Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2

In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold stand...

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Autores principales: Pham, David, Maddocks, Susan, Dwyer, Dominic E., Sintchenko, Vitali, Kok, Jen, Rockett, Rebecca J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9416591/
https://www.ncbi.nlm.nih.gov/pubmed/36016382
http://dx.doi.org/10.3390/v14081760
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author Pham, David
Maddocks, Susan
Dwyer, Dominic E.
Sintchenko, Vitali
Kok, Jen
Rockett, Rebecca J.
author_facet Pham, David
Maddocks, Susan
Dwyer, Dominic E.
Sintchenko, Vitali
Kok, Jen
Rockett, Rebecca J.
author_sort Pham, David
collection PubMed
description In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions.
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spelling pubmed-94165912022-08-27 Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2 Pham, David Maddocks, Susan Dwyer, Dominic E. Sintchenko, Vitali Kok, Jen Rockett, Rebecca J. Viruses Article In order to rapidly differentiate sublineages BA.1 and BA.2 of the SARS-CoV-2 variant of concern Omicron, we developed a real-time reverse-transcriptase polymerase chain reaction to target the discriminatory spike protein deletion at amino acid position 69–70 (S:del69–70). Compared to the gold standard of whole genome sequencing, the candidate assay was 100% sensitive and 99.4% specific. Sublineage typing by RT-PCR can provide a rapid, high throughput and cost-effective method to enhance surveillance as well as potentially guiding treatment and infection control decisions. MDPI 2022-08-12 /pmc/articles/PMC9416591/ /pubmed/36016382 http://dx.doi.org/10.3390/v14081760 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
Pham, David
Maddocks, Susan
Dwyer, Dominic E.
Sintchenko, Vitali
Kok, Jen
Rockett, Rebecca J.
Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title_full Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title_fullStr Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title_full_unstemmed Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title_short Development and Validation of an In-House Real-Time Reverse-Transcriptase Polymerase Chain Reaction Assay for SARS-CoV-2 Omicron Lineage Subtyping between BA.1 and BA.2
title_sort development and validation of an in-house real-time reverse-transcriptase polymerase chain reaction assay for sars-cov-2 omicron lineage subtyping between ba.1 and ba.2
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9416591/
https://www.ncbi.nlm.nih.gov/pubmed/36016382
http://dx.doi.org/10.3390/v14081760
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