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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Autores principales: Yolshin, Nikita D., Komissarov, Andrey B., Varchenko, Kirill V., Musaeva, Tamila D., Fadeev, Artem V., Lioznov, Dmitry A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9784567/
https://www.ncbi.nlm.nih.gov/pubmed/36555794
http://dx.doi.org/10.3390/ijms232416153
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author Yolshin, Nikita D.
Komissarov, Andrey B.
Varchenko, Kirill V.
Musaeva, Tamila D.
Fadeev, Artem V.
Lioznov, Dmitry A.
author_facet Yolshin, Nikita D.
Komissarov, Andrey B.
Varchenko, Kirill V.
Musaeva, Tamila D.
Fadeev, Artem V.
Lioznov, Dmitry A.
author_sort Yolshin, Nikita D.
collection PubMed
description 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.
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spelling pubmed-97845672022-12-24 Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR Yolshin, Nikita D. Komissarov, Andrey B. Varchenko, Kirill V. Musaeva, Tamila D. Fadeev, Artem V. Lioznov, Dmitry A. Int J Mol Sci Article 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. MDPI 2022-12-18 /pmc/articles/PMC9784567/ /pubmed/36555794 http://dx.doi.org/10.3390/ijms232416153 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Yolshin, Nikita D.
Komissarov, Andrey B.
Varchenko, Kirill V.
Musaeva, Tamila D.
Fadeev, Artem V.
Lioznov, Dmitry A.
Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title_full Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title_fullStr Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title_full_unstemmed Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title_short Detection of the Omicron SARS-CoV-2 Lineage and Its BA.1 Variant with Multiplex RT-qPCR
title_sort detection of the omicron sars-cov-2 lineage and its ba.1 variant with multiplex rt-qpcr
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9784567/
https://www.ncbi.nlm.nih.gov/pubmed/36555794
http://dx.doi.org/10.3390/ijms232416153
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