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Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination
The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to bette...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9162366/ https://www.ncbi.nlm.nih.gov/pubmed/35500026 http://dx.doi.org/10.1371/journal.ppat.1010023 |
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author | Campbell, Kathryn Gifford, Robert J. Singer, Joshua Hill, Verity O’Toole, Aine Rambaut, Andrew Hampson, Katie Brunker, Kirstyn |
author_facet | Campbell, Kathryn Gifford, Robert J. Singer, Joshua Hill, Verity O’Toole, Aine Rambaut, Andrew Hampson, Katie Brunker, Kirstyn |
author_sort | Campbell, Kathryn |
collection | PubMed |
description | The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses. |
format | Online Article Text |
id | pubmed-9162366 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-91623662022-06-03 Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination Campbell, Kathryn Gifford, Robert J. Singer, Joshua Hill, Verity O’Toole, Aine Rambaut, Andrew Hampson, Katie Brunker, Kirstyn PLoS Pathog Research Article The availability of pathogen sequence data and use of genomic surveillance is rapidly increasing. Genomic tools and classification systems need updating to reflect this. Here, rabies virus is used as an example to showcase the potential value of updated genomic tools to enhance surveillance to better understand epidemiological dynamics and improve disease control. Previous studies have described the evolutionary history of rabies virus, however the resulting taxonomy lacks the definition necessary to identify incursions, lineage turnover and transmission routes at high resolution. Here we propose a lineage classification system based on the dynamic nomenclature used for SARS-CoV-2, defining a lineage by phylogenetic methods for tracking virus spread and comparing sequences across geographic areas. We demonstrate this system through application to the globally distributed Cosmopolitan clade of rabies virus, defining 96 total lineages within the clade, beyond the 22 previously reported. We further show how integration of this tool with a new rabies virus sequence data resource (RABV-GLUE) enables rapid application, for example, highlighting lineage dynamics relevant to control and elimination programmes, such as identifying importations and their sources, as well as areas of persistence and routes of virus movement, including transboundary incursions. This system and the tools developed should be useful for coordinating and targeting control programmes and monitoring progress as countries work towards eliminating dog-mediated rabies, as well as having potential for broader application to the surveillance of other viruses. Public Library of Science 2022-05-02 /pmc/articles/PMC9162366/ /pubmed/35500026 http://dx.doi.org/10.1371/journal.ppat.1010023 Text en © 2022 Campbell et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Campbell, Kathryn Gifford, Robert J. Singer, Joshua Hill, Verity O’Toole, Aine Rambaut, Andrew Hampson, Katie Brunker, Kirstyn Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title | Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title_full | Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title_fullStr | Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title_full_unstemmed | Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title_short | Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination |
title_sort | making genomic surveillance deliver: a lineage classification and nomenclature system to inform rabies elimination |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9162366/ https://www.ncbi.nlm.nih.gov/pubmed/35500026 http://dx.doi.org/10.1371/journal.ppat.1010023 |
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