A universal microarray for detection of SARS coronavirus
Identifieur interne : 000A48 ( Ncbi/Checkpoint ); précédent : 000A47; suivant : 000A49A universal microarray for detection of SARS coronavirus
Auteurs : Wei-Hong Long [République populaire de Chine] ; Hua-Sheng Xiao [République populaire de Chine] ; Xiao-Mei Gu [République populaire de Chine] ; Qing-Hua Zhang [République populaire de Chine] ; Hong-Jun Yang [République populaire de Chine] ; Guo-Ping Zhao [République populaire de Chine] ; Jian-Hua Liu [République populaire de Chine]Source :
- Journal of Virological Methods [ 0166-0934 ] ; 2004.
Descripteurs français
- KwdFr :
- Génotype, Humains, Hybridation d'acides nucléiques, Mutation ponctuelle, RT-PCR, Réaction en chaîne par ligase, Substitution d'acide aminé, Syndrome respiratoire aigu sévère (diagnostic), Syndrome respiratoire aigu sévère (virologie), Séquençage par oligonucléotides en batterie, Techniques de diagnostic moléculaire, Variation génétique, Virus du SRAS (génétique), Virus du SRAS (isolement et purification), Épidémiologie moléculaire.
- MESH :
- diagnostic : Syndrome respiratoire aigu sévère.
- génétique : Virus du SRAS.
- isolement et purification : Virus du SRAS.
- virologie : Syndrome respiratoire aigu sévère.
- Génotype, Humains, Hybridation d'acides nucléiques, Mutation ponctuelle, RT-PCR, Réaction en chaîne par ligase, Substitution d'acide aminé, Séquençage par oligonucléotides en batterie, Techniques de diagnostic moléculaire, Variation génétique, Épidémiologie moléculaire.
English descriptors
- KwdEn :
- Amino Acid Substitution, Genetic Variation, Genotype, Humans, Ligase Chain Reaction, Molecular Diagnostic Techniques, Molecular Epidemiology, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Point Mutation, Reverse Transcriptase Polymerase Chain Reaction, SARS Virus (genetics), SARS Virus (isolation & purification), Severe Acute Respiratory Syndrome (diagnosis), Severe Acute Respiratory Syndrome (virology).
- MESH :
- diagnosis : Severe Acute Respiratory Syndrome.
- genetics : SARS Virus.
- isolation & purification : SARS Virus.
- virology : Severe Acute Respiratory Syndrome.
- Amino Acid Substitution, Genetic Variation, Genotype, Humans, Ligase Chain Reaction, Molecular Diagnostic Techniques, Molecular Epidemiology, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Point Mutation, Reverse Transcriptase Polymerase Chain Reaction.
Abstract
Severe acute respiratory syndrome (SARS) is caused by the SARS coronavirus (SARS-CoV). There are many point mutations among SARS-CoV genome sequences. Previous studies suggested that the mutations are correlated closely with the SARS epidemic. It was found that the bases of six nucleotide positions (nt9404, nt9479, nt19838, nt21721, nt22222 and nt27827) with high-mutation rate have an important relationship with the SARS epidemic. For viral detection as well as genotyping, a universal microarray system was developed that combines RT-PCR and ligase detection reaction (LDR). The Zip Codes attached covalently to a slide remain constant and their complementary Zip Codes (cZip Codes) can be used for tagging target sequence, making the microarrays universal. The discriminating oligonucleotides contain on the 5′ end “cZip Codes” that are used to direct LDR product to specific Zip Codes attached covalently to a slide. Since Zip Codes have no homology to either the target sequence or to other sequences in the genomes of both human host and SARS-CoV, there was no false signal due to mismatch hybridizations. 20 samples assayed with the universal microarray were confirmed by DNA sequencing, demonstrating that this microarray system is a promising diagnostic tool for detection and genotyping of the SARS-CoV.
Url:
DOI: 10.1016/j.jviromet.2004.06.016
PubMed: 15350733
PubMed Central: 7112900
Affiliations:
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Ltd., 151 Li-Bing Road, Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203</wicri:regionArea><wicri:noRegion>Shanghai 201203</wicri:noRegion></affiliation></author><author><name sortKey="Gu, Xiao Mei" sort="Gu, Xiao Mei" uniqKey="Gu X" first="Xiao-Mei" last="Gu">Xiao-Mei Gu</name><affiliation wicri:level="1"><nlm:aff id="aff2">Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203</wicri:regionArea><wicri:noRegion>Shanghai 201203</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Qing Hua" sort="Zhang, Qing Hua" uniqKey="Zhang Q" first="Qing-Hua" last="Zhang">Qing-Hua Zhang</name><affiliation wicri:level="1"><nlm:aff id="aff2">Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203</wicri:regionArea><wicri:noRegion>Shanghai 201203</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Hong Jun" sort="Yang, Hong Jun" uniqKey="Yang H" first="Hong-Jun" last="Yang">Hong-Jun Yang</name><affiliation wicri:level="1"><nlm:aff id="aff2">Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203</wicri:regionArea><wicri:noRegion>Shanghai 201203</wicri:noRegion></affiliation></author><author><name sortKey="Zhao, Guo Ping" sort="Zhao, Guo Ping" uniqKey="Zhao G" first="Guo-Ping" last="Zhao">Guo-Ping Zhao</name><affiliation wicri:level="1"><nlm:aff id="aff2">Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai BioChip Co. Ltd., 151 Li-Bing Road, Shanghai 201203</wicri:regionArea><wicri:noRegion>Shanghai 201203</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Jian Hua" sort="Liu, Jian Hua" uniqKey="Liu J" first="Jian-Hua" last="Liu">Jian-Hua Liu</name><affiliation wicri:level="1"><nlm:aff id="aff1">School of Life Science and Technology, Shanghai JiaoTong University, 1954 Hua-Shan Road, Shanghai 200030, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Science and Technology, Shanghai JiaoTong University, 1954 Hua-Shan Road, Shanghai 200030</wicri:regionArea><wicri:noRegion>Shanghai 200030</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Virological Methods</title><idno type="ISSN">0166-0934</idno><idno type="eISSN">1879-0984</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Substitution</term><term>Genetic Variation</term><term>Genotype</term><term>Humans</term><term>Ligase Chain Reaction</term><term>Molecular Diagnostic Techniques</term><term>Molecular Epidemiology</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Point Mutation</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Severe Acute Respiratory Syndrome (diagnosis)</term><term>Severe Acute Respiratory Syndrome (virology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Génotype</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Mutation ponctuelle</term><term>RT-PCR</term><term>Réaction en chaîne par ligase</term><term>Substitution d'acide aminé</term><term>Syndrome respiratoire aigu sévère (diagnostic)</term><term>Syndrome respiratoire aigu sévère (virologie)</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques de diagnostic moléculaire</term><term>Variation génétique</term><term>Virus du SRAS (génétique)</term><term>Virus du SRAS (isolement et purification)</term><term>Épidémiologie moléculaire</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>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Virus du SRAS</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Syndrome respiratoire aigu sévère</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Substitution</term><term>Genetic Variation</term><term>Genotype</term><term>Humans</term><term>Ligase Chain Reaction</term><term>Molecular Diagnostic Techniques</term><term>Molecular Epidemiology</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Point Mutation</term><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génotype</term><term>Humains</term><term>Hybridation d'acides nucléiques</term><term>Mutation ponctuelle</term><term>RT-PCR</term><term>Réaction en chaîne par ligase</term><term>Substitution d'acide aminé</term><term>Séquençage par oligonucléotides en batterie</term><term>Techniques de diagnostic moléculaire</term><term>Variation génétique</term><term>Épidémiologie moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Severe acute respiratory syndrome (SARS) is caused by the SARS coronavirus (SARS-CoV). There are many point mutations among SARS-CoV genome sequences. Previous studies suggested that the mutations are correlated closely with the SARS epidemic. It was found that the bases of six nucleotide positions (nt9404, nt9479, nt19838, nt21721, nt22222 and nt27827) with high-mutation rate have an important relationship with the SARS epidemic. For viral detection as well as genotyping, a universal microarray system was developed that combines RT-PCR and ligase detection reaction (LDR). The Zip Codes attached covalently to a slide remain constant and their complementary Zip Codes (cZip Codes) can be used for tagging target sequence, making the microarrays universal. The discriminating oligonucleotides contain on the 5′ end “cZip Codes” that are used to direct LDR product to specific Zip Codes attached covalently to a slide. Since Zip Codes have no homology to either the target sequence or to other sequences in the genomes of both human host and SARS-CoV, there was no false signal due to mismatch hybridizations. 20 samples assayed with the universal microarray were confirmed by DNA sequencing, demonstrating that this microarray system is a promising diagnostic tool for detection and genotyping of the SARS-CoV.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bellis, D G" uniqKey="Bellis D">D.G. Bellis</name></author><author><name sortKey="Castiglioni, B" uniqKey="Castiglioni B">B. Castiglioni</name></author><author><name sortKey="Bordoni, R" uniqKey="Bordoni R">R. Bordoni</name></author><author><name sortKey="Rossi, L" uniqKey="Rossi L">L. Rossi</name></author><author><name sortKey="Mezzelani, A" uniqKey="Mezzelani A">A. Mezzelani</name></author><author><name sortKey="Rizzi, E" uniqKey="Rizzi E">E. 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Lin</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Long, Wei Hong" sort="Long, Wei Hong" uniqKey="Long W" first="Wei-Hong" last="Long">Wei-Hong Long</name></noRegion><name sortKey="Gu, Xiao Mei" sort="Gu, Xiao Mei" uniqKey="Gu X" first="Xiao-Mei" last="Gu">Xiao-Mei Gu</name><name sortKey="Liu, Jian Hua" sort="Liu, Jian Hua" uniqKey="Liu J" first="Jian-Hua" last="Liu">Jian-Hua Liu</name><name sortKey="Xiao, Hua Sheng" sort="Xiao, Hua Sheng" uniqKey="Xiao H" first="Hua-Sheng" last="Xiao">Hua-Sheng Xiao</name><name sortKey="Yang, Hong Jun" sort="Yang, Hong Jun" uniqKey="Yang H" first="Hong-Jun" last="Yang">Hong-Jun Yang</name><name sortKey="Zhang, Qing Hua" sort="Zhang, Qing Hua" uniqKey="Zhang Q" first="Qing-Hua" last="Zhang">Qing-Hua Zhang</name><name sortKey="Zhao, Guo Ping" sort="Zhao, Guo Ping" uniqKey="Zhao G" first="Guo-Ping" last="Zhao">Guo-Ping Zhao</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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