Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus.
Identifieur interne : 002E66 ( PubMed/Corpus ); précédent : 002E65; suivant : 002E67Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus.
Auteurs : James B. Mahony ; Astrid Petrich ; Lisa Louie ; Xinyu Song ; Sylvia Chong ; Marek Smieja ; Max Chernesky ; Mark Loeb ; Susan RichardsonSource :
- Journal of clinical microbiology [ 0095-1137 ] ; 2004.
English descriptors
- KwdEn :
- Costs and Cost Analysis, Humans, RNA, Viral (analysis), Reagent Kits, Diagnostic (economics), Reverse Transcriptase Polymerase Chain Reaction (economics), Reverse Transcriptase Polymerase Chain Reaction (methods), SARS Virus (genetics), SARS Virus (isolation & purification), Sensitivity and Specificity, Severe Acute Respiratory Syndrome (virology).
- MESH :
- chemical , analysis : RNA, Viral.
- chemical , economics : Reagent Kits, Diagnostic.
- economics : Reverse Transcriptase Polymerase Chain Reaction.
- genetics : SARS Virus.
- isolation & purification : SARS Virus.
- methods : Reverse Transcriptase Polymerase Chain Reaction.
- virology : Severe Acute Respiratory Syndrome.
- Costs and Cost Analysis, Humans, Sensitivity and Specificity.
Abstract
We evaluated seven reverse transcription-PCR (RT-PCR) assays, including six in-house assays and one commercial assay for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV) RNA in clinical specimens. RT-PCR assays targeted different genomic regions and included three conventional assays (one nested and two non-nested) run on a conventional heat block and four real-time assays performed in a LightCycler (LC; Roche Diagnostics). All in-house assays were optimized for assay parameters, including MgCl2, primer, and probe concentrations. The commercial assay was the RealArt HPA CoV RT-PCR assay (Artus), which was run in the LC. Testing serial dilutions of cultured SARS-CoV showed that the analytical sensitivity of the assays ranged from 10(-8) to 10(-6), corresponding to 1 and 100 copies of viral RNA, respectively. Significant differences in analytical sensitivities were observed between assays (P < 0.01, probit regression analysis for 50% sensitivity levels for the top two assays versus the others). Testing 68 clinical specimens (including 17 respiratory tract specimens, 29 urine samples, and 22 stools or rectal swabs) demonstrated that six of the seven assays detected at least 17 of 18 positives (defined as positive in at least two assays), and two of the assays had a sensitivity of 100%. There were no significant differences in sensitivity between the assays (P = 0.5 [Cochrance Q test, least sensitive 15 of 18 versus 18 of 18]). The specificities of the assays ranged from 94.0 to 100% without significant differences (P = 0.25 to 0.5 [McNemar test]). The reagent and technologist cost of performing the in-house PCR assays ranged from $5.46 to $9.81 Canadian dollars (CDN) per test. The commercial assay cost was considerably higher at $40.37 per test. The results demonstrated good performance for all assays, providing laboratories that need to do SARS RNA testing with a choice of assay formats.
DOI: 10.1128/jcm.42.4.1471-1476.2004
PubMed: 15070991
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pubmed:15070991Le document en format XML
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Mahony</name><affiliation><nlm:affiliation>McMaster University, Toronto, Ontario L8N 4A6, Canada. mahonyj@mcmaster.ca</nlm:affiliation></affiliation></author><author><name sortKey="Petrich, Astrid" sort="Petrich, Astrid" uniqKey="Petrich A" first="Astrid" last="Petrich">Astrid Petrich</name></author><author><name sortKey="Louie, Lisa" sort="Louie, Lisa" uniqKey="Louie L" first="Lisa" last="Louie">Lisa Louie</name></author><author><name sortKey="Song, Xinyu" sort="Song, Xinyu" uniqKey="Song X" first="Xinyu" last="Song">Xinyu Song</name></author><author><name sortKey="Chong, Sylvia" sort="Chong, Sylvia" uniqKey="Chong S" first="Sylvia" last="Chong">Sylvia Chong</name></author><author><name sortKey="Smieja, Marek" sort="Smieja, Marek" uniqKey="Smieja M" first="Marek" last="Smieja">Marek Smieja</name></author><author><name sortKey="Chernesky, Max" sort="Chernesky, Max" uniqKey="Chernesky M" first="Max" last="Chernesky">Max Chernesky</name></author><author><name sortKey="Loeb, Mark" sort="Loeb, Mark" uniqKey="Loeb M" first="Mark" last="Loeb">Mark Loeb</name></author><author><name sortKey="Richardson, Susan" sort="Richardson, Susan" uniqKey="Richardson S" first="Susan" last="Richardson">Susan Richardson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2004">2004</date><idno type="RBID">pubmed:15070991</idno><idno type="pmid">15070991</idno><idno type="doi">10.1128/jcm.42.4.1471-1476.2004</idno><idno type="wicri:Area/PubMed/Corpus">002E66</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002E66</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus.</title><author><name sortKey="Mahony, James B" sort="Mahony, James B" uniqKey="Mahony J" first="James B" last="Mahony">James B. Mahony</name><affiliation><nlm:affiliation>McMaster University, Toronto, Ontario L8N 4A6, Canada. mahonyj@mcmaster.ca</nlm:affiliation></affiliation></author><author><name sortKey="Petrich, Astrid" sort="Petrich, Astrid" uniqKey="Petrich A" first="Astrid" last="Petrich">Astrid Petrich</name></author><author><name sortKey="Louie, Lisa" sort="Louie, Lisa" uniqKey="Louie L" first="Lisa" last="Louie">Lisa Louie</name></author><author><name sortKey="Song, Xinyu" sort="Song, Xinyu" uniqKey="Song X" first="Xinyu" last="Song">Xinyu Song</name></author><author><name sortKey="Chong, Sylvia" sort="Chong, Sylvia" uniqKey="Chong S" first="Sylvia" last="Chong">Sylvia Chong</name></author><author><name sortKey="Smieja, Marek" sort="Smieja, Marek" uniqKey="Smieja M" first="Marek" last="Smieja">Marek Smieja</name></author><author><name sortKey="Chernesky, Max" sort="Chernesky, Max" uniqKey="Chernesky M" first="Max" last="Chernesky">Max Chernesky</name></author><author><name sortKey="Loeb, Mark" sort="Loeb, Mark" uniqKey="Loeb M" first="Mark" last="Loeb">Mark Loeb</name></author><author><name sortKey="Richardson, Susan" sort="Richardson, Susan" uniqKey="Richardson S" first="Susan" last="Richardson">Susan Richardson</name></author></analytic><series><title level="j">Journal of clinical microbiology</title><idno type="ISSN">0095-1137</idno><imprint><date when="2004" type="published">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Costs and Cost Analysis</term><term>Humans</term><term>RNA, Viral (analysis)</term><term>Reagent Kits, Diagnostic (economics)</term><term>Reverse Transcriptase Polymerase Chain Reaction (economics)</term><term>Reverse Transcriptase Polymerase Chain Reaction (methods)</term><term>SARS Virus (genetics)</term><term>SARS Virus (isolation & purification)</term><term>Sensitivity and Specificity</term><term>Severe Acute Respiratory Syndrome (virology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" type="chemical" qualifier="economics" xml:lang="en"><term>Reagent Kits, Diagnostic</term></keywords><keywords scheme="MESH" qualifier="economics" xml:lang="en"><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>SARS Virus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Severe Acute Respiratory Syndrome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Costs and Cost Analysis</term><term>Humans</term><term>Sensitivity and Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We evaluated seven reverse transcription-PCR (RT-PCR) assays, including six in-house assays and one commercial assay for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV) RNA in clinical specimens. RT-PCR assays targeted different genomic regions and included three conventional assays (one nested and two non-nested) run on a conventional heat block and four real-time assays performed in a LightCycler (LC; Roche Diagnostics). All in-house assays were optimized for assay parameters, including MgCl2, primer, and probe concentrations. The commercial assay was the RealArt HPA CoV RT-PCR assay (Artus), which was run in the LC. Testing serial dilutions of cultured SARS-CoV showed that the analytical sensitivity of the assays ranged from 10(-8) to 10(-6), corresponding to 1 and 100 copies of viral RNA, respectively. Significant differences in analytical sensitivities were observed between assays (P < 0.01, probit regression analysis for 50% sensitivity levels for the top two assays versus the others). Testing 68 clinical specimens (including 17 respiratory tract specimens, 29 urine samples, and 22 stools or rectal swabs) demonstrated that six of the seven assays detected at least 17 of 18 positives (defined as positive in at least two assays), and two of the assays had a sensitivity of 100%. There were no significant differences in sensitivity between the assays (P = 0.5 [Cochrance Q test, least sensitive 15 of 18 versus 18 of 18]). The specificities of the assays ranged from 94.0 to 100% without significant differences (P = 0.25 to 0.5 [McNemar test]). The reagent and technologist cost of performing the in-house PCR assays ranged from $5.46 to $9.81 Canadian dollars (CDN) per test. The commercial assay cost was considerably higher at $40.37 per test. The results demonstrated good performance for all assays, providing laboratories that need to do SARS RNA testing with a choice of assay formats.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15070991</PMID><DateCompleted><Year>2004</Year><Month>07</Month><Day>19</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0095-1137</ISSN><JournalIssue CitedMedium="Print"><Volume>42</Volume><Issue>4</Issue><PubDate><Year>2004</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Journal of clinical microbiology</Title><ISOAbbreviation>J. Clin. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>Performance and Cost evaluation of one commercial and six in-house conventional and real-time reverse transcription-pcr assays for detection of severe acute respiratory syndrome coronavirus.</ArticleTitle><Pagination><MedlinePgn>1471-6</MedlinePgn></Pagination><Abstract><AbstractText>We evaluated seven reverse transcription-PCR (RT-PCR) assays, including six in-house assays and one commercial assay for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV) RNA in clinical specimens. RT-PCR assays targeted different genomic regions and included three conventional assays (one nested and two non-nested) run on a conventional heat block and four real-time assays performed in a LightCycler (LC; Roche Diagnostics). All in-house assays were optimized for assay parameters, including MgCl2, primer, and probe concentrations. The commercial assay was the RealArt HPA CoV RT-PCR assay (Artus), which was run in the LC. Testing serial dilutions of cultured SARS-CoV showed that the analytical sensitivity of the assays ranged from 10(-8) to 10(-6), corresponding to 1 and 100 copies of viral RNA, respectively. Significant differences in analytical sensitivities were observed between assays (P < 0.01, probit regression analysis for 50% sensitivity levels for the top two assays versus the others). Testing 68 clinical specimens (including 17 respiratory tract specimens, 29 urine samples, and 22 stools or rectal swabs) demonstrated that six of the seven assays detected at least 17 of 18 positives (defined as positive in at least two assays), and two of the assays had a sensitivity of 100%. There were no significant differences in sensitivity between the assays (P = 0.5 [Cochrance Q test, least sensitive 15 of 18 versus 18 of 18]). The specificities of the assays ranged from 94.0 to 100% without significant differences (P = 0.25 to 0.5 [McNemar test]). The reagent and technologist cost of performing the in-house PCR assays ranged from $5.46 to $9.81 Canadian dollars (CDN) per test. The commercial assay cost was considerably higher at $40.37 per test. The results demonstrated good performance for all assays, providing laboratories that need to do SARS RNA testing with a choice of assay formats.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mahony</LastName><ForeName>James B</ForeName><Initials>JB</Initials><AffiliationInfo><Affiliation>McMaster University, Toronto, Ontario L8N 4A6, Canada. mahonyj@mcmaster.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Petrich</LastName><ForeName>Astrid</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Louie</LastName><ForeName>Lisa</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Xinyu</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Chong</LastName><ForeName>Sylvia</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Smieja</LastName><ForeName>Marek</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Chernesky</LastName><ForeName>Max</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Loeb</LastName><ForeName>Mark</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Richardson</LastName><ForeName>Susan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><CollectiveName>Ontario Laboratory Working Group for the Rapid Diagnosis of Emerging Infections</CollectiveName></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Clin Microbiol</MedlineTA><NlmUniqueID>7505564</NlmUniqueID><ISSNLinking>0095-1137</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011933">Reagent Kits, Diagnostic</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003365" MajorTopicYN="N">Costs and Cost Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011933" MajorTopicYN="N">Reagent Kits, Diagnostic</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="N">economics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000191" MajorTopicYN="Y">economics</QualifierName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D045473" MajorTopicYN="N">SARS Virus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012680" MajorTopicYN="N">Sensitivity and Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D045169" MajorTopicYN="N">Severe Acute Respiratory Syndrome</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2004</Year><Month>4</Month><Day>9</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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