CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants

SUMMARY: The CoV-Spectrum website supports the identification of new SARS-CoV-2 variants of concern and the tracking of known variants. Its flexible amino acid and nucleotide mutation search allows querying of variants before they are designated by a lineage nomenclature system. The platform brings...

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Detalles Bibliográficos
Autores principales: Chen, Chaoran, Nadeau, Sarah, Yared, Michael, Voinov, Philippe, Xie, Ning, Roemer, Cornelius, Stadler, Tanja
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896605/
https://www.ncbi.nlm.nih.gov/pubmed/34954792
http://dx.doi.org/10.1093/bioinformatics/btab856
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author Chen, Chaoran
Nadeau, Sarah
Yared, Michael
Voinov, Philippe
Xie, Ning
Roemer, Cornelius
Stadler, Tanja
author_facet Chen, Chaoran
Nadeau, Sarah
Yared, Michael
Voinov, Philippe
Xie, Ning
Roemer, Cornelius
Stadler, Tanja
author_sort Chen, Chaoran
collection PubMed
description SUMMARY: The CoV-Spectrum website supports the identification of new SARS-CoV-2 variants of concern and the tracking of known variants. Its flexible amino acid and nucleotide mutation search allows querying of variants before they are designated by a lineage nomenclature system. The platform brings together SARS-CoV-2 data from different sources and applies analyses. Results include the proportion of different variants over time, their demographic and geographic distributions, common mutations, hospitalization and mortality probabilities, estimates for transmission fitness advantage and insights obtained from wastewater samples. AVAILABILITY AND IMPLEMENTATION: CoV-Spectrum is available at https://cov-spectrum.org. The code is released under the GPL-3.0 license at https://github.com/cevo-public/cov-spectrum-website.
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spelling pubmed-88966052022-03-07 CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants Chen, Chaoran Nadeau, Sarah Yared, Michael Voinov, Philippe Xie, Ning Roemer, Cornelius Stadler, Tanja Bioinformatics Applications Notes SUMMARY: The CoV-Spectrum website supports the identification of new SARS-CoV-2 variants of concern and the tracking of known variants. Its flexible amino acid and nucleotide mutation search allows querying of variants before they are designated by a lineage nomenclature system. The platform brings together SARS-CoV-2 data from different sources and applies analyses. Results include the proportion of different variants over time, their demographic and geographic distributions, common mutations, hospitalization and mortality probabilities, estimates for transmission fitness advantage and insights obtained from wastewater samples. AVAILABILITY AND IMPLEMENTATION: CoV-Spectrum is available at https://cov-spectrum.org. The code is released under the GPL-3.0 license at https://github.com/cevo-public/cov-spectrum-website. Oxford University Press 2021-12-25 /pmc/articles/PMC8896605/ /pubmed/34954792 http://dx.doi.org/10.1093/bioinformatics/btab856 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Chen, Chaoran
Nadeau, Sarah
Yared, Michael
Voinov, Philippe
Xie, Ning
Roemer, Cornelius
Stadler, Tanja
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title_full CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title_fullStr CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title_full_unstemmed CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title_short CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
title_sort cov-spectrum: analysis of globally shared sars-cov-2 data to identify and characterize new variants
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8896605/
https://www.ncbi.nlm.nih.gov/pubmed/34954792
http://dx.doi.org/10.1093/bioinformatics/btab856
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