Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2.
Identifieur interne : 000678 ( Main/Exploration ); précédent : 000677; suivant : 000679Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2.
Auteurs : Philip L. Bulterys [États-Unis] ; Natasha Garamani [États-Unis] ; Bryan Stevens [États-Unis] ; Malaya K. Sahoo [États-Unis] ; Chunhong Huang [États-Unis] ; Catherine A. Hogan [États-Unis] ; James Zehnder [États-Unis] ; Benjamin A. Pinsky [États-Unis]Source :
- Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology [ 1873-5967 ] ; 2020.
Descripteurs français
- KwdFr :
- Betacoronavirus (génétique), Humains (MeSH), Infections à coronavirus (diagnostic), Pandémies (MeSH), Pneumopathie virale (diagnostic), Protéines de l'enveloppe virale (génétique), Protéines nucléocapside (génétique), Techniques d'amplification d'acides nucléiques (méthodes), Techniques de diagnostic moléculaire (méthodes), Techniques de laboratoire clinique (méthodes).
- MESH :
English descriptors
- KwdEn :
- Betacoronavirus (genetics), COVID-19 (MeSH), COVID-19 Testing (MeSH), COVID-19 Vaccines (MeSH), Clinical Laboratory Techniques (methods), Coronavirus Infections (diagnosis), Humans (MeSH), Molecular Diagnostic Techniques (methods), Nucleic Acid Amplification Techniques (methods), Nucleocapsid Proteins (genetics), Pandemics (MeSH), Pneumonia, Viral (diagnosis), SARS-CoV-2 (MeSH), Viral Envelope Proteins (genetics).
- MESH :
- chemical , genetics : Nucleocapsid Proteins, Viral Envelope Proteins.
- chemical : COVID-19 Vaccines.
- diagnosis : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- methods : Clinical Laboratory Techniques, Molecular Diagnostic Techniques, Nucleic Acid Amplification Techniques.
- COVID-19, COVID-19 Testing, Humans, Pandemics, SARS-CoV-2.
Abstract
BACKGROUND
Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.
OBJECTIVES
The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.
STUDY DESIGN
A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.
RESULTS
Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.
CONCLUSIONS
Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.
DOI: 10.1016/j.jcv.2020.104427
PubMed: 32535398
PubMed Central: PMC7207111
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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<term>COVID-19 (MeSH)</term>
<term>COVID-19 Testing (MeSH)</term>
<term>COVID-19 Vaccines (MeSH)</term>
<term>Clinical Laboratory Techniques (methods)</term>
<term>Coronavirus Infections (diagnosis)</term>
<term>Humans (MeSH)</term>
<term>Molecular Diagnostic Techniques (methods)</term>
<term>Nucleic Acid Amplification Techniques (methods)</term>
<term>Nucleocapsid Proteins (genetics)</term>
<term>Pandemics (MeSH)</term>
<term>Pneumonia, Viral (diagnosis)</term>
<term>SARS-CoV-2 (MeSH)</term>
<term>Viral Envelope Proteins (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Betacoronavirus (génétique)</term>
<term>Humains (MeSH)</term>
<term>Infections à coronavirus (diagnostic)</term>
<term>Pandémies (MeSH)</term>
<term>Pneumopathie virale (diagnostic)</term>
<term>Protéines de l'enveloppe virale (génétique)</term>
<term>Protéines nucléocapside (génétique)</term>
<term>Techniques d'amplification d'acides nucléiques (méthodes)</term>
<term>Techniques de diagnostic moléculaire (méthodes)</term>
<term>Techniques de laboratoire clinique (méthodes)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Nucleocapsid Proteins</term>
<term>Viral Envelope Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>COVID-19 Vaccines</term>
</keywords>
<keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Coronavirus Infections</term>
<term>Pneumonia, Viral</term>
</keywords>
<keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Infections à coronavirus</term>
<term>Pneumopathie virale</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Betacoronavirus</term>
<term>Protéines de l'enveloppe virale</term>
<term>Protéines nucléocapside</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Clinical Laboratory Techniques</term>
<term>Molecular Diagnostic Techniques</term>
<term>Nucleic Acid Amplification Techniques</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Techniques d'amplification d'acides nucléiques</term>
<term>Techniques de diagnostic moléculaire</term>
<term>Techniques de laboratoire clinique</term>
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<term>COVID-19 Testing</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>OBJECTIVES</b>
</p>
<p>The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>STUDY DESIGN</b>
</p>
<p>A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.</p>
</div>
</front>
</TEI>
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<ArticleTitle>Comparison of a laboratory-developed test targeting the envelope gene with three nucleic acid amplification tests for detection of SARS-CoV-2.</ArticleTitle>
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<Abstract><AbstractText Label="BACKGROUND">Numerous nucleic acid amplification tests, including real-time, reverse transcription PCR (rRT-PCR) and isothermal amplification methods, have been developed to detect SARS-CoV-2 RNA, including many that have received emergency use authorization (EUA). There is a need to assess their test performance relative to one another.</AbstractText>
<AbstractText Label="OBJECTIVES">The aim of this study was to compare the test performance of a high complexity laboratory-developed rRT-PCR EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene with other tests: the Atila isothermal amplification assay targeting the nucleocapsid (N) gene and open reading frame 1ab (ORF1ab), the Altona E and spike (S) multiplex, real-time RT-PCR, and the US Centers for Disease Control and Prevention (CDC) N1 and N2 rRT-PCRs.</AbstractText>
<AbstractText Label="STUDY DESIGN">A diagnostic comparison study was performed by testing nasopharyngeal samples from persons under investigation for coronavirus disease 2019 (COVID-19). Assay performance was assessed by percent agreement and Cohen's kappa coefficient.</AbstractText>
<AbstractText Label="RESULTS">Positive percent agreement with the SHC EUA reference assay was 82.8 % (95 % confidence interval (CI) 65.0 to 92.9) for Atila, 86.7 % (95 % CI 69.7 to 95.3) for the Altona E and S targets, and 86.7 % (95 % CI 69.7 to 95.3) and 90.0 % (95 % CI 73.6 to 97.3), for the CDC N1 and N2 targets, respectively. All assays demonstrated 100 % negative percent agreement. Kappa coefficients ranged from 0.86 to 0.92, indicating excellent agreement.</AbstractText>
<AbstractText Label="CONCLUSIONS">Performance was comparable among the SARS-CoV-2 nucleic acid amplification methods tested, with a limited number of discrepancies observed in specimens with low viral loads.</AbstractText>
<CopyrightInformation>Copyright © 2020 Elsevier B.V. All rights reserved.</CopyrightInformation>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bulterys</LastName>
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</AffiliationInfo>
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</AffiliationInfo>
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<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Sahoo</LastName>
<ForeName>Malaya K</ForeName>
<Initials>MK</Initials>
<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Huang</LastName>
<ForeName>ChunHong</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zehnder</LastName>
<ForeName>James</ForeName>
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<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
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<ForeName>Benjamin A</ForeName>
<Initials>BA</Initials>
<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Clinical Virology Laboratory, Stanford Health Care, Stanford, CA, USA; Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA. Electronic address: bpinsky@stanford.edu.</Affiliation>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName>
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<MeshHeading><DescriptorName UI="D000086382" MajorTopicYN="N">COVID-19</DescriptorName>
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<MeshHeading><DescriptorName UI="D000086742" MajorTopicYN="N">COVID-19 Testing</DescriptorName>
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<MeshHeading><DescriptorName UI="D000086663" MajorTopicYN="N">COVID-19 Vaccines</DescriptorName>
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<MeshHeading><DescriptorName UI="D019411" MajorTopicYN="N">Clinical Laboratory Techniques</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName>
<QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D025202" MajorTopicYN="N">Molecular Diagnostic Techniques</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D021141" MajorTopicYN="N">Nucleic Acid Amplification Techniques</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019590" MajorTopicYN="N">Nucleocapsid Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName>
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<MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName>
<QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName>
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<MeshHeading><DescriptorName UI="D000086402" MajorTopicYN="N">SARS-CoV-2</DescriptorName>
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<MeshHeading><DescriptorName UI="D014759" MajorTopicYN="N">Viral Envelope Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">COVID-19</Keyword>
<Keyword MajorTopicYN="Y">Coronavirus</Keyword>
<Keyword MajorTopicYN="Y">Diagnostics</Keyword>
<Keyword MajorTopicYN="Y">SARS-CoV-2</Keyword>
</KeywordList>
<CoiStatement>Declaration of Competing Interest The authors declare no conflicts of interest.</CoiStatement>
</MedlineCitation>
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<Month>04</Month>
<Day>25</Day>
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<PubMedPubDate PubStatus="revised"><Year>2020</Year>
<Month>05</Month>
<Day>03</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted"><Year>2020</Year>
<Month>05</Month>
<Day>05</Day>
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<Month>6</Month>
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<ArticleId IdType="doi">10.1016/j.jcv.2020.104427</ArticleId>
<ArticleId IdType="pmc">PMC7207111</ArticleId>
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<ReferenceList><Reference><Citation>J Clin Virol. 2020 Jun;127:104383</Citation>
<ArticleIdList><ArticleId IdType="pubmed">32353760</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Euro Surveill. 2020 Jan;25(3):</Citation>
<ArticleIdList><ArticleId IdType="pubmed">31992387</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Emerg Infect Dis. 2020 Jul;26(7):1633-1635</Citation>
<ArticleIdList><ArticleId IdType="pubmed">32294051</ArticleId>
</ArticleIdList>
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<Reference><Citation>J Clin Microbiol. 2020 May 26;58(6):</Citation>
<ArticleIdList><ArticleId IdType="pubmed">32269100</ArticleId>
</ArticleIdList>
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<Reference><Citation>Biometrics. 1977 Mar;33(1):159-74</Citation>
<ArticleIdList><ArticleId IdType="pubmed">843571</ArticleId>
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<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Californie</li>
</region>
</list>
<tree><country name="États-Unis"><region name="Californie"><name sortKey="Bulterys, Philip L" sort="Bulterys, Philip L" uniqKey="Bulterys P" first="Philip L" last="Bulterys">Philip L. Bulterys</name>
</region>
<name sortKey="Garamani, Natasha" sort="Garamani, Natasha" uniqKey="Garamani N" first="Natasha" last="Garamani">Natasha Garamani</name>
<name sortKey="Hogan, Catherine A" sort="Hogan, Catherine A" uniqKey="Hogan C" first="Catherine A" last="Hogan">Catherine A. Hogan</name>
<name sortKey="Huang, Chunhong" sort="Huang, Chunhong" uniqKey="Huang C" first="Chunhong" last="Huang">Chunhong Huang</name>
<name sortKey="Pinsky, Benjamin A" sort="Pinsky, Benjamin A" uniqKey="Pinsky B" first="Benjamin A" last="Pinsky">Benjamin A. Pinsky</name>
<name sortKey="Sahoo, Malaya K" sort="Sahoo, Malaya K" uniqKey="Sahoo M" first="Malaya K" last="Sahoo">Malaya K. Sahoo</name>
<name sortKey="Stevens, Bryan" sort="Stevens, Bryan" uniqKey="Stevens B" first="Bryan" last="Stevens">Bryan Stevens</name>
<name sortKey="Zehnder, James" sort="Zehnder, James" uniqKey="Zehnder J" first="James" last="Zehnder">James Zehnder</name>
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