Serveur d'exploration sur le Covid à Stanford

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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 : 000679

Comparison 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 :

RBID : pubmed:32535398

Descripteurs français

English descriptors

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:


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<term>Clinical Laboratory Techniques (methods)</term>
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<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>
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<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>
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<Keyword MajorTopicYN="Y">COVID-19</Keyword>
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<Keyword MajorTopicYN="Y">SARS-CoV-2</Keyword>
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<CoiStatement>Declaration of Competing Interest The authors declare no conflicts of interest.</CoiStatement>
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<Year>2020</Year>
<Month>05</Month>
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<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>
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<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>
</Reference>
<Reference>
<Citation>J Clin Microbiol. 2020 May 26;58(6):</Citation>
<ArticleIdList>
<ArticleId IdType="pubmed">32269100</ArticleId>
</ArticleIdList>
</Reference>
<Reference>
<Citation>Biometrics. 1977 Mar;33(1):159-74</Citation>
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<ArticleId IdType="pubmed">843571</ArticleId>
</ArticleIdList>
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<li>États-Unis</li>
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<name sortKey="Bulterys, Philip L" sort="Bulterys, Philip L" uniqKey="Bulterys P" first="Philip L" last="Bulterys">Philip L. Bulterys</name>
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<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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