Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR

Whole genome sequencing (WGS) is considered the best instrument to track both virus evolution and the spread of new, emerging variants. However, WGS still does not allow the analysis of as many samples as qPCR does. Epidemiological and clinical research needs to develop advanced qPCR methods to iden...

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Bibliographic Details
Published in:International journal of molecular sciences 2022-12, Vol.23 (24), p.16153
Main Authors: Yolshin, Nikita D, Komissarov, Andrey B, Varchenko, Kirill V, Musaeva, Tamila D, Fadeev, Artem V, Lioznov, Dmitry A
Format: Article
Language:English
Subjects:
BA qPCR
BA.1 qPCR
Biological Assay
Coronaviruses
COVID-19 - diagnosis
COVID-19 vaccines
Design
Disease transmission
Efficiency
Epidemics
Epidemiology
Genomes
Humans
Identification methods
Influenza
Multiplexing
Mutation
Omicron detection
Omicron RT-qPCR
Pandemics
Proteins
Public Health
SARS-CoV-2 - genetics
SARS-CoV-2 RT-qPCR
SARS-CoV-2 variants detection
Severe acute respiratory syndrome coronavirus 2
Whole genome sequencing
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Summary:Whole genome sequencing (WGS) is considered the best instrument to track both virus evolution and the spread of new, emerging variants. However, WGS still does not allow the analysis of as many samples as qPCR does. Epidemiological and clinical research needs to develop advanced qPCR methods to identify emerging variants of SARS-CoV-2 while collecting data on their spreading in a faster and cheaper way, which is critical for introducing public health measures. This study aimed at designing a one-step RT-qPCR assay for multiplex detection of the Omicron lineage and providing additional data on its subvariants in clinical samples. The RT-qPCR assay demonstrated high sensitivity and specificity on multiple SARS-CoV-2 variants and was cross-validated by WGS.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms232416153