Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater

As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are thre...

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Autores principales: Sapoval, Nicolae, Liu, Yunxi, Lou, Esther G., Hopkins, Loren, Ensor, Katherine B., Schneider, Rebecca, Stadler, Lauren B., Treangen, Todd J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191095/
https://www.ncbi.nlm.nih.gov/pubmed/37198181
http://dx.doi.org/10.1038/s41467-023-38184-3
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author Sapoval, Nicolae
Liu, Yunxi
Lou, Esther G.
Hopkins, Loren
Ensor, Katherine B.
Schneider, Rebecca
Stadler, Lauren B.
Treangen, Todd J.
author_facet Sapoval, Nicolae
Liu, Yunxi
Lou, Esther G.
Hopkins, Loren
Ensor, Katherine B.
Schneider, Rebecca
Stadler, Lauren B.
Treangen, Todd J.
author_sort Sapoval, Nicolae
collection PubMed
description As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions).
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spelling pubmed-101910952023-05-19 Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater Sapoval, Nicolae Liu, Yunxi Lou, Esther G. Hopkins, Loren Ensor, Katherine B. Schneider, Rebecca Stadler, Lauren B. Treangen, Todd J. Nat Commun Article As clinical testing declines, wastewater monitoring can provide crucial surveillance on the emergence of SARS-CoV-2 variant of concerns (VoCs) in communities. In this paper we present QuaID, a novel bioinformatics tool for VoC detection based on quasi-unique mutations. The benefits of QuaID are three-fold: (i) provides up to 3-week earlier VoC detection, (ii) accurate VoC detection (>95% precision on simulated benchmarks), and (iii) leverages all mutational signatures (including insertions & deletions). Nature Publishing Group UK 2023-05-17 /pmc/articles/PMC10191095/ /pubmed/37198181 http://dx.doi.org/10.1038/s41467-023-38184-3 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Sapoval, Nicolae
Liu, Yunxi
Lou, Esther G.
Hopkins, Loren
Ensor, Katherine B.
Schneider, Rebecca
Stadler, Lauren B.
Treangen, Todd J.
Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title_full Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title_fullStr Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title_full_unstemmed Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title_short Enabling accurate and early detection of recently emerged SARS-CoV-2 variants of concern in wastewater
title_sort enabling accurate and early detection of recently emerged sars-cov-2 variants of concern in wastewater
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10191095/
https://www.ncbi.nlm.nih.gov/pubmed/37198181
http://dx.doi.org/10.1038/s41467-023-38184-3
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