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

Mandy Bloemen; Annabel Rector; Jill Swinnen; Marc Van Ranst; Piet Maes; Bert Vanmechelen; Elke Wollants

doi:10.1016/j.jviromet.2022.114512

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

J Virol Methods. 2022 Jun:304:114512. doi: 10.1016/j.jviromet.2022.114512. Epub 2022 Mar 4.

Authors

Mandy Bloemen¹, Annabel Rector¹, Jill Swinnen¹, Marc Van Ranst², Piet Maes¹, Bert Vanmechelen¹, Elke Wollants³

Affiliations

¹ KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, 3000 Leuven, Belgium.
² KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, 3000 Leuven, Belgium; University Hospitals Leuven, Department of Laboratory Medicine, National Reference Center for Respiratory Pathogens, 3000 Leuven, Belgium.
³ KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, 3000 Leuven, Belgium. Electronic address: elke.wollants@kuleuven.be.

Abstract

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.

Keywords: Easy detection of variants of concern; RT-PCR; SARS-CoV-2 Omicron; Sanger sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19* / diagnosis
Humans
Mutation
Reverse Transcriptase Polymerase Chain Reaction
SARS-CoV-2* / genetics

Supplementary concepts

SARS-CoV-2 variants