Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants

Summary: Since the beginning of the COVID-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the receptor-binding motif (RBM), close to the interface with...

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Autores principales:	Eva Lopez, Margot Barthélémy, Cécile Baronti, Shirley Masse, Alessandra Falchi, Fabien Durbesson, Renaud Vincentelli, Xavier de Lamballerie, Rémi Charrel, Bruno Coutard
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Virology Methodology in biological sciences Science Q
Acceso en línea:	https://doaj.org/article/40e3d47cc36e438991142d8e8cfecf7a
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spelling	oai:doaj.org-article:40e3d47cc36e438991142d8e8cfecf7a2021-11-20T05:10:00ZEndonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants2589-004210.1016/j.isci.2021.103329https://doaj.org/article/40e3d47cc36e438991142d8e8cfecf7a2021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2589004221012980https://doaj.org/toc/2589-0042Summary: Since the beginning of the COVID-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the receptor-binding motif (RBM), close to the interface with the receptor ACE2. We thus developed a fast molecular assay to detect mutations in the RBM coding sequence. After amplification, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation can be detected using a mismatch-specific endonuclease and the cleavage pattern is analyzed by capillary electrophoresis. The method was validated on RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants produced in vitro before being implemented for clinical samples. The assay showed 97.8% sensitivity and 97.8% specificity. The procedure can be set up for high-throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.Eva LopezMargot BarthélémyCécile BarontiShirley MasseAlessandra FalchiFabien DurbessonRenaud VincentelliXavier de LamballerieRémi CharrelBruno CoutardElsevierarticleVirologyMethodology in biological sciencesScienceQENiScience, Vol 24, Iss 11, Pp 103329- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Virology Methodology in biological sciences Science Q
spellingShingle	Virology Methodology in biological sciences Science Q Eva Lopez Margot Barthélémy Cécile Baronti Shirley Masse Alessandra Falchi Fabien Durbesson Renaud Vincentelli Xavier de Lamballerie Rémi Charrel Bruno Coutard Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
description	Summary: Since the beginning of the COVID-19 pandemics, variants have emerged. Some of them display increased transmissibility and/or resistance to immune response. Most of the mutations involved in the functional adaptation are found in the receptor-binding motif (RBM), close to the interface with the receptor ACE2. We thus developed a fast molecular assay to detect mutations in the RBM coding sequence. After amplification, the amplicon is heat-denatured and hybridized with an amplicon of reference. The presence of a mutation can be detected using a mismatch-specific endonuclease and the cleavage pattern is analyzed by capillary electrophoresis. The method was validated on RNA of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants produced in vitro before being implemented for clinical samples. The assay showed 97.8% sensitivity and 97.8% specificity. The procedure can be set up for high-throughput identification of the presence of mutations and serve as a first-line screening to select the samples for full genome sequencing.
format	article
author	Eva Lopez Margot Barthélémy Cécile Baronti Shirley Masse Alessandra Falchi Fabien Durbesson Renaud Vincentelli Xavier de Lamballerie Rémi Charrel Bruno Coutard
author_facet	Eva Lopez Margot Barthélémy Cécile Baronti Shirley Masse Alessandra Falchi Fabien Durbesson Renaud Vincentelli Xavier de Lamballerie Rémi Charrel Bruno Coutard
author_sort	Eva Lopez
title	Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
title_short	Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
title_full	Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
title_fullStr	Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
title_full_unstemmed	Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants
title_sort	endonuclease-based genotyping of the rbm as a method to track the emergence or evolution of sars-cov-2 variants
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/40e3d47cc36e438991142d8e8cfecf7a
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Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants

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