Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
Identifieur interne : 005001 ( Main/Exploration ); précédent : 005000; suivant : 005002Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays
Auteurs : Christopher W. Wong ; Thomas J. Albert ; Vinsensius B. Vega ; Jason E. Norton ; David J. Cutler ; Todd A. Richmond ; Lawrence W. Stanton ; Edison T. Liu ; Lance D. MillerSource :
- Genome Research [ 1088-9051 ] ; 2004.
Descripteurs français
- KwdFr :
- ADN viral (génétique), ADN viral (métabolisme), ARN viral (génétique), ARN viral (métabolisme), Amorces ADN (génétique), Amorces ADN (métabolisme), Analyse de séquence d'ARN (), Animaux, Cellules Vero (virologie), Composition en bases nucléiques (génétique), Coronavirus (), Coronavirus (génétique), Coronavirus (isolement et purification), Génome viral, Humains, Hybridation d'acides nucléiques (génétique), Lignée cellulaire, Mésappariement de bases (génétique), Syndrome respiratoire aigu sévère (diagnostic), Syndrome respiratoire aigu sévère (virologie), Séquence consensus (génétique), Séquençage par oligonucléotides en batterie, Virus du SRAS (), Virus du SRAS (génétique), Évolution moléculaire.
- MESH :
- diagnostic : Syndrome respiratoire aigu sévère.
- génétique : ADN viral, ARN viral, Amorces ADN, Composition en bases nucléiques, Coronavirus, Hybridation d'acides nucléiques, Mésappariement de bases, Séquence consensus, Virus du SRAS.
- isolement et purification : Coronavirus.
- métabolisme : ADN viral, ARN viral, Amorces ADN.
- virologie : Cellules Vero, Syndrome respiratoire aigu sévère.
- Analyse de séquence d'ARN, Animaux, Coronavirus, Génome viral, Humains, Lignée cellulaire, Séquençage par oligonucléotides en batterie, Virus du SRAS, Évolution moléculaire.
English descriptors
- KwdEn :
- Animals, Base Composition (genetics), Base Pair Mismatch (genetics), Cell Line, Chlorocebus aethiops (genetics), Consensus Sequence (genetics), Coronavirus (classification), Coronavirus (genetics), Coronavirus (isolation & purification), DNA Primers (genetics), DNA Primers (metabolism), DNA, Viral (genetics), DNA, Viral (metabolism), Evolution, Molecular, Genome, Viral, Humans, Nucleic Acid Hybridization (genetics), Oligonucleotide Array Sequence Analysis, RNA, Viral (genetics), RNA, Viral (metabolism), SARS Virus (classification), SARS Virus (genetics), Sequence Analysis, RNA (methods), Severe Acute Respiratory Syndrome (diagnosis), Severe Acute Respiratory Syndrome (virology), Vero Cells (virology).
- MESH :
- chemical , genetics : DNA Primers, DNA, Viral, RNA, Viral.
- classification : Coronavirus, SARS Virus.
- diagnosis : Severe Acute Respiratory Syndrome.
- genetics : Base Composition, Base Pair Mismatch, Chlorocebus aethiops, Consensus Sequence, Coronavirus, Nucleic Acid Hybridization, SARS Virus.
- isolation & purification : Coronavirus.
- chemical , metabolism : DNA Primers, DNA, Viral, RNA, Viral.
- methods : Sequence Analysis, RNA.
- virology : Severe Acute Respiratory Syndrome, Vero Cells.
- Animals, Cell Line, Evolution, Molecular, Genome, Viral, Humans, Oligonucleotide Array Sequence Analysis.
Abstract
Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the development and validation of an oligonucleotide resequencing array for interrogating the entire 30-kb SARS-CoV genome in a rapid, cost-effective fashion. Using this platform, we sequenced SARS-CoV genomes from Vero cell culture isolates of 12 patients and directly from four patient tissues. The sequence obtained from the array is highly reproducible, accurate (>99.99% accuracy) and capable of identifying known and novel variants of SARS-CoV. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable, and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale, making this an ideal platform for the global monitoring of SARS-CoV and other small-genome pathogens.
Url:
DOI: 10.1101/gr.2141004
PubMed: 14993206
PubMed Central: 353227
Affiliations:
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Le document en format XML
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Wong</name><affiliation><nlm:aff id="aff1"><italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic></nlm:aff></affiliation></author><author><name sortKey="Albert, Thomas J" sort="Albert, Thomas J" uniqKey="Albert T" first="Thomas J." last="Albert">Thomas J. Albert</name><affiliation><nlm:aff id="aff2"><italic>NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA</italic></nlm:aff></affiliation></author><author><name sortKey="Vega, Vinsensius B" sort="Vega, Vinsensius B" uniqKey="Vega V" first="Vinsensius B." last="Vega">Vinsensius B. Vega</name><affiliation><nlm:aff id="aff1"><italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic></nlm:aff></affiliation></author><author><name sortKey="Norton, Jason E" sort="Norton, Jason E" uniqKey="Norton J" first="Jason E." last="Norton">Jason E. 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Stanton</name><affiliation><nlm:aff id="aff1"><italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic></nlm:aff></affiliation></author><author><name sortKey="Liu, Edison T" sort="Liu, Edison T" uniqKey="Liu E" first="Edison T." last="Liu">Edison T. Liu</name><affiliation><nlm:aff id="aff1"><italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic></nlm:aff></affiliation></author><author><name sortKey="Miller, Lance D" sort="Miller, Lance D" uniqKey="Miller L" first="Lance D." last="Miller">Lance D. Miller</name><affiliation><nlm:aff id="aff1"><italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic></nlm:aff></affiliation></author></analytic><series><title level="j">Genome Research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Composition (genetics)</term><term>Base Pair Mismatch (genetics)</term><term>Cell Line</term><term>Chlorocebus aethiops (genetics)</term><term>Consensus Sequence (genetics)</term><term>Coronavirus (classification)</term><term>Coronavirus (genetics)</term><term>Coronavirus (isolation & purification)</term><term>DNA Primers (genetics)</term><term>DNA Primers (metabolism)</term><term>DNA, Viral (genetics)</term><term>DNA, Viral (metabolism)</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Nucleic Acid Hybridization (genetics)</term><term>Oligonucleotide Array Sequence Analysis</term><term>RNA, Viral (genetics)</term><term>RNA, Viral (metabolism)</term><term>SARS Virus (classification)</term><term>SARS Virus (genetics)</term><term>Sequence Analysis, RNA (methods)</term><term>Severe Acute Respiratory Syndrome (diagnosis)</term><term>Severe Acute Respiratory Syndrome (virology)</term><term>Vero Cells (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN viral (génétique)</term><term>ADN viral (métabolisme)</term><term>ARN viral (génétique)</term><term>ARN viral (métabolisme)</term><term>Amorces ADN (génétique)</term><term>Amorces ADN (métabolisme)</term><term>Analyse de séquence d'ARN ()</term><term>Animaux</term><term>Cellules Vero (virologie)</term><term>Composition en bases nucléiques (génétique)</term><term>Coronavirus ()</term><term>Coronavirus (génétique)</term><term>Coronavirus (isolement et purification)</term><term>Génome viral</term><term>Humains</term><term>Hybridation d'acides nucléiques (génétique)</term><term>Lignée cellulaire</term><term>Mésappariement de bases (génétique)</term><term>Syndrome respiratoire aigu sévère (diagnostic)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Séquence consensus (génétique)</term><term>Séquençage par oligonucléotides en batterie</term><term>Virus du SRAS ()</term><term>Virus du SRAS (génétique)</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Primers</term><term>DNA, Viral</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coronavirus</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Base Composition</term><term>Base Pair Mismatch</term><term>Chlorocebus aethiops</term><term>Consensus Sequence</term><term>Coronavirus</term><term>Nucleic Acid Hybridization</term><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN viral</term><term>ARN viral</term><term>Amorces ADN</term><term>Composition en bases nucléiques</term><term>Coronavirus</term><term>Hybridation d'acides nucléiques</term><term>Mésappariement de bases</term><term>Séquence consensus</term><term>Virus du SRAS</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" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA Primers</term><term>DNA, Viral</term><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN viral</term><term>ARN viral</term><term>Amorces ADN</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Cellules Vero</term><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term><term>Vero Cells</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cell Line</term><term>Evolution, Molecular</term><term>Genome, Viral</term><term>Humans</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Animaux</term><term>Coronavirus</term><term>Génome viral</term><term>Humains</term><term>Lignée cellulaire</term><term>Séquençage par oligonucléotides en batterie</term><term>Virus du SRAS</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Mutations in the SARS-Coronavirus (SARS-CoV) can alter its clinical presentation, and the study of its mutation patterns in human populations can facilitate contact tracing. Here, we describe the development and validation of an oligonucleotide resequencing array for interrogating the entire 30-kb SARS-CoV genome in a rapid, cost-effective fashion. Using this platform, we sequenced SARS-CoV genomes from Vero cell culture isolates of 12 patients and directly from four patient tissues. The sequence obtained from the array is highly reproducible, accurate (>99.99% accuracy) and capable of identifying known and novel variants of SARS-CoV. Notably, we applied this technology to a field specimen of probable SARS and rapidly deduced its infectious source. We demonstrate that array-based resequencing-by-hybridization is a fast, reliable, and economical alternative to capillary sequencing for obtaining SARS-CoV genomic sequence on a population scale, making this an ideal platform for the global monitoring of SARS-CoV and other small-genome pathogens.</p></div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Albert, Thomas J" sort="Albert, Thomas J" uniqKey="Albert T" first="Thomas J." last="Albert">Thomas J. Albert</name><name sortKey="Cutler, David J" sort="Cutler, David J" uniqKey="Cutler D" first="David J." last="Cutler">David J. Cutler</name><name sortKey="Liu, Edison T" sort="Liu, Edison T" uniqKey="Liu E" first="Edison T." last="Liu">Edison T. Liu</name><name sortKey="Miller, Lance D" sort="Miller, Lance D" uniqKey="Miller L" first="Lance D." last="Miller">Lance D. Miller</name><name sortKey="Norton, Jason E" sort="Norton, Jason E" uniqKey="Norton J" first="Jason E." last="Norton">Jason E. Norton</name><name sortKey="Richmond, Todd A" sort="Richmond, Todd A" uniqKey="Richmond T" first="Todd A." last="Richmond">Todd A. Richmond</name><name sortKey="Stanton, Lawrence W" sort="Stanton, Lawrence W" uniqKey="Stanton L" first="Lawrence W." last="Stanton">Lawrence W. Stanton</name><name sortKey="Vega, Vinsensius B" sort="Vega, Vinsensius B" uniqKey="Vega V" first="Vinsensius B." last="Vega">Vinsensius B. Vega</name><name sortKey="Wong, Christopher W" sort="Wong, Christopher W" uniqKey="Wong C" first="Christopher W." last="Wong">Christopher W. Wong</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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