Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
Identifieur interne : 001308 ( Pmc/Curation ); précédent : 001307; suivant : 001309Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
Auteurs : Christine M. Malboeuf [États-Unis] ; Xiao Yang [États-Unis] ; Patrick Charlebois [États-Unis] ; James Qu [États-Unis] ; Aaron M. Berlin [États-Unis] ; Monica Casali [États-Unis] ; Kendra N. Pesko [États-Unis] ; Christian L. Boutwell [États-Unis] ; John P. Devincenzo [États-Unis] ; Gregory D. Ebel [États-Unis] ; Todd M. Allen [États-Unis] ; Michael C. Zody [États-Unis] ; Matthew R. Henn [États-Unis] ; Joshua Z. Levin [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2012.
Abstract
RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and
Url:
DOI: 10.1093/nar/gks794
PubMed: 22962364
PubMed Central: 3592391
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John P. Devincenzo<affiliation><nlm:aff id="gks794-AFF1">Department of Pediatrics, University of Tennessee School of Medicine,</nlm:aff><wicri:noCountry code="subfield">University of Tennessee School of Medicine</wicri:noCountry></affiliation><affiliation><nlm:aff id="gks794-AFF1">LeBonheur Children's Medical Center,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="gks794-AFF1">The Children's Foundation Research Center</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Department of Molecular Sciences, University of Tennessee Graduate School of Health Sciences, Memphis, TN, 38103 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Sciences, University of Tennessee Graduate School of Health Sciences, Memphis, TN</wicri:regionArea></affiliation>Le document en format XML
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Levin</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22962364</idno><idno type="pmc">3592391</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592391</idno><idno type="RBID">PMC:3592391</idno><idno type="doi">10.1093/nar/gks794</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">001308</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001308</idno><idno type="wicri:Area/Pmc/Curation">001308</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001308</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification</title><author><name sortKey="Malboeuf, Christine M" sort="Malboeuf, Christine M" uniqKey="Malboeuf C" first="Christine M." last="Malboeuf">Christine M. Malboeuf</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Charlebois, Patrick" sort="Charlebois, Patrick" uniqKey="Charlebois P" first="Patrick" last="Charlebois">Patrick Charlebois</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Qu, James" sort="Qu, James" uniqKey="Qu J" first="James" last="Qu">James Qu</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Berlin, Aaron M" sort="Berlin, Aaron M" uniqKey="Berlin A" first="Aaron M." last="Berlin">Aaron M. Berlin</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Casali, Monica" sort="Casali, Monica" uniqKey="Casali M" first="Monica" last="Casali">Monica Casali</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Pesko, Kendra N" sort="Pesko, Kendra N" uniqKey="Pesko K" first="Kendra N." last="Pesko">Kendra N. Pesko</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131</wicri:regionArea></affiliation></author><author><name sortKey="Boutwell, Christian L" sort="Boutwell, Christian L" uniqKey="Boutwell C" first="Christian L." last="Boutwell">Christian L. Boutwell</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Ragon Institute of MGH, MIT and Harvard, Boston, MA, 02129 USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ragon Institute of MGH, MIT and Harvard, Boston, MA</wicri:regionArea></affiliation></author><author><name sortKey="Devincenzo, John P" sort="Devincenzo, John P" uniqKey="Devincenzo J" first="John P." last="Devincenzo">John P. Devincenzo</name><affiliation><nlm:aff id="gks794-AFF1">Department of Pediatrics, University of Tennessee School of Medicine,</nlm:aff><wicri:noCountry code="subfield">University of Tennessee School of Medicine</wicri:noCountry></affiliation><affiliation><nlm:aff id="gks794-AFF1">LeBonheur Children's Medical Center,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="gks794-AFF1">The Children's Foundation Research Center</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Department of Molecular Sciences, University of Tennessee Graduate School of Health Sciences, Memphis, TN, 38103 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Sciences, University of Tennessee Graduate School of Health Sciences, Memphis, TN</wicri:regionArea></affiliation></author><author><name sortKey="Ebel, Gregory D" sort="Ebel, Gregory D" uniqKey="Ebel G" first="Gregory D." last="Ebel">Gregory D. Ebel</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131</wicri:regionArea></affiliation></author><author><name sortKey="Allen, Todd M" sort="Allen, Todd M" uniqKey="Allen T" first="Todd M." last="Allen">Todd M. Allen</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Ragon Institute of MGH, MIT and Harvard, Boston, MA, 02129 USA,</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Ragon Institute of MGH, MIT and Harvard, Boston, MA</wicri:regionArea></affiliation></author><author><name sortKey="Zody, Michael C" sort="Zody, Michael C" uniqKey="Zody M" first="Michael C." last="Zody">Michael C. Zody</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Henn, Matthew R" sort="Henn, Matthew R" uniqKey="Henn M" first="Matthew R." last="Henn">Matthew R. Henn</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author><author><name sortKey="Levin, Joshua Z" sort="Levin, Joshua Z" uniqKey="Levin J" first="Joshua Z." last="Levin">Joshua Z. Levin</name><affiliation wicri:level="1"><nlm:aff id="gks794-AFF1">Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Broad Institute of MIT and Harvard, Cambridge, MA, 02142</wicri:regionArea></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and <italic>de novo</italic> assembly optimized for viral genomes. With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bimber, Bn" uniqKey="Bimber B">BN Bimber</name></author><author><name sortKey="Dudley, Dm" uniqKey="Dudley D">DM Dudley</name></author><author><name sortKey="Lauck, M" uniqKey="Lauck M">M Lauck</name></author><author><name sortKey="Becker, Ea" uniqKey="Becker E">EA Becker</name></author><author><name sortKey="Chin, En" uniqKey="Chin E">EN Chin</name></author><author><name sortKey="Lank, Sm" uniqKey="Lank S">SM Lank</name></author><author><name sortKey="Grunenwald, Hl" uniqKey="Grunenwald H">HL Grunenwald</name></author><author><name sortKey="Caruccio, Nc" uniqKey="Caruccio N">NC 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22962364</article-id><article-id pub-id-type="pmc">3592391</article-id><article-id pub-id-type="doi">10.1093/nar/gks794</article-id><article-id pub-id-type="publisher-id">gks794</article-id><article-categories><subj-group subj-group-type="heading"><subject>Methods Online</subject></subj-group></article-categories><title-group><article-title>Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Malboeuf</surname><given-names>Christine M.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="gks794-COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Yang</surname><given-names>Xiao</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Charlebois</surname><given-names>Patrick</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Qu</surname><given-names>James</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Berlin</surname><given-names>Aaron M.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Casali</surname><given-names>Monica</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Pesko</surname><given-names>Kendra N.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Boutwell</surname><given-names>Christian L.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>DeVincenzo</surname><given-names>John P.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>4</sup></xref><xref ref-type="aff" rid="gks794-AFF1"><sup>5</sup></xref><xref ref-type="aff" rid="gks794-AFF1"><sup>6</sup></xref><xref ref-type="aff" rid="gks794-AFF1"><sup>7</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ebel</surname><given-names>Gregory D.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Allen</surname><given-names>Todd M.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Zody</surname><given-names>Michael C.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Henn</surname><given-names>Matthew R.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Levin</surname><given-names>Joshua Z.</given-names></name><xref ref-type="aff" rid="gks794-AFF1"><sup>1</sup></xref></contrib></contrib-group><aff id="gks794-AFF1"><sup>1</sup>Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA<sup>2</sup>Department of Pathology, University of New Mexico School of Medicine, Albuquerque, NM, 87131, USA<sup>3</sup>Ragon Institute of MGH, MIT and Harvard, Boston, MA, 02129 USA,<sup>4</sup>Department of Pediatrics, University of Tennessee School of Medicine,<sup>5</sup>LeBonheur Children's Medical Center,<sup>6</sup>The Children's Foundation Research Center and<sup>7</sup>Department of Molecular Sciences, University of Tennessee Graduate School of Health Sciences, Memphis, TN, 38103 USA</aff><author-notes><corresp id="gks794-COR1">*To whom correspondence should be addressed. Tel: <phone>+1 617 714 8342</phone>; Fax: <fax>+1 617 714 8002</fax>; Email: <email>malboeuf@broadinstitute.org</email></corresp><fn id="gks794-FN1"><p>Present addresses: Kendra Pesko, Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.</p></fn><fn id="gks794-FN2"><p>Gregory D. Ebel, Department of Microbiology Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.</p></fn></author-notes><pub-date pub-type="ppub"><month>1</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>8</day><month>9</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>8</day><month>9</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>41</volume><issue>1</issue><fpage>e13</fpage><lpage>e13</lpage><history><date date-type="received"><day>5</day><month>4</month><year>2012</year></date><date date-type="rev-recd"><day>29</day><month>6</month><year>2012</year></date><date date-type="accepted"><day>31</day><month>7</month><year>2012</year></date></history><permissions><copyright-statement>© The Author(s) 2012. Published by Oxford University Press.</copyright-statement><copyright-year>2012</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>RNA viruses are the causative agents for AIDS, influenza, SARS, and other serious health threats. Development of rapid and broadly applicable methods for complete viral genome sequencing is highly desirable to fully understand all aspects of these infectious agents as well as for surveillance of viral pandemic threats and emerging pathogens. However, traditional viral detection methods rely on prior sequence or antigen knowledge. In this study, we describe sequence-independent amplification for samples containing ultra-low amounts of viral RNA coupled with Illumina sequencing and <italic>de novo</italic> assembly optimized for viral genomes. With 5 million reads, we capture 96 to 100% of the viral protein coding region of HIV, respiratory syncytial and West Nile viral samples from as little as 100 copies of viral RNA. The methods presented here are scalable to large numbers of samples and capable of generating full or near full length viral genomes from clone and clinical samples with low amounts of viral RNA, without prior sequence information and in the presence of substantial host contamination.</p></abstract><counts><page-count count="10"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>7 January 2013</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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