Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing

Brunker, K. et al. (2015) Elucidating the phylodynamics of endemic rabies virus in eastern Africa using whole-genome sequencing. Virus Evolution, 1(1), pp. 1-11. (doi: 10.1093/ve/vev011)

Abstract

Many of the pathogens perceived to pose the greatest risk to humans are viral zoonoses, responsible for a range of emerging and endemic infectious diseases. Phylogeography is a useful tool to understand the processes that give rise to spatial patterns and drive dynamics in virus populations. Increasingly, whole-genome information is being used to uncover these patterns, but the limits of phylogenetic resolution that can be achieved with this are unclear. Here, whole-genome variation was used to uncover fine-scale population structure in endemic canine rabies virus circulating in Tanzania. This is the first whole-genome population study of rabies virus and the first comprehensive phylogenetic analysis of rabies virus in East Africa, providing important insights into rabies transmission in an endemic system. In addition, sub-continental scale patterns of population structure were identified using partial gene data and used to determine population structure at larger spatial scales in Africa. While rabies virus has a defined spatial structure at large scales, increasingly frequent levels of admixture were observed at regional and local levels. Discrete phylogeographic analysis revealed long-distance dispersal within Tanzania, which could be attributed to human-mediated movement, and we found evidence of multiple persistent, co-circulating lineages at a very local scale in a single district, despite on-going mass dog vaccination campaigns. This may reflect the wider endemic circulation of these lineages over several decades alongside increased admixture due to human-mediated introductions. These data indicate that successful rabies control in Tanzania could be established at a national level, since most dispersal appears to be restricted within the confines of country borders but some coordination with neighbouring countries may be required to limit transboundary movements. Evidence of complex patterns of rabies circulation within Tanzania necessitates the use of whole-genome sequencing to delineate finer scale population structure that can that can guide interventions, such as the spatial scale and design of dog vaccination campaigns and dog movement controls to achieve and maintain freedom from disease.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Lembo, Dr Tiziana and Hampson, Professor Katie and Wilkie, Dr Gavin and Biek, Professor Roman and Cleaveland, Professor Sarah and Brunker, Dr Kirstyn
• Authors: Brunker, K., Marston, D. A., Horton, D. L., Cleaveland, S., Fooks, A., Kazwala, R., Ngeleja, C., Lembo, T., Sambo, M., Mtema, Z. J., Sikana, L., Wilkie, G., Biek, R., and Hampson, K.
• College/School: College of Medical Veterinary and Life Sciences > School of Life Sciences; College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: Virus Evolution
• Publisher: Oxford University Press
• ISSN: 2057-1577
• ISSN (Online): 2057-1577
• Copyright Holders: Copyright © 2015 The Authors
• First Published: First published in Virus Evolution 1(1):1-11
• Publisher Policy: Reproduced under a Creative Commons License