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Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

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Tracking 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. Miller

Source :

Genome Research [ 1088-9051 ] ; 2004.

RBID : PMC:353227

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:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC353227

DOI: 10.1101/gr.2141004
PubMed: 14993206
PubMed Central: 353227

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Le document en format XML

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<author><name sortKey="Wong, Christopher W" sort="Wong, Christopher W" uniqKey="Wong C" first="Christopher W." last="Wong">Christopher W. 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>
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<author><name sortKey="Vega, Vinsensius B" sort="Vega, Vinsensius B" uniqKey="Vega V" first="Vinsensius B." last="Vega">Vinsensius B. Vega</name>
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<author><name sortKey="Norton, Jason E" sort="Norton, Jason E" uniqKey="Norton J" first="Jason E." last="Norton">Jason E. Norton</name>
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<author><name sortKey="Cutler, David J" sort="Cutler, David J" uniqKey="Cutler D" first="David J." last="Cutler">David J. Cutler</name>
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<author><name sortKey="Richmond, Todd A" sort="Richmond, Todd A" uniqKey="Richmond T" first="Todd A." last="Richmond">Todd A. Richmond</name>
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<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>
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<author><name sortKey="Norton, Jason E" sort="Norton, Jason E" uniqKey="Norton J" first="Jason E." last="Norton">Jason E. Norton</name>
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</affiliation>
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<author><name sortKey="Cutler, David J" sort="Cutler, David J" uniqKey="Cutler D" first="David J." last="Cutler">David J. Cutler</name>
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<author><name sortKey="Stanton, Lawrence W" sort="Stanton, Lawrence W" uniqKey="Stanton L" first="Lawrence W." last="Stanton">Lawrence W. Stanton</name>
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<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>
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<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
  <front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Res</journal-id>
<journal-id journal-id-type="publisher-id">genome</journal-id>
<journal-title>Genome Research</journal-title>
<issn pub-type="ppub">1088-9051</issn>
<publisher><publisher-name>Cold Spring Harbor Laboratory Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">14993206</article-id>
<article-id pub-id-type="pmc">353227</article-id>
<article-id pub-id-type="publisher-id">0140398</article-id>
<article-id pub-id-type="doi">10.1101/gr.2141004</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Methods</subject>
</subj-group>
</article-categories>
<title-group><article-title>Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Wong</surname>
<given-names>Christopher W.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="fn" rid="fn1">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Albert</surname>
<given-names>Thomas J.</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vega</surname>
<given-names>Vinsensius B.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Norton</surname>
<given-names>Jason E.</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cutler</surname>
<given-names>David J.</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Richmond</surname>
<given-names>Todd A.</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Stanton</surname>
<given-names>Lawrence W.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Liu</surname>
<given-names>Edison T.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Miller</surname>
<given-names>Lance D.</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="fn" rid="fn1">4</xref>
</contrib>
</contrib-group>
<aff id="aff1"><label>1</label>
<italic>Genome Institute of Singapore, Singapore 138672, Republic of Singapore</italic>
</aff>
<aff id="aff2"><label>2</label>
<italic>NimbleGen Systems, Inc., Madison, Wisconsin 53711, USA</italic>
</aff>
<aff id="aff3"><label>3</label>
<italic>Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA</italic>
</aff>
<author-notes><fn id="fn1"><label>4</label>
<p><bold>Corresponding authors.</bold>
<bold>E-MAIL </bold>
<email>wongc@gis.a-star.edu.sg</email>
<bold>; FAX +65-64789060. E-MAIL </bold>
<email>millerl@gis.a-star.edu.sg</email>
<bold>; FAX +65-64789060.</bold>
</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>3</month>
<year>2004</year>
</pub-date>
<volume>14</volume>
<issue>3</issue>
<fpage>398</fpage>
<lpage>405</lpage>
<history><date date-type="received"><day>3</day>
<month>11</month>
<year>2003</year>
</date>
<date date-type="accepted"><day>28</day>
<month>12</month>
<year>2003</year>
</date>
</history>
<copyright-statement>Copyright © 2004, Cold Spring Harbor Laboratory Press</copyright-statement>
<copyright-year>2004</copyright-year>
<abstract><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>
</abstract>
</article-meta>
<notes><fn-group><fn><p>Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2141004.</p>
</fn>
</fn-group>
</notes>
</front>
</pmc>
</record>

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Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

Tracking the Evolution of the SARS Coronavirus Using High-Throughput, High-Density Resequencing Arrays

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