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Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants

The emergence of variants of SARS-CoV-2 has created challenges for the testing infrastructure. Although large-scale genome sequencing of SARS-CoV-2 has facilitated hospital and public health responses, access to sequencing facilities globally is variable and turnaround times can be significant, so t...

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Autores principales: Hale, Richard, Crowley, Peter, Dervisevic, Samir, Coupland, Lindsay, Cliff, Penelope R., Ebie, Saidat, Snell, Luke B., Paul, Joel, Williams, Cheryl, Randell, Paul, Pond, Marcus, Stanley, Keith
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8537371/
https://www.ncbi.nlm.nih.gov/pubmed/34696458
http://dx.doi.org/10.3390/v13102028
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author Hale, Richard
Crowley, Peter
Dervisevic, Samir
Coupland, Lindsay
Cliff, Penelope R.
Ebie, Saidat
Snell, Luke B.
Paul, Joel
Williams, Cheryl
Randell, Paul
Pond, Marcus
Stanley, Keith
author_facet Hale, Richard
Crowley, Peter
Dervisevic, Samir
Coupland, Lindsay
Cliff, Penelope R.
Ebie, Saidat
Snell, Luke B.
Paul, Joel
Williams, Cheryl
Randell, Paul
Pond, Marcus
Stanley, Keith
author_sort Hale, Richard
collection PubMed
description The emergence of variants of SARS-CoV-2 has created challenges for the testing infrastructure. Although large-scale genome sequencing of SARS-CoV-2 has facilitated hospital and public health responses, access to sequencing facilities globally is variable and turnaround times can be significant, so there is a requirement for rapid and cost-effective alternatives. Applying a polymerase chain reaction (PCR)-based single nucleotide polymorphism (SNP) approach enables rapid (<4 h) identification of SARS-CoV-2 lineages from nucleic acid extracts, through the presence or absence of a panel of defined of genomic polymorphisms. For example, the B.1.1.7 lineage (“UK”, “Alpha”, or “Kent” variant) is characterised by 23 mutations compared to the reference strain, and the most biologically significant of these are found in the S gene. We have developed a SARS-CoV-2 typing assay focused on five positions in the S gene (HV69/70, N501, K417, E484 and P681). This configuration can identify a range of variants, including all the “Variants of Concern” currently designated by national and international public health bodies. The panel has been evaluated using a range of clinical isolates and standardised control materials at four UK hospitals and shows excellent concordance with the known lineage information derived from full sequence analysis. The assay has a turnaround time of about three hours for a set of up to 24 samples and has been utilised to identify emerging variants in a clinical setting.
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spelling pubmed-85373712021-10-24 Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants Hale, Richard Crowley, Peter Dervisevic, Samir Coupland, Lindsay Cliff, Penelope R. Ebie, Saidat Snell, Luke B. Paul, Joel Williams, Cheryl Randell, Paul Pond, Marcus Stanley, Keith Viruses Communication The emergence of variants of SARS-CoV-2 has created challenges for the testing infrastructure. Although large-scale genome sequencing of SARS-CoV-2 has facilitated hospital and public health responses, access to sequencing facilities globally is variable and turnaround times can be significant, so there is a requirement for rapid and cost-effective alternatives. Applying a polymerase chain reaction (PCR)-based single nucleotide polymorphism (SNP) approach enables rapid (<4 h) identification of SARS-CoV-2 lineages from nucleic acid extracts, through the presence or absence of a panel of defined of genomic polymorphisms. For example, the B.1.1.7 lineage (“UK”, “Alpha”, or “Kent” variant) is characterised by 23 mutations compared to the reference strain, and the most biologically significant of these are found in the S gene. We have developed a SARS-CoV-2 typing assay focused on five positions in the S gene (HV69/70, N501, K417, E484 and P681). This configuration can identify a range of variants, including all the “Variants of Concern” currently designated by national and international public health bodies. The panel has been evaluated using a range of clinical isolates and standardised control materials at four UK hospitals and shows excellent concordance with the known lineage information derived from full sequence analysis. The assay has a turnaround time of about three hours for a set of up to 24 samples and has been utilised to identify emerging variants in a clinical setting. MDPI 2021-10-08 /pmc/articles/PMC8537371/ /pubmed/34696458 http://dx.doi.org/10.3390/v13102028 Text en © 2021 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 Communication
Hale, Richard
Crowley, Peter
Dervisevic, Samir
Coupland, Lindsay
Cliff, Penelope R.
Ebie, Saidat
Snell, Luke B.
Paul, Joel
Williams, Cheryl
Randell, Paul
Pond, Marcus
Stanley, Keith
Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title_full Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title_fullStr Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title_full_unstemmed Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title_short Development of a Multiplex Tandem PCR (MT-PCR) Assay for the Detection of Emerging SARS-CoV-2 Variants
title_sort development of a multiplex tandem pcr (mt-pcr) assay for the detection of emerging sars-cov-2 variants
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8537371/
https://www.ncbi.nlm.nih.gov/pubmed/34696458
http://dx.doi.org/10.3390/v13102028
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