Fast detection of SARS-CoV-2 variants including Omicron using one-step RT-PCR and Sanger sequencing

• Published in: Journal of virological methods Vol. 304; p. 114512
• Main Authors: Bloemen, Mandy, Rector, Annabel, Swinnen, Jill, Ranst, Marc Van, Maes, Piet, Vanmechelen, Bert, Wollants, Elke
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2022
• Subjects: COVID-19 - diagnosis; Easy detection of variants of concern; Humans; Mutation; Reverse Transcriptase Polymerase Chain Reaction; RT-PCR; Sanger sequencing; SARS-CoV-2 - genetics; SARS-CoV-2 Omicron; SARS-CoV-2 Omicron; Sanger sequencing; RT-PCR; Easy detection of variants of concern
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2022.114512

SARS-CoV-2 has kept the world in suspense for almost 2 years now. The virus spread rapidly worldwide and several variants of concern have emerged: Alpha, Beta, Gamma, Delta and recently Omicron. A rapid method to detect key mutations is needed because these variants may jeopardize the effectiveness of immune protection following vaccination or past infection. This article describes an easy, cheap and fast method for the detection of mutations in the spike protein that are indicative for specific variants. This method can easily distinguish Omicron from other variants. •Sanger sequencing to detect mutations in SARS-CoV-2 S gene receptor binding domain.•733 bp is sufficient for reliable identification of SARS-CoV-2 variants of concern.•Sequencing allows rapid identification of newly emerging variants.•Sanger is faster, cheaper and easier compared to whole genome sequencing.