><term>Gene Amplification</term><term>Genome</term><term>Genome, Viral</term><term>Genomics</term><term>Humans</term><term>Medicine</term><term>Middle East respiratory syndrome</term><term>Respiratory Tract Infections (epidemiology)</term><term>Respiratory Tract Infections (genetics)</term><term>Respiratory Tract Infections (transmission)</term><term>Saudi Arabia</term><term>Saudi Arabia (epidemiology)</term><term>Syndrome</term><term>Transmission</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Amplification de gène</term><term>Arabie saoudite (épidémiologie)</term><term>Coronavirus (génétique)</term><term>Flambées de maladies</term><term>Génome viral</term><term>Humains</term><term>Infections de l'appareil respiratoire (génétique)</term><term>Infections de l'appareil respiratoire (transmission)</term><term>Infections de l'appareil respiratoire (épidémiologie)</term><term>Infections à coronavirus (génétique)</term><term>Infections à coronavirus (transmission)</term><term>Infections à coronavirus (épidémiologie)</term><term>Syndrome</term><term>Séquence nucléotidique</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>Saudi Arabia</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term><term>Respiratory Tract Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term><term>Coronavirus Infections</term><term>Respiratory Tract Infections</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term><term>Infections de l'appareil respiratoire</term><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Coronavirus Infections</term><term>Respiratory Tract Infections</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Arabie saoudite</term><term>Infections de l'appareil respiratoire</term><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Disease Outbreaks</term><term>Evolution, Molecular</term><term>Gene Amplification</term><term>Genome, Viral</term><term>Humans</term><term>Syndrome</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Amplification de gène</term><term>Flambées de maladies</term><term>Génome viral</term><term>Humains</term><term>Syndrome</term><term>Séquence nucléotidique</term><term>Transmission</term><term>Evolution</term><term>Coronavirus</term><term>Arabie saoudite</term><term>Génomique</term><term>Génome</term><term>Médecine</term><term>Syndrome respiratoire du Moyen-Orient</term><term>Évolution moléculaire</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Arabie saoudite</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Médecine</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Background Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has, worldwide, caused 104 infections in people including 49 deaths, with 82 cases and 41 deaths reported from Saudi Arabia. In addition to confirming diagnosis, we generated the MERS-CoV genomic sequences obtained directly from patient samples to provide important information on MERS-CoV transmission, evolution, and origin. Methods Full genome deep sequencing was done on nucleic acid extracted directly from PCR-confirmed clinical samples. Viral genomes were obtained from 21 MERS cases of which 13 had 100%, four 85-95%, and four 30-50% genome coverage. Phylogenetic analysis of the 21 sequences, combined with nine published MERS-CoV genomes, was done. Findings Three distinct MERS-CoV genotypes were identified in Riyadh. Phylogeographic analyses suggest the MERS-CoV zoonotic reservoir is geographically disperse. Selection analysis of the MERS-CoV genomes reveals the expected accumulation of genetic diversity including changes in the S protein. The genetic diversity in the Al-Hasa cluster suggests that the hospital outbreak might have had more than one virus introduction. Interpretation We present the largest number of MERS-CoV genomes (21) described so far. MERS-CoV full genome sequences provide greater detail in tracking transmission. Multiple introductions of MERS-CoV are identified and suggest lower R<sub>0</sub> values. Transmission within Saudi Arabia is consistent with either movement of an animal reservoir, animal products, or movement of infected people. Further definition of the exposures responsible for the sporadic introductions of MERS-CoV into human populations is urgently needed. Funding Saudi Arabian Ministry of Health, Wellcome Trust, European Community, and National Institute of Health Research University College London Hospitals Biomedical Research Centre.</div></front></TEI><affiliations><list><country><li>Arabie saoudite</li><li>Royaume-Uni</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Grand Londres</li><li>Maryland</li><li>Écosse</li></region><settlement><li>Londres</li><li>Édimbourg</li></settlement><orgName><li>University College de Londres</li></orgName></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Cotten, Matthew" sort="Cotten, Matthew" uniqKey="Cotten M" first="Matthew" last="Cotten">Matthew Cotten</name></noRegion><name sortKey="Bashford Rogers, Rachael" sort="Bashford Rogers, Rachael" uniqKey="Bashford Rogers R" first="Rachael" last="Bashford-Rogers">Rachael Bashford-Rogers</name><name sortKey="Gall, Astrid" sort="Gall, Astrid" uniqKey="Gall A" first="Astrid" last="Gall">Astrid Gall</name><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</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="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><name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name></country><country name="Arabie saoudite"><noRegion><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></noRegion><name sortKey="Al Nassir, Wafa N" sort="Al Nassir, Wafa N" uniqKey="Al Nassir W" first="Wafa N." last="Al-Nassir">Wafa N. Al-Nassir</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="Alrabiah, Fahad A" sort="Alrabiah, Fahad A" uniqKey="Alrabiah F" first="Fahad A." last="Alrabiah">Fahad A. Alrabiah</name><name sortKey="Alsubaie, Sarah" sort="Alsubaie, Sarah" uniqKey="Alsubaie S" first="Sarah" last="Alsubaie">Sarah Alsubaie</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="Flemban, Hesham" sort="Flemban, Hesham" uniqKey="Flemban H" first="Hesham" last="Flemban">Hesham Flemban</name><name sortKey="Madani, Hossam" sort="Madani, Hossam" uniqKey="Madani H" first="Hossam" last="Madani">Hossam Madani</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="Sami Al Hajjar" sort="Sami Al Hajjar" uniqKey="Sami Al Hajjar" last="Sami Al Hajjar">SAMI AL HAJJAR</name><name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name></country><country name="États-Unis"><region name="Maryland"><name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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