Rapid detection of SARS-CoV-2 variants using allele-specific PCR

Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymera...

Descripción completa

Detalles Bibliográficos
Autores principales: Brito-Mutunayagam, Sanjita, Maloney, Daniel, McAllister, Gina, Dewar, Rebecca, McHugh, Martin, Templeton, Kate
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier B.V. 2022
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848537/
https://www.ncbi.nlm.nih.gov/pubmed/35182711
http://dx.doi.org/10.1016/j.jviromet.2022.114497
_version_ 1784652271508783104
author Brito-Mutunayagam, Sanjita
Maloney, Daniel
McAllister, Gina
Dewar, Rebecca
McHugh, Martin
Templeton, Kate
author_facet Brito-Mutunayagam, Sanjita
Maloney, Daniel
McAllister, Gina
Dewar, Rebecca
McHugh, Martin
Templeton, Kate
author_sort Brito-Mutunayagam, Sanjita
collection PubMed
description Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymerase chain reaction (ASP) variant assay to detect variants of concern (VOC). ASP sensitivity for detecting Delta, Alpha and Beta was 99.45 %, 100 %, and 66.67 %, respectively, compared with WGS. Specificity was 100 % in detecting all three VOC. ASP generated results 1.3 days faster compared with WGS. These findings suggest using variant assays such as ASP may enhance epidemiological surveillance and IPC measures.
format Online
Article
Text
id pubmed-8848537
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Elsevier B.V.
record_format MEDLINE/PubMed
spelling pubmed-88485372022-02-16 Rapid detection of SARS-CoV-2 variants using allele-specific PCR Brito-Mutunayagam, Sanjita Maloney, Daniel McAllister, Gina Dewar, Rebecca McHugh, Martin Templeton, Kate J Virol Methods Article Tracking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants through whole genome sequencing (WGS) is vital for effective infection control and prevention (IPC) measures, but can be time-consuming and resource-heavy. We describe an in-house validation of an allele-specific polymerase chain reaction (ASP) variant assay to detect variants of concern (VOC). ASP sensitivity for detecting Delta, Alpha and Beta was 99.45 %, 100 %, and 66.67 %, respectively, compared with WGS. Specificity was 100 % in detecting all three VOC. ASP generated results 1.3 days faster compared with WGS. These findings suggest using variant assays such as ASP may enhance epidemiological surveillance and IPC measures. Elsevier B.V. 2022-05 2022-02-16 /pmc/articles/PMC8848537/ /pubmed/35182711 http://dx.doi.org/10.1016/j.jviromet.2022.114497 Text en © 2022 Elsevier B.V. All rights reserved. Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.
spellingShingle Article
Brito-Mutunayagam, Sanjita
Maloney, Daniel
McAllister, Gina
Dewar, Rebecca
McHugh, Martin
Templeton, Kate
Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title_full Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title_fullStr Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title_full_unstemmed Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title_short Rapid detection of SARS-CoV-2 variants using allele-specific PCR
title_sort rapid detection of sars-cov-2 variants using allele-specific pcr
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8848537/
https://www.ncbi.nlm.nih.gov/pubmed/35182711
http://dx.doi.org/10.1016/j.jviromet.2022.114497
work_keys_str_mv AT britomutunayagamsanjita rapiddetectionofsarscov2variantsusingallelespecificpcr
AT maloneydaniel rapiddetectionofsarscov2variantsusingallelespecificpcr
AT mcallistergina rapiddetectionofsarscov2variantsusingallelespecificpcr
AT dewarrebecca rapiddetectionofsarscov2variantsusingallelespecificpcr
AT mchughmartin rapiddetectionofsarscov2variantsusingallelespecificpcr
AT templetonkate rapiddetectionofsarscov2variantsusingallelespecificpcr

Ejemplares similares