SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern

The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation...

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Autores principales: Lowry, Kym, Wang, Claire, Bordin, Amanda, Buckley, Cameron, Badman, Steven, Harris, Patrick, Mackay, Ian, Whiley, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9497716/
https://www.ncbi.nlm.nih.gov/pubmed/36140458
http://dx.doi.org/10.3390/diagnostics12092056
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author Lowry, Kym
Wang, Claire
Bordin, Amanda
Buckley, Cameron
Badman, Steven
Harris, Patrick
Mackay, Ian
Whiley, David
author_facet Lowry, Kym
Wang, Claire
Bordin, Amanda
Buckley, Cameron
Badman, Steven
Harris, Patrick
Mackay, Ian
Whiley, David
author_sort Lowry, Kym
collection PubMed
description The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance.
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spelling pubmed-94977162022-09-23 SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern Lowry, Kym Wang, Claire Bordin, Amanda Buckley, Cameron Badman, Steven Harris, Patrick Mackay, Ian Whiley, David Diagnostics (Basel) Communication The continuous transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has required that diagnostic capabilities be constantly monitored and updated as new variants emerge and prior variants disappear. Although whole genome sequencing provides full characterisation of SARS-CoV-2 directly from patient samples, this has limited throughput and requires sufficient resources. To enhance screening for circulating variants, we designed a rapid in-house RT-PCR assay to target a spike mutation (D950N) in Delta variants, which is not detected in the remaining variants of concern (VOCs). Assay sensitivity for detecting Delta variants was 93% and specificity was 100% using a sequenced sample bank of several lineages. As the D950N mutation is prevalent in >95% of the global Delta variant sequences deposited in GISAID, this assay has the potential to provide rapid results to determine if the samples are presumptively Delta variants and can support clinicians in timely clinical decision-making for effective treatments and surveillance. MDPI 2022-08-24 /pmc/articles/PMC9497716/ /pubmed/36140458 http://dx.doi.org/10.3390/diagnostics12092056 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 Communication
Lowry, Kym
Wang, Claire
Bordin, Amanda
Buckley, Cameron
Badman, Steven
Harris, Patrick
Mackay, Ian
Whiley, David
SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title_full SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title_fullStr SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title_full_unstemmed SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title_short SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern
title_sort sars-cov-2 rt-pcr to screen for b.1.617.2 (delta) variant of concern
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9497716/
https://www.ncbi.nlm.nih.gov/pubmed/36140458
http://dx.doi.org/10.3390/diagnostics12092056
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