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

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

Mandy Bloemen  1 , Annabel Rector  1 , Jill Swinnen  1 , Marc Van Ranst  2 , Piet Maes  1 , Bert Vanmechelen  1 , Elke Wollants  3
Affiliations

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

Mandy Bloemen et al. J Virol Methods. 2022 Jun.

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.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Fig. 1
Fig. 1
SARS-CoV-2 S-gene with indication of the amino acid mutations present in the Omicron variant and positions of primers used for Sanger sequencing. The mutation in blue is detected as S-gene target failure with the TaqPath COVID-19 RT-PCR test, mutations in red are detected with our Sanger sequencing method. Δ = deletion; ins=insertion; FW: forward primer (AA360); REV: reverse primer (AA588).
See this image and copyright information in PMC

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Publication types

Supplementary concepts