Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification
Identifieur interne : 001D46 ( Main/Exploration ); précédent : 001D45; suivant : 001D47Complete 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.
Descripteurs français
- KwdFr :
- ARN viral (), Analyse de séquence d'ARN, Données de séquences moléculaires, Génome viral, Humains, RT-PCR, Séquence nucléotidique, Techniques d'amplification d'acides nucléiques, VIH (Virus de l'Immunodéficience Humaine) (génétique), Virus du Nil occidental (génétique), Virus respiratoires syncytiaux (génétique).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : RNA, Viral.
- genetics : HIV, Respiratory Syncytial Viruses, West Nile virus.
- Base Sequence, Genome, Viral, Humans, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, RNA.
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
Affiliations:
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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><wicri:noRegion>02142</wicri:noRegion></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><wicri:noRegion>02142</wicri:noRegion></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><wicri:noRegion>02142</wicri:noRegion></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><wicri:noRegion>02142</wicri:noRegion></affiliation></author><author><name sortKey="Berlin, Aaron M" sort="Berlin, Aaron M" uniqKey="Berlin A" first="Aaron M." last="Berlin">Aaron M. 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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><wicri:noRegion>87131</wicri:noRegion></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="2"><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><placeName><region type="state">Massachusetts</region></placeName></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="2"><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><placeName><region type="state">Tennessee</region></placeName></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><wicri:noRegion>87131</wicri:noRegion></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="2"><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><placeName><region type="state">Massachusetts</region></placeName></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><wicri:noRegion>02142</wicri:noRegion></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><wicri:noRegion>02142</wicri:noRegion></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><wicri:noRegion>02142</wicri:noRegion></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><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Genome, Viral</term><term>HIV (genetics)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Amplification Techniques</term><term>RNA, Viral (chemistry)</term><term>Respiratory Syncytial Viruses (genetics)</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, RNA</term><term>West Nile virus (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN viral ()</term><term>Analyse de séquence d'ARN</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>RT-PCR</term><term>Séquence nucléotidique</term><term>Techniques d'amplification d'acides nucléiques</term><term>VIH (Virus de l'Immunodéficience Humaine) (génétique)</term><term>Virus du Nil occidental (génétique)</term><term>Virus respiratoires syncytiaux (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>HIV</term><term>Respiratory Syncytial Viruses</term><term>West Nile virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>VIH (Virus de l'Immunodéficience Humaine)</term><term>Virus du Nil occidental</term><term>Virus respiratoires syncytiaux</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Amplification Techniques</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN viral</term><term>Analyse de séquence d'ARN</term><term>Données de séquences moléculaires</term><term>Génome viral</term><term>Humains</term><term>RT-PCR</term><term>Séquence nucléotidique</term><term>Techniques d'amplification d'acides nucléiques</term></keywords></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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Marra</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Massachusetts</li><li>Tennessee</li></region></list><tree><country name="États-Unis"><noRegion><name sortKey="Malboeuf, Christine M" sort="Malboeuf, Christine M" uniqKey="Malboeuf C" first="Christine M." last="Malboeuf">Christine M. Malboeuf</name></noRegion><name sortKey="Allen, Todd M" sort="Allen, Todd M" uniqKey="Allen T" first="Todd M." last="Allen">Todd M. Allen</name><name sortKey="Berlin, Aaron M" sort="Berlin, Aaron M" uniqKey="Berlin A" first="Aaron M." last="Berlin">Aaron M. Berlin</name><name sortKey="Boutwell, Christian L" sort="Boutwell, Christian L" uniqKey="Boutwell C" first="Christian L." last="Boutwell">Christian L. Boutwell</name><name sortKey="Casali, Monica" sort="Casali, Monica" uniqKey="Casali M" first="Monica" last="Casali">Monica Casali</name><name sortKey="Charlebois, Patrick" sort="Charlebois, Patrick" uniqKey="Charlebois P" first="Patrick" last="Charlebois">Patrick Charlebois</name><name sortKey="Devincenzo, John P" sort="Devincenzo, John P" uniqKey="Devincenzo J" first="John P." last="Devincenzo">John P. Devincenzo</name><name sortKey="Ebel, Gregory D" sort="Ebel, Gregory D" uniqKey="Ebel G" first="Gregory D." last="Ebel">Gregory D. Ebel</name><name sortKey="Henn, Matthew R" sort="Henn, Matthew R" uniqKey="Henn M" first="Matthew R." last="Henn">Matthew R. Henn</name><name sortKey="Levin, Joshua Z" sort="Levin, Joshua Z" uniqKey="Levin J" first="Joshua Z." last="Levin">Joshua Z. Levin</name><name sortKey="Pesko, Kendra N" sort="Pesko, Kendra N" uniqKey="Pesko K" first="Kendra N." last="Pesko">Kendra N. Pesko</name><name sortKey="Qu, James" sort="Qu, James" uniqKey="Qu J" first="James" last="Qu">James Qu</name><name sortKey="Yang, Xiao" sort="Yang, Xiao" uniqKey="Yang X" first="Xiao" last="Yang">Xiao Yang</name><name sortKey="Zody, Michael C" sort="Zody, Michael C" uniqKey="Zody M" first="Michael C." last="Zody">Michael C. Zody</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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