Japanese Journal of Infectious Diseases
Online ISSN : 1884-2836
Print ISSN : 1344-6304
ISSN-L : 1344-6304

This article has now been updated. Please use the final version.

Development of new SNP genotyping assays to discriminate the Omicron variant of SARS-CoV-2
Nobuhiro TakemaeYen Hai DoanFumitaka MomoseTomoya SaitoTsutomu Kageyama
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JOURNAL FREE ACCESS Advance online publication

Article ID: JJID.2022.007

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Abstract

The World Health Organization (WHO) designated Omicron (B.1.1.529 lineage) of SARS-CoV-2 as a new variant of concern (VOC) on 26th of November 2021. The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations raise concern about its potential for increased transmissibility and immune escape. In this study, we describe our development of two single nucleotide polymorphism (SNP) genotyping assays targeting the G339D or T547K mutation of the spike protein for screening of the Omicron variant. A specificity test revealed that the two assays successfully discriminated the Omicron variant from the Delta variant and Alpha variant each with one nucleotide mismatch. In addition, a sensitivity test showed that the G339D and T547K assays detected at least 2.60 and 3.36 RNA copies of the Omicron variant, respectively, and 1.59 RNA copies of the Delta variant. These results demonstrated that both assays could be useful for detecting and discriminating the Omicron variant from other strains. In addition, because of the rapid and unpredictable evolution of SARS-CoV-2, combining our assays with previously developed assays for detecting other mutations may lead to a more accurate diagnosis system.

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