Making genomic surveillance deliver: a lineage classification and nomenclature system to inform rabies elimination

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) (Early Online Publication)

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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:Early Online Publication
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gifford, Dr Robert and Singer, Dr Josh and Hampson, Professor Katie and Brunker, Dr Kirstyn 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 > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
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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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
301620The Science of Rabies EliminationKatie HampsonWellcome Trust (WELLCOTR)207569/Z/17/ZInstitute of Biodiversity, Animal Health and Comparative Medicine