| dc.description |
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 humanmediated
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. |
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