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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...
Autores principales: | , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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MDPI
2021
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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. |
format | Online Article Text |
id | pubmed-8537371 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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