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

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.

Keywords: RNA virus; endemic; phylodynamics; rabies; translocation; zoonoses.

Figure 1.

ML trees derived from datasets of rabies virus sequences from the Africa 1b clade for increasing levels of genome coverage: (a) 430 sequences from African countries highlighted on the map for a 405 bp fragment of the nucleoprotein gene, (b) 100 sequences of full 1,350 bp nucleoprotein gene from the same countries (except Botswana, Ghana, Kenya, and Zimbabwe); and (c) sixty full or near-full genome sequences (range: 11,076–11,923 bp) from Tanzania. Trees are scaled by number of substitutions per site and node symbols indicate nodes with bootstrap support ≥ 0.8. Historical samples from the Serengeti District (∼20 years old) are circled in partial genome trees.

Figure 2.

Regional phylogeography among sixty rabies virus whole-genome sequences sampled in Tanzania from 2003 to 2012: (a) an MCC tree with branches coloured according to the most probable posterior location of its descendent node inferred by discrete-state phylogeographic reconstruction in BEAST. Five major phylogenetic groups (Tz1-5) are annotated on the tree and node symbols indicate node posterior support ≥0.9. (b) The four most significant dispersal pathways indicated by BF results from a BSSVS procedure in BEAST with the median number of transitions estimated by Markov jump counts indicated in cases where posterior support for a transition was >0.7. (c) Markov jump densities for total number of transitions through time. (d) Bayesian Skyline plot showing Neτ, the product of the effective population size (Ne), and the generation time in years (τ) through time.

Figure 3.

Spatial distribution of rabies virus lineages sampled from regions in Tanzania between 2003 and 2012 with a colour gradient (yellow to red) indicating the total number of lineages (low to high) sampled in each region.