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Endonuclease-based genotyping of the RBM as a method to track the emergence or evolution of SARS-CoV-2 variants.
Lopez, Eva; Barthélémy, Margot; Baronti, Cécile; Masse, Shirley; Falchi, Alessandra; Durbesson, Fabien; Vincentelli, Renaud; de Lamballerie, Xavier; Charrel, Rémi; Coutard, Bruno.
  • Lopez E; Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
  • Barthélémy M; Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
  • Baronti C; Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
  • Masse S; UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France.
  • Falchi A; UR7310, Laboratoire de Virologie, Université de Corse-Inserm, 20250 Corte, France.
  • Durbesson F; 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.
  • Vincentelli R; 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.
  • de Lamballerie X; Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
  • Charrel R; Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
  • Coutard B; Comité de Lutte contre les Infections Nosocomiales, Hôpitaux Universitaires de Marseille, AP-HM, Marseille, France.
iScience ; 24(11): 103329, 2021 Nov 19.
Article in English | MEDLINE | ID: covidwho-1474646
ABSTRACT
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.
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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Prognostic study Topics: Variants Language: English Journal: IScience Year: 2021 Document Type: Article Affiliation country: J.isci.2021.103329

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Diagnostic study / Prognostic study Topics: Variants Language: English Journal: IScience Year: 2021 Document Type: Article Affiliation country: J.isci.2021.103329