Abstract
The development of novel approaches that combine epidemiological and genomic data provides new opportunities to reveal the spatiotemporal dynamics of infectious diseases and determine the processes responsible for their spread and maintenance. Taking advantage of detailed epidemiological time series and viral sequence data from more than 20 years reported by the National Reference Centre for Rabies of Bangui, the capital city of Central African Republic, we used a combination of mathematical modeling and phylogenetic analysis to determine the spatiotemporal dynamics of rabies in domestic dogs as well as the frequency of extinction and introduction events in an African city. We show that although dog rabies virus (RABV) appears to be endemic in Bangui, its epidemiology is in fact shaped by the regular extinction of local chains of transmission coupled with the introduction of new lineages, generating successive waves of spread. Notably, the effective reproduction number during each wave was rarely above the critical value of 1, such that rabies is not self-sustaining in Bangui. In turn, this suggests that rabies at local geographic scales is driven by human-mediated dispersal of RABV among sparsely connected peri-urban and rural areas as opposed to dispersion in a relatively large homogenous urban dog population. This combined epidemiological and genomic approach enables development of a comprehensive framework for understanding disease persistence and informing control measures, indicating that control measures are probably best targeted towards areas neighbouring the city that appear as the source of frequent incursions seeding outbreaks in Bangui.
Highlights
Understanding the processes responsible for the maintenance and extinction of infectious diseases in specific geographic locations is essential for the establishment of locally relevant control strategies
Despite its importance for public health, little is known about the spatiotemporal dynamics of rabies in dogs in an urban setting
We document that rabies is not self-sustaining in the city, and that numerous reintroductions of the virus occur in the city, generating a succession of epidemic waves
Summary
Understanding the processes responsible for the maintenance and extinction of infectious diseases in specific geographic locations is essential for the establishment of locally relevant control strategies. The long-term presence of rabies relies on the zoonotic source of transmission and domestic dog populations remain the principal target for prevention and interventions [4]. Given the tight social and spatial structure of dog populations, the dynamics of rabies in dog populations are often considered in the context of meta-populations where endemic populations provide a source of infection for sink populations [11,12]. In such settings, targeted interventions would clearly benefit enormously from identifying these sources of infection
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