CovidStanfordV1, Main, Exploration, bibRecord, 000676

Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2.

Identifieur interne : 000676 ( Main/Exploration ); précédent : 000675; suivant : 000677

Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2.

Auteurs : Catherine A. Hogan [États-Unis] ; Malaya K. Sahoo [États-Unis] ; Chunhong Huang [États-Unis] ; Natasha Garamani [États-Unis] ; Bryan Stevens [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.

RBID : pubmed:32353760

Descripteurs français

KwdFr :
- Betacoronavirus (génétique), Humains (MeSH), Infections à coronavirus (diagnostic), Pandémies (MeSH), Partie nasale du pharynx (virologie), Pneumopathie virale (diagnostic), Protéines de l'enveloppe virale (génétique), Protéines de l'enveloppe virale (isolement et purification), Reproductibilité des résultats (MeSH), Techniques de diagnostic moléculaire (méthodes), Techniques de diagnostic moléculaire (normes), Trousses de réactifs pour diagnostic (normes).
MESH :
- diagnostic : Infections à coronavirus, Pneumopathie virale.
- génétique : Betacoronavirus, Protéines de l'enveloppe virale.
- isolement et purification : Protéines de l'enveloppe virale.
- méthodes : Techniques de diagnostic moléculaire.
- normes : Techniques de diagnostic moléculaire, Trousses de réactifs pour diagnostic.
- virologie : Partie nasale du pharynx.
- Humains, Pandémies, Reproductibilité des résultats.

English descriptors

KwdEn :
- Betacoronavirus (genetics), COVID-19 (MeSH), Coronavirus Envelope Proteins (MeSH), Coronavirus Infections (diagnosis), Humans (MeSH), Molecular Diagnostic Techniques (methods), Molecular Diagnostic Techniques (standards), Nasopharynx (virology), Pandemics (MeSH), Pneumonia, Viral (diagnosis), Reagent Kits, Diagnostic (standards), Reproducibility of Results (MeSH), SARS-CoV-2 (MeSH), Viral Envelope Proteins (genetics), Viral Envelope Proteins (isolation & purification).
MESH :
- chemical , genetics : Viral Envelope Proteins.
- chemical , isolation & purification : Viral Envelope Proteins.
- chemical , standards : Reagent Kits, Diagnostic.
- chemical : Coronavirus Envelope Proteins.
- diagnosis : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- methods : Molecular Diagnostic Techniques.
- standards : Molecular Diagnostic Techniques.
- virology : Nasopharynx.
- COVID-19, Humans, Pandemics, Reproducibility of Results, SARS-CoV-2.

Abstract

BACKGROUND

Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and 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 the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene.

STUDY DESIGN

We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient.

RESULTS

A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6.

CONCLUSION

The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.

DOI: 10.1016/j.jcv.2020.104383
PubMed: 32353760
PubMed Central: PMC7195328

Affiliations:

Links toward previous steps (curation, corpus...)

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Le document en format XML

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Betacoronavirus (genetics)</term>
<term>COVID-19 (MeSH)</term>
<term>Coronavirus Envelope Proteins (MeSH)</term>
<term>Coronavirus Infections (diagnosis)</term>
<term>Humans (MeSH)</term>
<term>Molecular Diagnostic Techniques (methods)</term>
<term>Molecular Diagnostic Techniques (standards)</term>
<term>Nasopharynx (virology)</term>
<term>Pandemics (MeSH)</term>
<term>Pneumonia, Viral (diagnosis)</term>
<term>Reagent Kits, Diagnostic (standards)</term>
<term>Reproducibility of Results (MeSH)</term>
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<term>Viral Envelope Proteins (isolation & purification)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>Betacoronavirus (génétique)</term>
<term>Humains (MeSH)</term>
<term>Infections à coronavirus (diagnostic)</term>
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<term>Partie nasale du pharynx (virologie)</term>
<term>Pneumopathie virale (diagnostic)</term>
<term>Protéines de l'enveloppe virale (génétique)</term>
<term>Protéines de l'enveloppe virale (isolement et purification)</term>
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<term>Techniques de diagnostic moléculaire (méthodes)</term>
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<term>Trousses de réactifs pour diagnostic (normes)</term>
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<keywords scheme="MESH" type="chemical" qualifier="standards" xml:lang="en"><term>Reagent Kits, Diagnostic</term>
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<keywords scheme="MESH" type="chemical" xml:lang="en"><term>Coronavirus Envelope Proteins</term>
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<term>Pneumonia, Viral</term>
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<keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Infections à coronavirus</term>
<term>Pneumopathie virale</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Betacoronavirus</term>
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<term>Protéines de l'enveloppe virale</term>
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<keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Techniques de diagnostic moléculaire</term>
<term>Trousses de réactifs pour diagnostic</term>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and 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 the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>STUDY DESIGN</b>
</p>
<p>We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSION</b>
</p>
<p>The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.</p>
</div>
</front>
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<Abstract><AbstractText Label="BACKGROUND">Numerous nucleic acid amplification assays have recently received emergency use authorization (EUA) for the diagnosis of SARS-CoV-2 infection, and 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 the Hologic Panther Fusion SARS-CoV-2 assay targeting two regions of open reading frame 1ab (ORF1ab) to a high complexity molecular-based, laboratory-developed EUA from Stanford Health Care (SHC) targeting the SARS-CoV-2 envelope (E) gene.</AbstractText>
<AbstractText Label="STUDY DESIGN">We performed a diagnostic comparison study by testing nasopharyngeal samples on the two assays. Assay agreement was assessed by overall percent agreement and Cohen's kappa coefficient.</AbstractText>
<AbstractText Label="RESULTS">A total of 184 nasopharyngeal samples were tested using the two assays, of which 180 showed valid results and were included for the comparative analysis. Overall percent agreement between the assays was 98.3 % (95 % confidence interval (CI) 95.2-99.7) and kappa coefficient was 0.97 (95 % CI 0.93-1.0). One sample was detected on the SHC laboratory developed test (LDT) and not on the Panther Fusion, and had a Ct of 35.9. Conversely, 2 samples were detected on the Panther Fusion and not on the LDT, and had Ct values of 37.2 and 36.6.</AbstractText>
<AbstractText Label="CONCLUSION">The Panther Fusion SARS-CoV-2 assay and the SHC LDT perform similarly on clinical nasopharyngeal swab specimens. Other considerations, including reagent availability, turnaround time, labor requirements, cost and instrument throughput should guide the decision of which assay to perform.</AbstractText>
<CopyrightInformation>Copyright © 2020 Elsevier B.V. All rights reserved.</CopyrightInformation>
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<ForeName>Catherine A</ForeName>
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</AffiliationInfo>
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</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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<Author ValidYN="Y"><LastName>Garamani</LastName>
<ForeName>Natasha</ForeName>
<Initials>N</Initials>
<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
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<Initials>B</Initials>
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</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Zehnder</LastName>
<ForeName>James</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Pinsky</LastName>
<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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<Month>04</Month>
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<NameOfSubstance UI="C000705509">envelope protein, SARS-CoV-2</NameOfSubstance>
</Chemical>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000073640" MajorTopicYN="N">Betacoronavirus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000086382" MajorTopicYN="N">COVID-19</DescriptorName>
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<MeshHeading><DescriptorName UI="D000086968" MajorTopicYN="N">Coronavirus Envelope Proteins</DescriptorName>
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<MeshHeading><DescriptorName UI="D018352" MajorTopicYN="N">Coronavirus Infections</DescriptorName>
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<MeshHeading><DescriptorName UI="D011933" MajorTopicYN="N">Reagent Kits, Diagnostic</DescriptorName>
<QualifierName UI="Q000592" MajorTopicYN="Y">standards</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName>
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<MeshHeading><DescriptorName UI="D000086402" MajorTopicYN="N">SARS-CoV-2</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014759" MajorTopicYN="N">Viral Envelope Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<Keyword MajorTopicYN="Y">QIAsymphony</Keyword>
<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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<Day>13</Day>
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<Month>04</Month>
<Day>18</Day>
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<Month>04</Month>
<Day>21</Day>
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<ArticleId IdType="doi">10.1016/j.jcv.2020.104383</ArticleId>
<ArticleId IdType="pmc">PMC7195328</ArticleId>
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<ReferenceList><Reference><Citation>Euro Surveill. 2020 Jan;25(3):</Citation>
<ArticleIdList><ArticleId IdType="pubmed">31992387</ArticleId>
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<Reference><Citation>J Clin Virol. 2020 Apr;125:104305</Citation>
<ArticleIdList><ArticleId IdType="pubmed">32143123</ArticleId>
</ArticleIdList>
</Reference>
<Reference><Citation>Biometrics. 1977 Mar;33(1):159-74</Citation>
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<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Californie</li>
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<tree><country name="États-Unis"><region name="Californie"><name sortKey="Hogan, Catherine A" sort="Hogan, Catherine A" uniqKey="Hogan C" first="Catherine A" last="Hogan">Catherine A. Hogan</name>
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<name sortKey="Sahoo, Malaya K" sort="Sahoo, Malaya K" uniqKey="Sahoo M" first="Malaya K" last="Sahoo">Malaya K. Sahoo</name>
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<name sortKey="Zehnder, James" sort="Zehnder, James" uniqKey="Zehnder J" first="James" last="Zehnder">James Zehnder</name>
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Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2.

Comparison of the Panther Fusion and a laboratory-developed test targeting the envelope gene for detection of SARS-CoV-2.

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