Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus
Identifieur interne : 000053 ( PascalFrancis/Checkpoint ); précédent : 000052; suivant : 000054Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus
Auteurs : Wasun Chantratita [Thaïlande] ; Wiroj Pongtanapisit [Thaïlande] ; Wantanich Piroj [Thaïlande] ; Chutatip Srichunrasmi [Thaïlande] ; Somying Seesuai [Thaïlande]Source :
- Southeast Asian journal of tropical medicine and public health [ 0125-1562 ] ; 2004.
Descripteurs français
- Pascal (Inist)
English descriptors
- KwdEn :
Abstract
The aim of this study was to develop a rapid, sensitive and robust procedure for the qualitative detection of SARS coronavirus RNA. Three unique detection formats were developed for real-time RNA amplification assays: a post amplification detection step with a virus-specific internal capture probe based on Taqman (RT-PCR TaqMan assay), hybridization probe (RT-PCR hybridization probe assay) and a real-time assay with virus-specific molecular beacon probes (NASBA-Beacon assay). The analytical sensitivity or reproducibility of the test results among those three assays was compared. All assays yielded results by detecting SARS coronavirus targeting the BNI-1 region in less than 2 hours. RNA detection by all the formats was unaffected by the presence of human sputum. The limits of detection were at least 10 copies of input RNA for both RT-PCR formats (RT-PCR TaqMan and RT-PCR hybridization probe assays), while the NASBA-Beacon assay could detect as little as 1 copy per reaction, with high reproducibility of the coefficient of variation (CV) of <10. These results demonstrate that real-time NASBA provides a rapid and sensitive alternative to RT-PCR for the routine qualitative assay of sputum for SARS corona viral RNA detection.
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
Pascal:04-0591783Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en" level="a">Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus</title><author><name sortKey="Chantratita, Wasun" sort="Chantratita, Wasun" uniqKey="Chantratita W" first="Wasun" last="Chantratita">Wasun Chantratita</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Pongtanapisit, Wiroj" sort="Pongtanapisit, Wiroj" uniqKey="Pongtanapisit W" first="Wiroj" last="Pongtanapisit">Wiroj Pongtanapisit</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Piroj, Wantanich" sort="Piroj, Wantanich" uniqKey="Piroj W" first="Wantanich" last="Piroj">Wantanich Piroj</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Srichunrasmi, Chutatip" sort="Srichunrasmi, Chutatip" uniqKey="Srichunrasmi C" first="Chutatip" last="Srichunrasmi">Chutatip Srichunrasmi</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Seesuai, Somying" sort="Seesuai, Somying" uniqKey="Seesuai S" first="Somying" last="Seesuai">Somying Seesuai</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">INIST</idno><idno type="inist">04-0591783</idno><date when="2004">2004</date><idno type="stanalyst">PASCAL 04-0591783 INIST</idno><idno type="RBID">Pascal:04-0591783</idno><idno type="wicri:Area/PascalFrancis/Corpus">000053</idno><idno type="wicri:Area/PascalFrancis/Curation">000006</idno><idno type="wicri:Area/PascalFrancis/Checkpoint">000053</idno><idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000053</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus</title><author><name sortKey="Chantratita, Wasun" sort="Chantratita, Wasun" uniqKey="Chantratita W" first="Wasun" last="Chantratita">Wasun Chantratita</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Pongtanapisit, Wiroj" sort="Pongtanapisit, Wiroj" uniqKey="Pongtanapisit W" first="Wiroj" last="Pongtanapisit">Wiroj Pongtanapisit</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Piroj, Wantanich" sort="Piroj, Wantanich" uniqKey="Piroj W" first="Wantanich" last="Piroj">Wantanich Piroj</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Srichunrasmi, Chutatip" sort="Srichunrasmi, Chutatip" uniqKey="Srichunrasmi C" first="Chutatip" last="Srichunrasmi">Chutatip Srichunrasmi</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Seesuai, Somying" sort="Seesuai, Somying" uniqKey="Seesuai S" first="Somying" last="Seesuai">Somying Seesuai</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>Thaïlande</country><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author></analytic><series><title level="j" type="main">Southeast Asian journal of tropical medicine and public health</title><title level="j" type="abbreviated">Southeast asian j. trop. med. public health</title><idno type="ISSN">0125-1562</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc><seriesStmt><title level="j" type="main">Southeast Asian journal of tropical medicine and public health</title><title level="j" type="abbreviated">Southeast asian j. trop. med. public health</title><idno type="ISSN">0125-1562</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Comparative study</term><term>Coronavirus</term><term>Probe</term><term>Reverse transcription polymerase chain reaction</term><term>Severe acute respiratory syndrome</term><term>Tropical medicine</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Etude comparative</term><term>Réaction chaîne polymérase RT</term><term>Sonde</term><term>Syndrome respiratoire aigu sévère</term><term>Coronavirus</term><term>Médecine tropicale</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The aim of this study was to develop a rapid, sensitive and robust procedure for the qualitative detection of SARS coronavirus RNA. Three unique detection formats were developed for real-time RNA amplification assays: a post amplification detection step with a virus-specific internal capture probe based on Taqman (RT-PCR TaqMan assay), hybridization probe (RT-PCR hybridization probe assay) and a real-time assay with virus-specific molecular beacon probes (NASBA-Beacon assay). The analytical sensitivity or reproducibility of the test results among those three assays was compared. All assays yielded results by detecting SARS coronavirus targeting the BNI-1 region in less than 2 hours. RNA detection by all the formats was unaffected by the presence of human sputum. The limits of detection were at least 10 copies of input RNA for both RT-PCR formats (RT-PCR TaqMan and RT-PCR hybridization probe assays), while the NASBA-Beacon assay could detect as little as 1 copy per reaction, with high reproducibility of the coefficient of variation (CV) of <10. These results demonstrate that real-time NASBA provides a rapid and sensitive alternative to RT-PCR for the routine qualitative assay of sputum for SARS corona viral RNA detection.</div></front></TEI><inist><standard h6="B"><pA><fA01 i1="01" i2="1"><s0>0125-1562</s0></fA01><fA02 i1="01"><s0>SJTMAK</s0></fA02><fA03 i2="1"><s0>Southeast asian j. trop. med. public health</s0></fA03><fA05><s2>35</s2></fA05><fA06><s2>3</s2></fA06><fA08 i1="01" i2="1" l="ENG"><s1>Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus</s1></fA08><fA11 i1="01" i2="1"><s1>CHANTRATITA (Wasun)</s1></fA11><fA11 i1="02" i2="1"><s1>PONGTANAPISIT (Wiroj)</s1></fA11><fA11 i1="03" i2="1"><s1>PIROJ (Wantanich)</s1></fA11><fA11 i1="04" i2="1"><s1>SRICHUNRASMI (Chutatip)</s1></fA11><fA11 i1="05" i2="1"><s1>SEESUAI (Somying)</s1></fA11><fA14 i1="01"><s1>Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University</s1><s2>Bangkok</s2><s3>THA</s3><sZ>1 aut.</sZ><sZ>2 aut.</sZ><sZ>3 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></fA14><fA20><s1>623-629</s1></fA20><fA21><s1>2004</s1></fA21><fA23 i1="01"><s0>ENG</s0></fA23><fA43 i1="01"><s1>INIST</s1><s2>19778</s2><s5>354000122499500230</s5></fA43><fA44><s0>0000</s0><s1>© 2004 INIST-CNRS. All rights reserved.</s1></fA44><fA45><s0>11 ref.</s0></fA45><fA47 i1="01" i2="1"><s0>04-0591783</s0></fA47><fA60><s1>P</s1></fA60><fA61><s0>A</s0></fA61><fA64 i1="01" i2="1"><s0>Southeast Asian journal of tropical medicine and public health</s0></fA64><fA66 i1="01"><s0>THA</s0></fA66><fC01 i1="01" l="ENG"><s0>The aim of this study was to develop a rapid, sensitive and robust procedure for the qualitative detection of SARS coronavirus RNA. Three unique detection formats were developed for real-time RNA amplification assays: a post amplification detection step with a virus-specific internal capture probe based on Taqman (RT-PCR TaqMan assay), hybridization probe (RT-PCR hybridization probe assay) and a real-time assay with virus-specific molecular beacon probes (NASBA-Beacon assay). The analytical sensitivity or reproducibility of the test results among those three assays was compared. All assays yielded results by detecting SARS coronavirus targeting the BNI-1 region in less than 2 hours. RNA detection by all the formats was unaffected by the presence of human sputum. The limits of detection were at least 10 copies of input RNA for both RT-PCR formats (RT-PCR TaqMan and RT-PCR hybridization probe assays), while the NASBA-Beacon assay could detect as little as 1 copy per reaction, with high reproducibility of the coefficient of variation (CV) of <10. These results demonstrate that real-time NASBA provides a rapid and sensitive alternative to RT-PCR for the routine qualitative assay of sputum for SARS corona viral RNA detection.</s0></fC01><fC02 i1="01" i2="X"><s0>002B01</s0></fC02><fC03 i1="01" i2="X" l="FRE"><s0>Etude comparative</s0><s5>02</s5></fC03><fC03 i1="01" i2="X" l="ENG"><s0>Comparative study</s0><s5>02</s5></fC03><fC03 i1="01" i2="X" l="SPA"><s0>Estudio comparativo</s0><s5>02</s5></fC03><fC03 i1="02" i2="X" l="FRE"><s0>Réaction chaîne polymérase RT</s0><s5>03</s5></fC03><fC03 i1="02" i2="X" l="ENG"><s0>Reverse transcription polymerase chain reaction</s0><s5>03</s5></fC03><fC03 i1="02" i2="X" l="SPA"><s0>Reacción cadena polimerasa transcripción inversa</s0><s5>03</s5></fC03><fC03 i1="03" i2="X" l="FRE"><s0>Sonde</s0><s5>05</s5></fC03><fC03 i1="03" i2="X" l="ENG"><s0>Probe</s0><s5>05</s5></fC03><fC03 i1="03" i2="X" l="SPA"><s0>Sonda</s0><s5>05</s5></fC03><fC03 i1="04" i2="X" l="FRE"><s0>Syndrome respiratoire aigu sévère</s0><s2>NM</s2><s5>06</s5></fC03><fC03 i1="04" i2="X" l="ENG"><s0>Severe acute respiratory syndrome</s0><s2>NM</s2><s5>06</s5></fC03><fC03 i1="04" i2="X" l="SPA"><s0>Síndrome respiratorio agudo severo</s0><s2>NM</s2><s5>06</s5></fC03><fC03 i1="05" i2="X" l="FRE"><s0>Coronavirus</s0><s2>NW</s2><s5>08</s5></fC03><fC03 i1="05" i2="X" l="ENG"><s0>Coronavirus</s0><s2>NW</s2><s5>08</s5></fC03><fC03 i1="05" i2="X" l="SPA"><s0>Coronavirus</s0><s2>NW</s2><s5>08</s5></fC03><fC03 i1="06" i2="X" l="FRE"><s0>Médecine tropicale</s0><s5>09</s5></fC03><fC03 i1="06" i2="X" l="ENG"><s0>Tropical medicine</s0><s5>09</s5></fC03><fC03 i1="06" i2="X" l="SPA"><s0>Medicina tropical</s0><s5>09</s5></fC03><fC07 i1="01" i2="X" l="FRE"><s0>Virose</s0><s2>NM</s2></fC07><fC07 i1="01" i2="X" l="ENG"><s0>Viral disease</s0><s2>NM</s2></fC07><fC07 i1="01" i2="X" l="SPA"><s0>Virosis</s0><s2>NM</s2></fC07><fC07 i1="02" i2="X" l="FRE"><s0>Infection</s0><s2>NM</s2></fC07><fC07 i1="02" i2="X" l="ENG"><s0>Infection</s0><s2>NM</s2></fC07><fC07 i1="02" i2="X" l="SPA"><s0>Infección</s0><s2>NM</s2></fC07><fC07 i1="03" i2="X" l="FRE"><s0>Coronaviridae</s0><s2>NW</s2></fC07><fC07 i1="03" i2="X" l="ENG"><s0>Coronaviridae</s0><s2>NW</s2></fC07><fC07 i1="03" i2="X" l="SPA"><s0>Coronaviridae</s0><s2>NW</s2></fC07><fC07 i1="04" i2="X" l="FRE"><s0>Nidovirales</s0><s2>NW</s2></fC07><fC07 i1="04" i2="X" l="ENG"><s0>Nidovirales</s0><s2>NW</s2></fC07><fC07 i1="04" i2="X" l="SPA"><s0>Nidovirales</s0><s2>NW</s2></fC07><fC07 i1="05" i2="X" l="FRE"><s0>Virus</s0><s2>NW</s2></fC07><fC07 i1="05" i2="X" l="ENG"><s0>Virus</s0><s2>NW</s2></fC07><fC07 i1="05" i2="X" l="SPA"><s0>Virus</s0><s2>NW</s2></fC07><fC07 i1="06" i2="X" l="FRE"><s0>Appareil respiratoire pathologie</s0><s5>37</s5></fC07><fC07 i1="06" i2="X" l="ENG"><s0>Respiratory disease</s0><s5>37</s5></fC07><fC07 i1="06" i2="X" l="SPA"><s0>Aparato respiratorio patología</s0><s5>37</s5></fC07><fC07 i1="07" i2="X" l="FRE"><s0>Poumon pathologie</s0><s5>38</s5></fC07><fC07 i1="07" i2="X" l="ENG"><s0>Lung disease</s0><s5>38</s5></fC07><fC07 i1="07" i2="X" l="SPA"><s0>Pulmón patología</s0><s5>38</s5></fC07><fN21><s1>341</s1></fN21><fN44 i1="01"><s1>OTO</s1></fN44><fN82><s1>OTO</s1></fN82></pA></standard></inist><affiliations><list><country><li>Thaïlande</li></country></list><tree><country name="Thaïlande"><noRegion><name sortKey="Chantratita, Wasun" sort="Chantratita, Wasun" uniqKey="Chantratita W" first="Wasun" last="Chantratita">Wasun Chantratita</name></noRegion><name sortKey="Piroj, Wantanich" sort="Piroj, Wantanich" uniqKey="Piroj W" first="Wantanich" last="Piroj">Wantanich Piroj</name><name sortKey="Pongtanapisit, Wiroj" sort="Pongtanapisit, Wiroj" uniqKey="Pongtanapisit W" first="Wiroj" last="Pongtanapisit">Wiroj Pongtanapisit</name><name sortKey="Seesuai, Somying" sort="Seesuai, Somying" uniqKey="Seesuai S" first="Somying" last="Seesuai">Somying Seesuai</name><name sortKey="Srichunrasmi, Chutatip" sort="Srichunrasmi, Chutatip" uniqKey="Srichunrasmi C" first="Chutatip" last="Srichunrasmi">Chutatip Srichunrasmi</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/CovidV1/Data/PascalFrancis/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000053 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PascalFrancis/Checkpoint/biblio.hfd -nk 000053 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= CovidV1
|flux= PascalFrancis
|étape= Checkpoint
|type= RBID
|clé= Pascal:04-0591783
|texte= Development and comparison of the real-time amplification based methods: NASBA-Beacon, RT-PCR Taqman and RT-PCR hybridization probe assays: For the qualitative detection of SARS coronavirus
}}
| This area was generated with Dilib version V0.6.33. |  |