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Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing

Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-ti...

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Autores principales: Zelyas, Nathan, Pabbaraju, Kanti, Croxen, Matthew A., Lynch, Tarah, McCullough, Emily, Murphy, Stephanie A., Shokoples, Sandy, Wong, Anita, Kanji, Jamil N., Tipples, Graham
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576821/
https://www.ncbi.nlm.nih.gov/pubmed/37838804
http://dx.doi.org/10.1038/s41598-023-44796-y
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author Zelyas, Nathan
Pabbaraju, Kanti
Croxen, Matthew A.
Lynch, Tarah
McCullough, Emily
Murphy, Stephanie A.
Shokoples, Sandy
Wong, Anita
Kanji, Jamil N.
Tipples, Graham
author_facet Zelyas, Nathan
Pabbaraju, Kanti
Croxen, Matthew A.
Lynch, Tarah
McCullough, Emily
Murphy, Stephanie A.
Shokoples, Sandy
Wong, Anita
Kanji, Jamil N.
Tipples, Graham
author_sort Zelyas, Nathan
collection PubMed
description Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9–100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period.
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spelling pubmed-105768212023-10-16 Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing Zelyas, Nathan Pabbaraju, Kanti Croxen, Matthew A. Lynch, Tarah McCullough, Emily Murphy, Stephanie A. Shokoples, Sandy Wong, Anita Kanji, Jamil N. Tipples, Graham Sci Rep Article Omicron has become the dominant SARS-CoV-2 variant globally since December 2021, with distinct waves being associated with separate Omicron sublineages. Rapid detection of BA.1, BA.2, BA.4, and BA.5 was accomplished in the province of Alberta, Canada, through the design and implementation of real-time reverse transcriptase PCR assays targeting S:N501Y, S:ins214EPE, S:H69/V70, ORF7b:L11F, and M:D3N. Using the combination of results for each of these markers, samples could be designated as belonging to sublineages within BA.1, BA.2, BA.4, or BA.5. The analytical sensitivity of these markers ranged from 132 to 2229 copies/mL and in-laboratory accuracy was 98.9–100%. A 97.3% agreement using 12,592 specimens was demonstrated for the assays compared to genome sequencing. The use of these assays, combined with genome sequencing, facilitated the surveillance of SARS-CoV-2 lineages throughout a BA.5-dominated period. Nature Publishing Group UK 2023-10-14 /pmc/articles/PMC10576821/ /pubmed/37838804 http://dx.doi.org/10.1038/s41598-023-44796-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zelyas, Nathan
Pabbaraju, Kanti
Croxen, Matthew A.
Lynch, Tarah
McCullough, Emily
Murphy, Stephanie A.
Shokoples, Sandy
Wong, Anita
Kanji, Jamil N.
Tipples, Graham
Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title_full Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title_fullStr Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title_full_unstemmed Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title_short Tracking SARS-CoV-2 Omicron lineages using real-time reverse transcriptase PCR assays and prospective comparison with genome sequencing
title_sort tracking sars-cov-2 omicron lineages using real-time reverse transcriptase pcr assays and prospective comparison with genome sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10576821/
https://www.ncbi.nlm.nih.gov/pubmed/37838804
http://dx.doi.org/10.1038/s41598-023-44796-y
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