Development of New SNP Genotyping Assays to Discriminate the Omicron Variant of SARS-CoV-2.
Jpn J Infect Dis
; 75(4): 411-414, 2022 Jul 22.
Article
in English
| MEDLINE | ID: covidwho-2100391
ABSTRACT
The World Health Organization designated Omicron (B.1.1.529 lineage) of SARS-CoV-2 as a new variant of concern on November 26, 2021. The risk to public health conferred by the Omicron variant is still not completely clear, although its numerous gene mutations have raised concerns regarding its potential for increased transmissibility and immune escape. In this study, we describe the development of two single-nucleotide polymorphism genotyping assays targeting the G339D or T547K mutations of the spike protein to screen for the Omicron variant. A specificity test revealed that the two assays successfully discriminated the Omicron variant from the Delta and Alpha variants, each with a single 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 demonstrate 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 diagnostic system.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Genotyping Techniques
/
COVID-19
Type of study:
Diagnostic study
/
Prognostic study
Topics:
Variants
Limits:
Humans
Language:
English
Journal:
Jpn J Infect Dis
Journal subject:
Communicable Diseases
Year:
2022
Document Type:
Article
Affiliation country:
Yoken.JJID.2022.007
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