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Abstract

We report the strategy leading to the first detection of variant of concern 202012/01 (VOC) in France (21 December 2020). First, the spike (S) deletion H69–V70 (ΔH69/ΔV70), identified in certain SARS-CoV-2 variants including VOC, is screened for. This deletion is associated with a S-gene target failure (SGTF) in the three-target RT-PCR assay (TaqPath kit). Subsequently, SGTF samples are whole genome sequenced. This approach revealed mutations co-occurring with ΔH69/ΔV70 including S:N501Y in the VOC.

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/content/10.2807/1560-7917.ES.2021.26.3.2100008
2021-01-21
2024-04-18
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2021.26.3.2100008
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Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Antonin+Bal&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bal Antonin</a>, <a href="/search?value1=Gregory+Destras&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Destras Gregory</a>, <a href="/search?value1=Alexandre+Gaymard&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gaymard Alexandre</a>, <a href="/search?value1=Karl+Stefic&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Stefic Karl</a>, <a href="/search?value1=Julien+Marlet&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Marlet Julien</a>, <a href="/search?value1=S%C3%A9bastien+Eymieux&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Eymieux Sébastien</a>, <a href="/search?value1=Hadrien+Regue&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Regue Hadrien</a>, <a href="/search?value1=Quentin+Semanas&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Semanas Quentin</a>, <a href="/search?value1=Constance+d%E2%80%99Aubarede&option1=author&noRedirect=true" class="nonDisambigAuthorLink">d’Aubarede Constance</a>, <a href="/search?value1=Genevi%C3%A8ve+Billaud&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Billaud Geneviève</a>, <a href="/search?value1=Fr%C3%A9d%C3%A9ric+Laurent&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Laurent Frédéric</a>, <a href="/search?value1=Claudia+Gonzalez&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gonzalez Claudia</a>, <a href="/search?value1=Yahia+Mekki&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mekki Yahia</a>, <a href="/search?value1=Martine+Valette&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Valette Martine</a>, <a href="/search?value1=Maude+Bouscambert&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Bouscambert Maude</a>, <a href="/search?value1=Catherine+Gaudy-Graffin&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Gaudy-Graffin Catherine</a>, <a href="/search?value1=Bruno+Lina&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lina Bruno</a>, <a href="/search?value1=Florence+Morfin&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Morfin Florence</a>, <a href="/search?value1=Laurence+Josset&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Josset Laurence</a>, <a href="/search?value1=the+COVID-Diagnosis+HCL+Study+Group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">the COVID-Diagnosis HCL Study Group</a></span>. Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69–V70, France, August to December 2020. <a href="/content/ecdc">Euro Surveill.</a> 2021;26(3):pii=2100008. <a href="https://doi.org/10.2807/1560-7917.ES.2021.26.3.2100008" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2021.26.3.2100008</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 05 Jan 2021;&nbsp;&nbsp; <span class="generated">Accepted</span>: 21 Jan 2021 </span> </p>
/content/10.2807/1560-7917.ES.2021.26.3.2100008
/content/10.2807/1560-7917.ES.2021.26.3.2100008
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