Spread, Circulation, and Evolution of the Middle East Respiratory Syndrome Coronavirus
Identifieur interne : 001A80 ( Main/Exploration ); précédent : 001A79; suivant : 001A81Spread, 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.
Descripteurs français
- KwdFr :
- ARN viral (génétique), Analyse de regroupements, Analyse de séquence d'ADN, Coronavirus (), Coronavirus (génétique), Coronavirus (isolement et purification), Données de séquences moléculaires, Génome viral, Humains, Infections à coronavirus (transmission), Infections à coronavirus (virologie), Infections à coronavirus (épidémiologie), Nombre de reproduction de base, Phylogénie, Sélection génétique, Évolution moléculaire.
- MESH :
- génétique : ARN viral, Coronavirus.
- isolement et purification : Coronavirus.
- virologie : Infections à coronavirus.
- épidémiologie : Infections à coronavirus.
- Analyse de regroupements, Analyse de séquence d'ADN, Coronavirus, Données de séquences moléculaires, Génome viral, Humains, Nombre de reproduction de base, Phylogénie, Sélection génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Basic Reproduction Number, Cluster Analysis, Coronavirus (classification), Coronavirus (genetics), Coronavirus (isolation & purification), Coronavirus Infections (epidemiology), Coronavirus Infections (transmission), Coronavirus Infections (virology), Evolution, Molecular, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, RNA, Viral (genetics), Selection, Genetic, Sequence Analysis, DNA.
- MESH :
- chemical , genetics : RNA, Viral.
- classification : Coronavirus.
- epidemiology : Coronavirus Infections.
- genetics : Coronavirus.
- isolation & purification : Coronavirus.
- transmission : Coronavirus Infections.
- virology : Coronavirus Infections.
- Basic Reproduction Number, Cluster Analysis, Evolution, Molecular, Genome, Viral, Humans, Molecular Sequence Data, Phylogeny, Selection, Genetic, Sequence Analysis, DNA.
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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Le document en format XML
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Watson</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zumla, Alimuddin I" sort="Zumla, Alimuddin I" uniqKey="Zumla A" first="Alimuddin I." last="Zumla">Alimuddin I. Zumla</name></author><author><name sortKey="Makhdoom, Hatem Q" sort="Makhdoom, Hatem Q" uniqKey="Makhdoom H" first="Hatem Q." last="Makhdoom">Hatem Q. Makhdoom</name><affiliation><nlm:aff id="aff5"></nlm:aff></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><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Ong, Swee Hoe" sort="Ong, Swee Hoe" uniqKey="Ong S" first="Swee Hoe" last="Ong">Swee Hoe Ong</name><affiliation><nlm:aff id="aff1"></nlm:aff></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><nlm:aff id="aff2"></nlm:aff></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><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Assiri, Abdullah" sort="Assiri, Abdullah" uniqKey="Assiri A" first="Abdullah" last="Assiri">Abdullah Assiri</name><affiliation><nlm:aff id="aff2"></nlm:aff></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><nlm:aff id="aff6"></nlm:aff></affiliation></author><author><name sortKey="Albarrak, Ali" sort="Albarrak, Ali" uniqKey="Albarrak A" first="Ali" last="Albarrak">Ali Albarrak</name><affiliation><nlm:aff id="aff7"></nlm:aff></affiliation></author><author><name sortKey="Barry, Mazin" sort="Barry, Mazin" uniqKey="Barry M" first="Mazin" last="Barry">Mazin Barry</name><affiliation><nlm:aff id="aff8"></nlm:aff></affiliation></author><author><name sortKey="Shibl, Atef" sort="Shibl, Atef" uniqKey="Shibl A" first="Atef" last="Shibl">Atef Shibl</name><affiliation><nlm:aff id="aff8"></nlm:aff></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><nlm:aff id="aff9"></nlm:aff></affiliation></author><author><name sortKey="Hajjar, Sami" sort="Hajjar, Sami" uniqKey="Hajjar S" first="Sami" last="Hajjar">Sami Hajjar</name><affiliation><nlm:aff id="aff9"></nlm:aff></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><nlm:aff id="aff10"></nlm:aff></affiliation></author><author><name sortKey="Flemban, Hesham" sort="Flemban, Hesham" uniqKey="Flemban H" first="Hesham" last="Flemban">Hesham Flemban</name><affiliation><nlm:aff id="aff11"></nlm:aff></affiliation></author><author><name sortKey="Rambaut, Andrew" sort="Rambaut, Andrew" uniqKey="Rambaut A" first="Andrew" last="Rambaut">Andrew Rambaut</name></author><author><name sortKey="Kellam, Paul" sort="Kellam, Paul" uniqKey="Kellam P" first="Paul" last="Kellam">Paul Kellam</name></author><author><name sortKey="Memish, Ziad A" sort="Memish, Ziad A" uniqKey="Memish Z" first="Ziad A." last="Memish">Ziad A. Memish</name></author></analytic><series><title level="j">mBio</title><idno type="eISSN">2150-7511</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Basic Reproduction Number</term><term>Cluster Analysis</term><term>Coronavirus (classification)</term><term>Coronavirus (genetics)</term><term>Coronavirus (isolation & purification)</term><term>Coronavirus Infections (epidemiology)</term><term>Coronavirus Infections (transmission)</term><term>Coronavirus Infections (virology)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>RNA, Viral (genetics)</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral (génétique)</term><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Coronavirus ()</term><term>Coronavirus (génétique)</term><term>Coronavirus (isolement et purification)</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Infections à coronavirus (transmission)</term><term>Infections à coronavirus (virologie)</term><term>Infections à coronavirus (épidémiologie)</term><term>Nombre de reproduction de base</term><term>Phylogénie</term><term>Sélection génétique</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN viral</term><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronavirus</term></keywords><keywords scheme="MESH" qualifier="transmission" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Basic Reproduction Number</term><term>Cluster Analysis</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Selection, Genetic</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Analyse de séquence d'ADN</term><term>Coronavirus</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>Nombre de reproduction de base</term><term>Phylogénie</term><term>Sélection génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><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><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zaki, Am" uniqKey="Zaki A">AM Zaki</name></author><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S van Boheemen</name></author><author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name></author><author><name sortKey="Osterhaus, Ad" uniqKey="Osterhaus A">AD Osterhaus</name></author><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Van Boheemen, S" uniqKey="Van Boheemen S">S van Boheemen</name></author><author><name sortKey="De Graaf, M" uniqKey="De Graaf M">M de Graaf</name></author><author><name sortKey="Lauber, C" uniqKey="Lauber C">C Lauber</name></author><author><name sortKey="Bestebroer, Tm" uniqKey="Bestebroer T">TM Bestebroer</name></author><author><name sortKey="Raj, Vs" uniqKey="Raj V">VS Raj</name></author><author><name sortKey="Zaki, Am" uniqKey="Zaki A">AM Zaki</name></author><author><name sortKey="Osterhaus, Ad" uniqKey="Osterhaus A">AD Osterhaus</name></author><author><name sortKey="Haagmans, Bl" uniqKey="Haagmans B">BL Haagmans</name></author><author><name sortKey="Gorbalenya, Ae" uniqKey="Gorbalenya A">AE Gorbalenya</name></author><author><name sortKey="Snijder, Ej" uniqKey="Snijder E">EJ Snijder</name></author><author><name sortKey="Fouchier, Ra" uniqKey="Fouchier R">RA Fouchier</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Albarrak, Am" uniqKey="Albarrak A">AM Albarrak</name></author><author><name sortKey="Stephens, Gm" uniqKey="Stephens G">GM Stephens</name></author><author><name sortKey="Hewson, R" uniqKey="Hewson R">R Hewson</name></author><author><name sortKey="Memish, Za" uniqKey="Memish Z">ZA Memish</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Memish, Za" uniqKey="Memish Z">ZA Memish</name></author><author><name sortKey="Zumla, Ai" uniqKey="Zumla A">AI Zumla</name></author><author><name sortKey="Al Hakeem, Rf" uniqKey="Al Hakeem R">RF Al-Hakeem</name></author><author><name sortKey="Al Rabeeah, Aa" uniqKey="Al Rabeeah A">AA Al-Rabeeah</name></author><author><name sortKey="Stephens, Gm" uniqKey="Stephens G">GM Stephens</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Guan, Y" uniqKey="Guan Y">Y Guan</name></author><author><name sortKey="Zheng, Bj" uniqKey="Zheng B">BJ Zheng</name></author><author><name sortKey="He, Yq" uniqKey="He Y">YQ He</name></author><author><name sortKey="Liu, Xl" uniqKey="Liu X">XL Liu</name></author><author><name sortKey="Zhuang, Zx" 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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)
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