SrasV1, PascalFrancis, Corpus, bibRecord, 000590

Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods

Identifieur interne : 000590 ( PascalFrancis/Corpus ); précédent : 000589; suivant : 000591

Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods

Auteurs : Linda Chui ; Michael Drebot ; Anton Andonov ; Astrid Petrich ; Martin Glushek ; James Mahony

Source :

Diagnostic microbiology and infectious disease [ 0732-8893 ] ; 2005.

RBID : Pascal:05-0463654

Descripteurs français

Pascal (Inist)
- Coronavirus, Réaction chaîne polymérase, Détection, Méthode, Temps réel, Réaction chaîne polymérase RT, Sensibilité, Spécificité, Microbiologie, Syndrome respiratoire aigu sévère.

English descriptors

KwdEn :
- Coronavirus, Detection, Method, Microbiology, Polymerase chain reaction, Real time, Reverse transcription polymerase chain reaction, Sensitivity, Severe acute respiratory syndrome, Specificity.

Abstract

The sensitivity and specificity of various severe acute respiratory syndrome coronavirus (SARS-CoV) PCR primer and probe sets were evaluated through the use of commercial kits and in-house amplification formats. Conventional and real-time PCR assays were performed using a heat-block thermocycler ABI 9600, the Roche LightCycler version 1.2, or the ABI 7000 Sequence Detection System. The sensitivity of all primers was between 0.0004 and 0.04 PFU with viral cell lysate and between 0.004 and 0.4 PFU in spiked stool specimen per PCR assay. The primer sets for real-time PCR assays were at one least 1 log more sensitive than the primer sets used in the conventional PCR. A panel of viruses including swine gastroenteritis virus, bovine coronavirus, avian bronchitis virus (Connecticut strain), avian bronchitis virus (Massachusetts strain), human coronaviruses 229E and OC43, parainfluenza virus (type III), human metapneumovirus, adenovirus, respiratory syncytial virus, and influenza A were tested by all assays. All real-time PCR assays used probe-based detection, and no cross-reactivity was observed. With conventional PCR, analysis was performed using agarose gel electrophoresis and multiple nonspecific bands were observed. Two commercial extraction methods, magnetic particle capture and silica-based procedure were evaluated and the results were comparable. The former was less laborious with shorter time for completion and can easily be adapted to an automated system such as the MagNa Pure-LC, which can extract nucleic acid from clinical samples and load it into the sample capillaries of the LightCycler. As exemplified by this study, the continued refinement and evaluation of PCR procedures will greatly benefit the diagnostic laboratory during an outbreak of SARS.

Notice en format standard (ISO 2709)

Pour connaître la documentation sur le format Inist Standard.

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Format Inist (serveur)

NO :	PASCAL 05-0463654 INIST
ET :	Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods
AU :	CHUI (Linda); DREBOT (Michael); ANDONOV (Anton); PETRICH (Astrid); GLUSHEK (Martin); MAHONY (James)
AF :	Provincial Laboratory for Public Health (Microbiology), University of Alberta Hospital/Edmonton, Alberta, T6G 2J2/Canada (1 aut., 5 aut.); National Microbiology Laboratory/Winnipeg, Manitoba, R3E 2R2/Canada (2 aut., 3 aut.); St. Joseph's Healthcare, McMaster University/Hamilton Ontario, L8N 4A6/Canada (4 aut., 6 aut.)
DT :	Publication en série; Niveau analytique
SO :	Diagnostic microbiology and infectious disease; ISSN 0732-8893; Coden DMIDDZ; Etats-Unis; Da. 2005; Vol. 53; No. 1; Pp. 47-55; Bibl. 19 ref.
LA :	Anglais
EA :	The sensitivity and specificity of various severe acute respiratory syndrome coronavirus (SARS-CoV) PCR primer and probe sets were evaluated through the use of commercial kits and in-house amplification formats. Conventional and real-time PCR assays were performed using a heat-block thermocycler ABI 9600, the Roche LightCycler version 1.2, or the ABI 7000 Sequence Detection System. The sensitivity of all primers was between 0.0004 and 0.04 PFU with viral cell lysate and between 0.004 and 0.4 PFU in spiked stool specimen per PCR assay. The primer sets for real-time PCR assays were at one least 1 log more sensitive than the primer sets used in the conventional PCR. A panel of viruses including swine gastroenteritis virus, bovine coronavirus, avian bronchitis virus (Connecticut strain), avian bronchitis virus (Massachusetts strain), human coronaviruses 229E and OC43, parainfluenza virus (type III), human metapneumovirus, adenovirus, respiratory syncytial virus, and influenza A were tested by all assays. All real-time PCR assays used probe-based detection, and no cross-reactivity was observed. With conventional PCR, analysis was performed using agarose gel electrophoresis and multiple nonspecific bands were observed. Two commercial extraction methods, magnetic particle capture and silica-based procedure were evaluated and the results were comparable. The former was less laborious with shorter time for completion and can easily be adapted to an automated system such as the MagNa Pure-LC, which can extract nucleic acid from clinical samples and load it into the sample capillaries of the LightCycler. As exemplified by this study, the continued refinement and evaluation of PCR procedures will greatly benefit the diagnostic laboratory during an outbreak of SARS.
CC :	002A05C10; 002B05
FD :	Coronavirus; Réaction chaîne polymérase; Détection; Méthode; Temps réel; Réaction chaîne polymérase RT; Sensibilité; Spécificité; Microbiologie; Syndrome respiratoire aigu sévère
FG :	Coronaviridae; Nidovirales; Virus; Appareil respiratoire pathologie; Virose; Infection; Poumon pathologie
ED :	Coronavirus; Polymerase chain reaction; Detection; Method; Real time; Reverse transcription polymerase chain reaction; Sensitivity; Specificity; Microbiology; Severe acute respiratory syndrome
EG :	Coronaviridae; Nidovirales; Virus; Respiratory disease; Viral disease; Infection; Lung disease
SD :	Coronavirus; Reacción cadena polimerasa; Detección; Método; Tiempo real; Reacción cadena polimerasa transcripción inversa; Sensibilidad; Especificidad; Microbiología; Síndrome respiratorio agudo severo
LO :	INIST-20217.354000132776120080
ID :	05-0463654

Links to Exploration step

Pascal:05-0463654

Le document en format XML

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<front><div type="abstract" xml:lang="en">The sensitivity and specificity of various severe acute respiratory syndrome coronavirus (SARS-CoV) PCR primer and probe sets were evaluated through the use of commercial kits and in-house amplification formats. Conventional and real-time PCR assays were performed using a heat-block thermocycler ABI 9600, the Roche LightCycler version 1.2, or the ABI 7000 Sequence Detection System. The sensitivity of all primers was between 0.0004 and 0.04 PFU with viral cell lysate and between 0.004 and 0.4 PFU in spiked stool specimen per PCR assay. The primer sets for real-time PCR assays were at one least 1 log more sensitive than the primer sets used in the conventional PCR. A panel of viruses including swine gastroenteritis virus, bovine coronavirus, avian bronchitis virus (Connecticut strain), avian bronchitis virus (Massachusetts strain), human coronaviruses 229E and OC43, parainfluenza virus (type III), human metapneumovirus, adenovirus, respiratory syncytial virus, and influenza A were tested by all assays. All real-time PCR assays used probe-based detection, and no cross-reactivity was observed. With conventional PCR, analysis was performed using agarose gel electrophoresis and multiple nonspecific bands were observed. Two commercial extraction methods, magnetic particle capture and silica-based procedure were evaluated and the results were comparable. The former was less laborious with shorter time for completion and can easily be adapted to an automated system such as the MagNa Pure-LC, which can extract nucleic acid from clinical samples and load it into the sample capillaries of the LightCycler. As exemplified by this study, the continued refinement and evaluation of PCR procedures will greatly benefit the diagnostic laboratory during an outbreak of SARS.</div>
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<fA64 i1="01" i2="1"><s0>Diagnostic microbiology and infectious disease</s0>
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<fA66 i1="01"><s0>USA</s0>
</fA66>
<fC01 i1="01" l="ENG"><s0>The sensitivity and specificity of various severe acute respiratory syndrome coronavirus (SARS-CoV) PCR primer and probe sets were evaluated through the use of commercial kits and in-house amplification formats. Conventional and real-time PCR assays were performed using a heat-block thermocycler ABI 9600, the Roche LightCycler version 1.2, or the ABI 7000 Sequence Detection System. The sensitivity of all primers was between 0.0004 and 0.04 PFU with viral cell lysate and between 0.004 and 0.4 PFU in spiked stool specimen per PCR assay. The primer sets for real-time PCR assays were at one least 1 log more sensitive than the primer sets used in the conventional PCR. A panel of viruses including swine gastroenteritis virus, bovine coronavirus, avian bronchitis virus (Connecticut strain), avian bronchitis virus (Massachusetts strain), human coronaviruses 229E and OC43, parainfluenza virus (type III), human metapneumovirus, adenovirus, respiratory syncytial virus, and influenza A were tested by all assays. All real-time PCR assays used probe-based detection, and no cross-reactivity was observed. With conventional PCR, analysis was performed using agarose gel electrophoresis and multiple nonspecific bands were observed. Two commercial extraction methods, magnetic particle capture and silica-based procedure were evaluated and the results were comparable. The former was less laborious with shorter time for completion and can easily be adapted to an automated system such as the MagNa Pure-LC, which can extract nucleic acid from clinical samples and load it into the sample capillaries of the LightCycler. As exemplified by this study, the continued refinement and evaluation of PCR procedures will greatly benefit the diagnostic laboratory during an outbreak of SARS.</s0>
</fC01>
<fC02 i1="01" i2="X"><s0>002A05C10</s0>
</fC02>
<fC02 i1="02" i2="X"><s0>002B05</s0>
</fC02>
<fC03 i1="01" i2="X" l="FRE"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>01</s5>
</fC03>
<fC03 i1="01" i2="X" l="ENG"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>01</s5>
</fC03>
<fC03 i1="01" i2="X" l="SPA"><s0>Coronavirus</s0>
<s2>NW</s2>
<s5>01</s5>
</fC03>
<fC03 i1="02" i2="X" l="FRE"><s0>Réaction chaîne polymérase</s0>
<s5>05</s5>
</fC03>
<fC03 i1="02" i2="X" l="ENG"><s0>Polymerase chain reaction</s0>
<s5>05</s5>
</fC03>
<fC03 i1="02" i2="X" l="SPA"><s0>Reacción cadena polimerasa</s0>
<s5>05</s5>
</fC03>
<fC03 i1="03" i2="X" l="FRE"><s0>Détection</s0>
<s5>06</s5>
</fC03>
<fC03 i1="03" i2="X" l="ENG"><s0>Detection</s0>
<s5>06</s5>
</fC03>
<fC03 i1="03" i2="X" l="SPA"><s0>Detección</s0>
<s5>06</s5>
</fC03>
<fC03 i1="04" i2="X" l="FRE"><s0>Méthode</s0>
<s5>07</s5>
</fC03>
<fC03 i1="04" i2="X" l="ENG"><s0>Method</s0>
<s5>07</s5>
</fC03>
<fC03 i1="04" i2="X" l="SPA"><s0>Método</s0>
<s5>07</s5>
</fC03>
<fC03 i1="05" i2="X" l="FRE"><s0>Temps réel</s0>
<s5>08</s5>
</fC03>
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<s5>08</s5>
</fC03>
<fC03 i1="05" i2="X" l="SPA"><s0>Tiempo real</s0>
<s5>08</s5>
</fC03>
<fC03 i1="06" i2="X" l="FRE"><s0>Réaction chaîne polymérase RT</s0>
<s5>09</s5>
</fC03>
<fC03 i1="06" i2="X" l="ENG"><s0>Reverse transcription polymerase chain reaction</s0>
<s5>09</s5>
</fC03>
<fC03 i1="06" i2="X" l="SPA"><s0>Reacción cadena polimerasa transcripción inversa</s0>
<s5>09</s5>
</fC03>
<fC03 i1="07" i2="X" l="FRE"><s0>Sensibilité</s0>
<s5>10</s5>
</fC03>
<fC03 i1="07" i2="X" l="ENG"><s0>Sensitivity</s0>
<s5>10</s5>
</fC03>
<fC03 i1="07" i2="X" l="SPA"><s0>Sensibilidad</s0>
<s5>10</s5>
</fC03>
<fC03 i1="08" i2="X" l="FRE"><s0>Spécificité</s0>
<s5>11</s5>
</fC03>
<fC03 i1="08" i2="X" l="ENG"><s0>Specificity</s0>
<s5>11</s5>
</fC03>
<fC03 i1="08" i2="X" l="SPA"><s0>Especificidad</s0>
<s5>11</s5>
</fC03>
<fC03 i1="09" i2="X" l="FRE"><s0>Microbiologie</s0>
<s5>12</s5>
</fC03>
<fC03 i1="09" i2="X" l="ENG"><s0>Microbiology</s0>
<s5>12</s5>
</fC03>
<fC03 i1="09" i2="X" l="SPA"><s0>Microbiología</s0>
<s5>12</s5>
</fC03>
<fC03 i1="10" i2="X" l="FRE"><s0>Syndrome respiratoire aigu sévère</s0>
<s2>NM</s2>
<s5>14</s5>
</fC03>
<fC03 i1="10" i2="X" l="ENG"><s0>Severe acute respiratory syndrome</s0>
<s2>NM</s2>
<s5>14</s5>
</fC03>
<fC03 i1="10" i2="X" l="SPA"><s0>Síndrome respiratorio agudo severo</s0>
<s2>NM</s2>
<s5>14</s5>
</fC03>
<fC07 i1="01" i2="X" l="FRE"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="01" i2="X" l="ENG"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="01" i2="X" l="SPA"><s0>Coronaviridae</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="FRE"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="ENG"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="02" i2="X" l="SPA"><s0>Nidovirales</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="FRE"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="ENG"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="03" i2="X" l="SPA"><s0>Virus</s0>
<s2>NW</s2>
</fC07>
<fC07 i1="04" i2="X" l="FRE"><s0>Appareil respiratoire pathologie</s0>
<s5>13</s5>
</fC07>
<fC07 i1="04" i2="X" l="ENG"><s0>Respiratory disease</s0>
<s5>13</s5>
</fC07>
<fC07 i1="04" i2="X" l="SPA"><s0>Aparato respiratorio patología</s0>
<s5>13</s5>
</fC07>
<fC07 i1="05" i2="X" l="FRE"><s0>Virose</s0>
</fC07>
<fC07 i1="05" i2="X" l="ENG"><s0>Viral disease</s0>
</fC07>
<fC07 i1="05" i2="X" l="SPA"><s0>Virosis</s0>
</fC07>
<fC07 i1="06" i2="X" l="FRE"><s0>Infection</s0>
</fC07>
<fC07 i1="06" i2="X" l="ENG"><s0>Infection</s0>
</fC07>
<fC07 i1="06" i2="X" l="SPA"><s0>Infección</s0>
</fC07>
<fC07 i1="07" i2="X" l="FRE"><s0>Poumon pathologie</s0>
<s5>16</s5>
</fC07>
<fC07 i1="07" i2="X" l="ENG"><s0>Lung disease</s0>
<s5>16</s5>
</fC07>
<fC07 i1="07" i2="X" l="SPA"><s0>Pulmón patología</s0>
<s5>16</s5>
</fC07>
<fN21><s1>325</s1>
</fN21>
<fN44 i1="01"><s1>OTO</s1>
</fN44>
<fN82><s1>OTO</s1>
</fN82>
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<server><NO>PASCAL 05-0463654 INIST</NO>
<ET>Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods</ET>
<AU>CHUI (Linda); DREBOT (Michael); ANDONOV (Anton); PETRICH (Astrid); GLUSHEK (Martin); MAHONY (James)</AU>
<AF>Provincial Laboratory for Public Health (Microbiology), University of Alberta Hospital/Edmonton, Alberta, T6G 2J2/Canada (1 aut., 5 aut.); National Microbiology Laboratory/Winnipeg, Manitoba, R3E 2R2/Canada (2 aut., 3 aut.); St. Joseph's Healthcare, McMaster University/Hamilton Ontario, L8N 4A6/Canada (4 aut., 6 aut.)</AF>
<DT>Publication en série; Niveau analytique</DT>
<SO>Diagnostic microbiology and infectious disease; ISSN 0732-8893; Coden DMIDDZ; Etats-Unis; Da. 2005; Vol. 53; No. 1; Pp. 47-55; Bibl. 19 ref.</SO>
<LA>Anglais</LA>
<EA>The sensitivity and specificity of various severe acute respiratory syndrome coronavirus (SARS-CoV) PCR primer and probe sets were evaluated through the use of commercial kits and in-house amplification formats. Conventional and real-time PCR assays were performed using a heat-block thermocycler ABI 9600, the Roche LightCycler version 1.2, or the ABI 7000 Sequence Detection System. The sensitivity of all primers was between 0.0004 and 0.04 PFU with viral cell lysate and between 0.004 and 0.4 PFU in spiked stool specimen per PCR assay. The primer sets for real-time PCR assays were at one least 1 log more sensitive than the primer sets used in the conventional PCR. A panel of viruses including swine gastroenteritis virus, bovine coronavirus, avian bronchitis virus (Connecticut strain), avian bronchitis virus (Massachusetts strain), human coronaviruses 229E and OC43, parainfluenza virus (type III), human metapneumovirus, adenovirus, respiratory syncytial virus, and influenza A were tested by all assays. All real-time PCR assays used probe-based detection, and no cross-reactivity was observed. With conventional PCR, analysis was performed using agarose gel electrophoresis and multiple nonspecific bands were observed. Two commercial extraction methods, magnetic particle capture and silica-based procedure were evaluated and the results were comparable. The former was less laborious with shorter time for completion and can easily be adapted to an automated system such as the MagNa Pure-LC, which can extract nucleic acid from clinical samples and load it into the sample capillaries of the LightCycler. As exemplified by this study, the continued refinement and evaluation of PCR procedures will greatly benefit the diagnostic laboratory during an outbreak of SARS.</EA>
<CC>002A05C10; 002B05</CC>
<FD>Coronavirus; Réaction chaîne polymérase; Détection; Méthode; Temps réel; Réaction chaîne polymérase RT; Sensibilité; Spécificité; Microbiologie; Syndrome respiratoire aigu sévère</FD>
<FG>Coronaviridae; Nidovirales; Virus; Appareil respiratoire pathologie; Virose; Infection; Poumon pathologie</FG>
<ED>Coronavirus; Polymerase chain reaction; Detection; Method; Real time; Reverse transcription polymerase chain reaction; Sensitivity; Specificity; Microbiology; Severe acute respiratory syndrome</ED>
<EG>Coronaviridae; Nidovirales; Virus; Respiratory disease; Viral disease; Infection; Lung disease</EG>
<SD>Coronavirus; Reacción cadena polimerasa; Detección; Método; Tiempo real; Reacción cadena polimerasa transcripción inversa; Sensibilidad; Especificidad; Microbiología; Síndrome respiratorio agudo severo</SD>
<LO>INIST-20217.354000132776120080</LO>
<ID>05-0463654</ID>
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Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods

Comparison of 9 different PCR primers for the rapid detection of severe acute respiratory syndrome coronavirus using 2 RNA extraction methods

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