The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
Identifieur interne : 000494 ( Main/Exploration ); précédent : 000493; suivant : 000495The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
Auteurs : Eric Farfour [France] ; Philippe Lesprit [France] ; Benoit Visseaux [France] ; Tiffany Pascreau [France] ; Emilie Jolly [France] ; Nadira Houhou [France] ; Laurence Mazaux [France] ; Marianne Asso-Bonnet [France] ; Marc Vasse [France]Source :
- European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology [ 1435-4373 ] ; 2020.
Descripteurs français
- KwdFr :
- Betacoronavirus (génétique), France (MeSH), Humains (MeSH), Infections à coronavirus (diagnostic), Pandémies (MeSH), Partie nasale du pharynx (virologie), Pneumopathie virale (diagnostic), Protéines de l'enveloppe virale (génétique), Protéines nucléocapside (génétique), Protéines virales non structurales (génétique), RNA replicase (génétique), RT-PCR (méthodes), Techniques de laboratoire clinique (méthodes), Études prospectives (MeSH).
- MESH :
- diagnostic : Infections à coronavirus, Pneumopathie virale.
- génétique : Betacoronavirus, Protéines de l'enveloppe virale, Protéines nucléocapside, Protéines virales non structurales, RNA replicase.
- méthodes : RT-PCR, Techniques de laboratoire clinique.
- virologie : Partie nasale du pharynx.
- France, Humains, Pandémies, Études prospectives.
- Wicri :
- geographic : France.
English descriptors
- KwdEn :
- Betacoronavirus (genetics), Clinical Laboratory Techniques (methods), Coronavirus Infections (diagnosis), France (MeSH), Humans (MeSH), Nasopharynx (virology), Nucleocapsid Proteins (genetics), Pandemics (MeSH), Pneumonia, Viral (diagnosis), Prospective Studies (MeSH), RNA Replicase (genetics), Reverse Transcriptase Polymerase Chain Reaction (methods), Viral Envelope Proteins (genetics), Viral Nonstructural Proteins (genetics).
- MESH :
- chemical , genetics : Nucleocapsid Proteins, RNA Replicase, Viral Envelope Proteins, Viral Nonstructural Proteins.
- geographic : France.
- diagnosis : Coronavirus Infections, Pneumonia, Viral.
- genetics : Betacoronavirus.
- methods : Clinical Laboratory Techniques, Reverse Transcriptase Polymerase Chain Reaction.
- virology : Nasopharynx.
- Humans, Pandemics, Prospective Studies.
Abstract
Several commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct < 22.0 for the E and RdRp genes while the N gene was not detected, suggesting a variability of the viral sequence. There was no cross-reactivity with other respiratory viruses. The Allplex 2019-nCoV appears as a reliable method, but additional evaluations using more samples are needed. RT-PCR assays should probably include at least 2 viral targets.
DOI: 10.1007/s10096-020-03930-8
PubMed: 32462501
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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xml:lang="fr"><term>RT-PCR</term><term>Techniques de laboratoire clinique</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Partie nasale du pharynx</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Nasopharynx</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Humans</term><term>Pandemics</term><term>Prospective Studies</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>France</term><term>Humains</term><term>Pandémies</term><term>Études prospectives</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>France</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Several commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct < 22.0 for the E and RdRp genes while the N gene was not detected, suggesting a variability of the viral sequence. There was no cross-reactivity with other respiratory viruses. The Allplex 2019-nCoV appears as a reliable method, but additional evaluations using more samples are needed. RT-PCR assays should probably include at least 2 viral targets.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">32462501</PMID><DateCompleted><Year>2020</Year><Month>09</Month><Day>23</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1435-4373</ISSN><JournalIssue CitedMedium="Internet"><Volume>39</Volume><Issue>10</Issue><PubDate><Year>2020</Year><Month>Oct</Month></PubDate></JournalIssue><Title>European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology</Title><ISOAbbreviation>Eur. J. Clin. Microbiol. Infect. Dis.</ISOAbbreviation></Journal><ArticleTitle>The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?</ArticleTitle><Pagination><MedlinePgn>1997-2000</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s10096-020-03930-8</ELocationID><Abstract><AbstractText>Several commercial assays for SARS-CoV-2 RT-PCR are available but few of them were assessed. We evaluate the Allplex 2019-nCoV (Seegene) assay using 41 nasopharyngeal samples. The rates of agreement were 92.7% and 100% with the GeneFinder COVID-19 plus (Elitech) and the diagnosis of the infectious disease specialist respectively. Four samples display a Ct < 22.0 for the E and RdRp genes while the N gene was not detected, suggesting a variability of the viral sequence. There was no cross-reactivity with other respiratory viruses. The Allplex 2019-nCoV appears as a reliable method, but additional evaluations using more samples are needed. RT-PCR assays should probably include at least 2 viral targets.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Farfour</LastName><ForeName>Eric</ForeName><Initials>E</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3243-8018</Identifier><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France. e.farfour@hopital-foch.org.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lesprit</LastName><ForeName>Philippe</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Visseaux</LastName><ForeName>Benoit</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Service de virologie, Hôpital Bichat, Saint-Ouen, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pascreau</LastName><ForeName>Tiffany</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jolly</LastName><ForeName>Emilie</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Houhou</LastName><ForeName>Nadira</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Service de virologie, Hôpital Bichat, Saint-Ouen, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mazaux</LastName><ForeName>Laurence</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Asso-Bonnet</LastName><ForeName>Marianne</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vasse</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Service de biologie Clinique, Hôpital Foch, Suresnes, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><CollectiveName>SARS-CoV-2 Foch Hospital study group</CollectiveName></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>05</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Eur J Clin Microbiol Infect 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UI="D005602" MajorTopicYN="N" Type="Geographic">France</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009305" MajorTopicYN="N">Nasopharynx</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019590" MajorTopicYN="N">Nucleocapsid Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011024" MajorTopicYN="N">Pneumonia, Viral</DescriptorName><QualifierName UI="Q000175" MajorTopicYN="Y">diagnosis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011446" MajorTopicYN="N">Prospective Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012324" MajorTopicYN="N">RNA Replicase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014759" MajorTopicYN="N">Viral Envelope Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017361" MajorTopicYN="N">Viral Nonstructural Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Allplex 2019-nCoV (Seegene)</Keyword><Keyword MajorTopicYN="N">COVID-19</Keyword><Keyword MajorTopicYN="N">Nasopharyngeal swab</Keyword><Keyword MajorTopicYN="N">RT-PCR</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2</Keyword><Keyword MajorTopicYN="N">Sensitivity</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>04</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>05</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>5</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>9</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>5</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32462501</ArticleId><ArticleId IdType="doi">10.1007/s10096-020-03930-8</ArticleId><ArticleId IdType="pii">10.1007/s10096-020-03930-8</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country></list><tree><country name="France"><noRegion><name sortKey="Farfour, Eric" sort="Farfour, Eric" uniqKey="Farfour E" first="Eric" last="Farfour">Eric Farfour</name></noRegion><name sortKey="Asso Bonnet, Marianne" sort="Asso Bonnet, Marianne" uniqKey="Asso Bonnet M" first="Marianne" last="Asso-Bonnet">Marianne Asso-Bonnet</name><name sortKey="Houhou, Nadira" sort="Houhou, Nadira" uniqKey="Houhou N" first="Nadira" last="Houhou">Nadira Houhou</name><name sortKey="Jolly, Emilie" sort="Jolly, Emilie" uniqKey="Jolly E" first="Emilie" last="Jolly">Emilie Jolly</name><name sortKey="Lesprit, Philippe" sort="Lesprit, Philippe" uniqKey="Lesprit P" first="Philippe" last="Lesprit">Philippe Lesprit</name><name sortKey="Mazaux, Laurence" sort="Mazaux, Laurence" uniqKey="Mazaux L" first="Laurence" last="Mazaux">Laurence Mazaux</name><name sortKey="Pascreau, Tiffany" sort="Pascreau, Tiffany" uniqKey="Pascreau T" first="Tiffany" last="Pascreau">Tiffany Pascreau</name><name sortKey="Vasse, Marc" sort="Vasse, Marc" uniqKey="Vasse M" first="Marc" last="Vasse">Marc Vasse</name><name sortKey="Visseaux, Benoit" sort="Visseaux, Benoit" uniqKey="Visseaux B" first="Benoit" last="Visseaux">Benoit Visseaux</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/CovidFranceV1/Data/Main/Exploration
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{{Explor lien
|wiki= Sante
|area= CovidFranceV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:32462501
|texte= The Allplex 2019-nCoV (Seegene) assay: which performances are for SARS-CoV-2 infection diagnosis?
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:32462501" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CovidFranceV1
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