Viral Discovery and Sequence Recovery Using DNA Microarrays
Identifieur interne : 005D05 ( Main/Exploration ); précédent : 005D04; suivant : 005D06Viral Discovery and Sequence Recovery Using DNA Microarrays
Auteurs : David Wang ; Anatoly Urisman ; Yu-Tsueng Liu ; Michael Springer ; Thomas G. Ksiazek ; Dean D. Erdman ; Elaine R. Mardis ; Matthew Hickenbotham ; Vincent Magrini ; James Eldred ; J. Phillipe Latreille ; Richard K. Wilson ; Don Ganem ; Joseph L. DerisiSource :
- PLoS Biology [ 1544-9173 ] ; 2003.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN, Données de séquences moléculaires, Gènes viraux, Génome viral, Humains, Hybridation d'acides nucléiques, Maladies transmissibles émergentes (diagnostic), Maladies transmissibles émergentes (virologie), Réaction de polymérisation en chaîne, Syndrome respiratoire aigu sévère (génétique), Séquence nucléotidique, Séquençage par oligonucléotides en batterie (), Techniques génétiques, Virus du SRAS (génétique).
- MESH :
- diagnostic : Maladies transmissibles émergentes.
- génétique : Syndrome respiratoire aigu sévère, Virus du SRAS.
- virologie : Maladies transmissibles émergentes.
- Analyse de séquence d'ADN, Données de séquences moléculaires, Gènes viraux, Génome viral, Humains, Hybridation d'acides nucléiques, Réaction de polymérisation en chaîne, Séquence nucléotidique, Séquençage par oligonucléotides en batterie, Techniques génétiques.
English descriptors
- KwdEn :
- Base Sequence, Communicable Diseases, Emerging (diagnosis), Communicable Diseases, Emerging (virology), Genes, Viral, Genetic Techniques, Genome, Viral, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis (methods), Polymerase Chain Reaction, SARS Virus (genetics), Sequence Analysis, DNA, Severe Acute Respiratory Syndrome (genetics).
- MESH :
- diagnosis : Communicable Diseases, Emerging.
- genetics : SARS Virus, Severe Acute Respiratory Syndrome.
- methods : Oligonucleotide Array Sequence Analysis.
- virology : Communicable Diseases, Emerging.
- Base Sequence, Genes, Viral, Genetic Techniques, Genome, Viral, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Polymerase Chain Reaction, Sequence Analysis, DNA.
Abstract
Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.
Url:
DOI: 10.1371/journal.pbio.0000002
PubMed: 14624234
PubMed Central: 261870
Affiliations:
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Le document en format XML
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Phillipe Latreille</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Wilson, Richard K" sort="Wilson, Richard K" uniqKey="Wilson R" first="Richard K" last="Wilson">Richard K. Wilson</name><affiliation><nlm:aff id="aff4"></nlm:aff></affiliation></author><author><name sortKey="Ganem, Don" sort="Ganem, Don" uniqKey="Ganem D" first="Don" last="Ganem">Don Ganem</name><affiliation><nlm:aff id="aff2"></nlm:aff></affiliation></author><author><name sortKey="Derisi, Joseph L" sort="Derisi, Joseph L" uniqKey="Derisi J" first="Joseph L" last="Derisi">Joseph L. Derisi</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Biology</title><idno type="ISSN">1544-9173</idno><idno type="eISSN">1545-7885</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Communicable Diseases, Emerging (diagnosis)</term><term>Communicable Diseases, Emerging (virology)</term><term>Genes, Viral</term><term>Genetic Techniques</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Polymerase Chain Reaction</term><term>SARS Virus (genetics)</term><term>Sequence Analysis, DNA</term><term>Severe Acute Respiratory Syndrome (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Gènes viraux</term><term>Génome viral</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Maladies transmissibles émergentes (diagnostic)</term><term>Maladies transmissibles émergentes (virologie)</term><term>Réaction de polymérisation en chaîne</term><term>Syndrome respiratoire aigu sévère (génétique)</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Techniques génétiques</term><term>Virus du SRAS (génétique)</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Communicable Diseases, Emerging</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Maladies transmissibles émergentes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Maladies transmissibles émergentes</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Communicable Diseases, Emerging</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Genes, Viral</term><term>Genetic Techniques</term><term>Genome, Viral</term><term>Humans</term><term>Molecular Sequence Data</term><term>Nucleic Acid Hybridization</term><term>Polymerase Chain Reaction</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Gènes viraux</term><term>Génome viral</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Réaction de polymérisation en chaîne</term><term>Séquence nucléotidique</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques génétiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Because of the constant threat posed by emerging infectious diseases and the limitations of existing approaches used to identify new pathogens, there is a great demand for new technological methods for viral discovery. We describe herein a DNA microarray-based platform for novel virus identification and characterization. Central to this approach was a DNA microarray designed to detect a wide range of known viruses as well as novel members of existing viral families; this microarray contained the most highly conserved 70mer sequences from every fully sequenced reference viral genome in GenBank. During an outbreak of severe acute respiratory syndrome (SARS) in March 2003, hybridization to this microarray revealed the presence of a previously uncharacterized coronavirus in a viral isolate cultivated from a SARS patient. To further characterize this new virus, approximately 1 kb of the unknown virus genome was cloned by physically recovering viral sequences hybridized to individual array elements. Sequencing of these fragments confirmed that the virus was indeed a new member of the coronavirus family. This combination of array hybridization followed by direct viral sequence recovery should prove to be a general strategy for the rapid identification and characterization of novel viruses and emerging infectious disease.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Chang, Y" uniqKey="Chang Y">Y Chang</name></author><author><name sortKey="Cesarman, E" uniqKey="Cesarman E">E Cesarman</name></author><author><name sortKey="Pessin, Ms" uniqKey="Pessin M">MS Pessin</name></author><author><name sortKey="Lee, F" uniqKey="Lee F">F Lee</name></author><author><name sortKey="Culpepper, J" uniqKey="Culpepper J">J Culpepper</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Choo, Ql" uniqKey="Choo Q">QL Choo</name></author><author><name sortKey="Kuo, G" uniqKey="Kuo G">G Kuo</name></author><author><name sortKey="Weiner, Aj" uniqKey="Weiner A">AJ Weiner</name></author><author><name sortKey="Overby, Lr" uniqKey="Overby L">LR Overby</name></author><author><name sortKey="Bradley, Dw" uniqKey="Bradley D">DW Bradley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Jonassen, Cm" uniqKey="Jonassen C">CM Jonassen</name></author><author><name sortKey="Jonassen, To" uniqKey="Jonassen T">TO Jonassen</name></author><author><name sortKey="Grinde, B" uniqKey="Grinde B">B Grinde</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kellam, P" uniqKey="Kellam P">P Kellam</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ksiazek, Tg" uniqKey="Ksiazek T">TG Ksiazek</name></author><author><name sortKey="Erdman, D" uniqKey="Erdman D">D Erdman</name></author><author><name sortKey="Goldsmith, Cs" uniqKey="Goldsmith C">CS Goldsmith</name></author><author><name sortKey="Zaki, Sr" uniqKey="Zaki S">SR Zaki</name></author><author><name sortKey="Peret, T" uniqKey="Peret T">T Peret</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Marra, Ma" uniqKey="Marra M">MA Marra</name></author><author><name sortKey="Jones, Sj" uniqKey="Jones S">SJ Jones</name></author><author><name sortKey="Astell, Cr" uniqKey="Astell C">CR Astell</name></author><author><name sortKey="Holt, Ra" uniqKey="Holt R">RA Holt</name></author><author><name sortKey="Brooks Wilson, A" uniqKey="Brooks Wilson A">A Brooks-Wilson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Muerhoff, As" uniqKey="Muerhoff A">AS Muerhoff</name></author><author><name sortKey="Leary, Tp" uniqKey="Leary T">TP Leary</name></author><author><name sortKey="Desai, Sm" uniqKey="Desai S">SM Desai</name></author><author><name sortKey="Mushahwar, Ik" uniqKey="Mushahwar I">IK\ Mushahwar</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nichol, St" uniqKey="Nichol S">ST Nichol</name></author><author><name sortKey="Spiropoulou, Cf" uniqKey="Spiropoulou C">CF Spiropoulou</name></author><author><name sortKey="Morzunov, S" uniqKey="Morzunov S">S Morzunov</name></author><author><name sortKey="Rollin, Pe" uniqKey="Rollin P">PE Rollin</name></author><author><name sortKey="Ksiazek, Tg" uniqKey="Ksiazek T">TG Ksiazek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rota, Pa" uniqKey="Rota P">PA Rota</name></author><author><name sortKey="Oberste, Ms" uniqKey="Oberste M">MS Oberste</name></author><author><name sortKey="Monroe, Ss" uniqKey="Monroe S">SS Monroe</name></author><author><name sortKey="Nix, Wa" uniqKey="Nix W">WA Nix</name></author><author><name sortKey="Campagnoli, R" uniqKey="Campagnoli R">R Campagnoli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, D" uniqKey="Wang D">D Wang</name></author><author><name sortKey="Coscoy, L" uniqKey="Coscoy L">L Coscoy</name></author><author><name sortKey="Zylberberg, M" uniqKey="Zylberberg M">M Zylberberg</name></author><author><name sortKey="Avila, Pc" uniqKey="Avila P">PC Avila</name></author><author><name sortKey="Boushey, Ha" uniqKey="Boushey H">HA Boushey</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Derisi, Joseph L" sort="Derisi, Joseph L" uniqKey="Derisi J" first="Joseph L" last="Derisi">Joseph L. Derisi</name><name sortKey="Eldred, James" sort="Eldred, James" uniqKey="Eldred J" first="James" last="Eldred">James Eldred</name><name sortKey="Erdman, Dean D" sort="Erdman, Dean D" uniqKey="Erdman D" first="Dean D" last="Erdman">Dean D. Erdman</name><name sortKey="Ganem, Don" sort="Ganem, Don" uniqKey="Ganem D" first="Don" last="Ganem">Don Ganem</name><name sortKey="Hickenbotham, Matthew" sort="Hickenbotham, Matthew" uniqKey="Hickenbotham M" first="Matthew" last="Hickenbotham">Matthew Hickenbotham</name><name sortKey="Ksiazek, Thomas G" sort="Ksiazek, Thomas G" uniqKey="Ksiazek T" first="Thomas G" last="Ksiazek">Thomas G. Ksiazek</name><name sortKey="Latreille, J Phillipe" sort="Latreille, J Phillipe" uniqKey="Latreille J" first="J. Phillipe" last="Latreille">J. Phillipe Latreille</name><name sortKey="Liu, Yu Tsueng" sort="Liu, Yu Tsueng" uniqKey="Liu Y" first="Yu-Tsueng" last="Liu">Yu-Tsueng Liu</name><name sortKey="Magrini, Vincent" sort="Magrini, Vincent" uniqKey="Magrini V" first="Vincent" last="Magrini">Vincent Magrini</name><name sortKey="Mardis, Elaine R" sort="Mardis, Elaine R" uniqKey="Mardis E" first="Elaine R" last="Mardis">Elaine R. Mardis</name><name sortKey="Springer, Michael" sort="Springer, Michael" uniqKey="Springer M" first="Michael" last="Springer">Michael Springer</name><name sortKey="Urisman, Anatoly" sort="Urisman, Anatoly" uniqKey="Urisman A" first="Anatoly" last="Urisman">Anatoly Urisman</name><name sortKey="Wang, David" sort="Wang, David" uniqKey="Wang D" first="David" last="Wang">David Wang</name><name sortKey="Wilson, Richard K" sort="Wilson, Richard K" uniqKey="Wilson R" first="Richard K" last="Wilson">Richard K. Wilson</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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