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

iScience

卷:24

Bruno Coutard¹  Shirley Masse²  Alessandra Falchi²  Renaud Vincentelli³  Fabien Durbesson³  Cécile Baronti⁴  Margot Barthélémy⁴  Eva Lopez⁴  Xavier de Lamballerie⁴  Rémi Charrel⁴ 

[1] Comité de Lutte contre les Infections Nosocomiales, Hôpitaux Universitaires de Marseille, AP-HM, Marseille, France;

[2] UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France;

[3] Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France;

[4] Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France;

关键词: Virology;    Methodology in biological sciences;   

DOI  :  

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown