Literature DB >> 33478625

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.

Antonin Bal1,2,3, Gregory Destras1,2,3, Alexandre Gaymard1,2,3, Karl Stefic4, Julien Marlet4, Sébastien Eymieux4, Hadrien Regue1, Quentin Semanas1, Constance d'Aubarede5, Geneviève Billaud1, Frédéric Laurent6,7, Claudia Gonzalez1, Yahia Mekki1, Martine Valette1, Maude Bouscambert1, Catherine Gaudy-Graffin4, Bruno Lina1,3, Florence Morfin1,3, Laurence Josset1,3.   

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.

Entities:  

Keywords:  COVID-19, whole genome sequencing; SARS-CoV-2; spike protein, variants, deletion

Mesh：

Substances：

Year:  2021        PMID： 33478625      PMCID： PMC7848679          DOI： 10.2807/1560-7917.ES.2021.26.3.2100008

Source DB:  PubMed          Journal:  Euro Surveill        ISSN： 1025-496X


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3.  Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

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6.  Molecular characterization of SARS-CoV-2 in the first COVID-19 cluster in France reveals an amino acid deletion in nsp2 (Asp268del).

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