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Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations

SARS-CoV-2 variants of concern (VOCs) that increase transmission or disease severity or reduce diagnostic or vaccine efficacy continue to emerge across the world. Current methods available to rapidly detect these can be resource intensive and thus sub-optimal for large-scale deployment needed during...

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Detalles Bibliográficos
Autores principales: Ning, Bo, Youngquist, Brady M., Li, Diane D., Lyon, Christopher J., Zelazny, Adrian, Maness, Nicholas J., Tian, Di, Hu, Tony Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8818353/
https://www.ncbi.nlm.nih.gov/pubmed/35156077
http://dx.doi.org/10.1016/j.crmeth.2022.100173
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author Ning, Bo
Youngquist, Brady M.
Li, Diane D.
Lyon, Christopher J.
Zelazny, Adrian
Maness, Nicholas J.
Tian, Di
Hu, Tony Y.
author_facet Ning, Bo
Youngquist, Brady M.
Li, Diane D.
Lyon, Christopher J.
Zelazny, Adrian
Maness, Nicholas J.
Tian, Di
Hu, Tony Y.
author_sort Ning, Bo
collection PubMed
description SARS-CoV-2 variants of concern (VOCs) that increase transmission or disease severity or reduce diagnostic or vaccine efficacy continue to emerge across the world. Current methods available to rapidly detect these can be resource intensive and thus sub-optimal for large-scale deployment needed during a pandemic response. Here, we describe a CRISPR-based assay that detects mutations in spike gene CRISPR PAM motif or seed regions to identify a pan-specific VOC single-nucleotide polymorphism (SNP)) ((D614G) and Alpha- and Delta-specific (S982A and D950N) SNPs. This assay exhibits good diagnostic sensitivity and strain specificity with nasal swabs and is designed for use in laboratory and point-of-care settings. This should enable rapid, high-throughput VOC identification required for surveillance and characterization efforts to inform clinical and public health decisions. Furthermore, the assay can be adapted to target similar SNPs associated with emerging SARS-CoV-2 VOCs, or other rapidly evolving viruses.
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spelling pubmed-88183532022-02-07 Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations Ning, Bo Youngquist, Brady M. Li, Diane D. Lyon, Christopher J. Zelazny, Adrian Maness, Nicholas J. Tian, Di Hu, Tony Y. Cell Rep Methods Article SARS-CoV-2 variants of concern (VOCs) that increase transmission or disease severity or reduce diagnostic or vaccine efficacy continue to emerge across the world. Current methods available to rapidly detect these can be resource intensive and thus sub-optimal for large-scale deployment needed during a pandemic response. Here, we describe a CRISPR-based assay that detects mutations in spike gene CRISPR PAM motif or seed regions to identify a pan-specific VOC single-nucleotide polymorphism (SNP)) ((D614G) and Alpha- and Delta-specific (S982A and D950N) SNPs. This assay exhibits good diagnostic sensitivity and strain specificity with nasal swabs and is designed for use in laboratory and point-of-care settings. This should enable rapid, high-throughput VOC identification required for surveillance and characterization efforts to inform clinical and public health decisions. Furthermore, the assay can be adapted to target similar SNPs associated with emerging SARS-CoV-2 VOCs, or other rapidly evolving viruses. Elsevier 2022-02-07 /pmc/articles/PMC8818353/ /pubmed/35156077 http://dx.doi.org/10.1016/j.crmeth.2022.100173 Text en © 2022. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Ning, Bo
Youngquist, Brady M.
Li, Diane D.
Lyon, Christopher J.
Zelazny, Adrian
Maness, Nicholas J.
Tian, Di
Hu, Tony Y.
Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title_full Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title_fullStr Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title_full_unstemmed Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title_short Rapid detection of multiple SARS-CoV-2 variants of concern by PAM-targeting mutations
title_sort rapid detection of multiple sars-cov-2 variants of concern by pam-targeting mutations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8818353/
https://www.ncbi.nlm.nih.gov/pubmed/35156077
http://dx.doi.org/10.1016/j.crmeth.2022.100173
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