Campbell, K., Gifford, R. J. , Singer, J., Hill, V., O'Toole, A., Rambaut, A., Hampson, K. and Brunker, K. (2022) Making genomic surveillance deliver: a lineage classification and nomenclature system to inform rabies elimination. PLoS Pathogens, 18(5), e1010023. (doi: 10.1371/journal.ppat.1010023) (PMID:35500026) (PMCID:PMC9162366)
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Abstract
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.
| Item Type: | Articles |
|---|---|
| Additional Information: | This work was supported by The University of Glasgow (MVLS DTP studentship 125638-06 https://www.gla.ac.uk/colleges/mvls/graduateschool/mvlsdtp/) to KC and the Wellcome Trust (research grant 207569/Z/17/Z https://wellcome.org/) to KH. |
| Status: | Published |
| Refereed: | Yes |
| Glasgow Author(s) Enlighten ID: | Gifford, Dr Robert and Singer, Dr Josh and Brunker, Dr Kirstyn and Hampson, Professor Katie and Campbell, Kathryn |
| Creator Roles: | Campbell, K.Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Visualization, Writing – original draft, Writing – review and editing Gifford, R. J.Software, Writing – review and editing Singer, J.Software Hampson, K.Supervision, Writing – review and editing Brunker, K.Supervision, Writing – review and editing |
| Authors: | Campbell, K., Gifford, R. J., Singer, J., Hill, V., O'Toole, A., Rambaut, A., Hampson, K., and Brunker, K. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine College of Medical Veterinary and Life Sciences > School of Infection & Immunity College of Medical Veterinary and Life Sciences > School of Infection & Immunity > Centre for Virus Research |
| Journal Name: | PLoS Pathogens |
| Publisher: | Public Library of Science |
| ISSN: | 1553-7366 |
| ISSN (Online): | 1553-7374 |
| Published Online: | 02 May 2022 |
| Copyright Holders: | Copyright © 2022 Campbell et al. |
| First Published: | First published in PLoS Pathogens 18(5): e1010023 |
| Publisher Policy: | Reproduced under a Creative Commons License |
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