Abstract
Variation in disease incidence in wildlife is often assumed to reflect environmental or demographic changes acting on an endemic pathogen. However, apparent endemicity might instead arise from spatial processes that are challenging to identify from traditional data sources including time series and field studies. Here, we analysed longitudinal sequence data collected from rabies virus outbreaks over 14 years in Costa Rica, a Central American country that has recorded continuous vampire bat-transmitted rabies outbreaks in humans and livestock since 1985. We identified five phylogenetically distinct lineages which shared most recent common ancestors with viruses from North and South America. Bayesian phylogeographic reconstructions supported bidirectional viral dispersals involving countries to the north and south of Costa Rica at different time points. Within Costa Rica, viruses showed little contemporaneous spatial overlap and no lineage was detected across all years of surveillance. Statistical models suggested that lineage disappearances were more likely to be explained by viral extinctions than undetected viral circulation. Our results highlight the importance of international viral dispersal for shaping the burden of rabies in Costa Rica, suggest a Central American corridor of rabies virus invasions between continents, and show that apparent disease endemicity may arise through recurrent pathogen extinctions and reinvasions which can be readily detected in relatively small datasets by joining phylodynamic and modelling approaches.
Highlights
Many newly emerging and historically important human pathogens originate from wildlife [1]
Using virus sequence data obtained from domestic animals that succumbed to rabies over a 14-year period, we (i) identified the time scale of evolutionary relationships between VBRVs from Costa Rica and other North, Central and South American countries, (ii) reconstructed the histories of international and inter-continental viral dispersals through Central America, and (iii) examined whether the dynamics of viral lineage residence in Costa Rica were better explained by endemic circulation of resident viruses or extinction–recolonization dynamics
The VBRV nucleoprotein evolved at a median rate of 4.86 × 10−4 substitutions per site per year (95% highest posterior density (HPD) = 3.54–6.34 × 10−4), which was similar to previous estimates [18]
Summary
Many newly emerging and historically important human pathogens originate from wildlife [1]. Most knowledge of the transmission dynamics of VBRV is derived from large countries in North (i.e. Mexico) and South America (e.g. Argentina, Brazil, Peru) that sustain high incidence of human and/or livestock rabies [17,18,19] These studies have revealed that single bat colonies cannot maintain VBRV indefinitely, implying that bat dispersal among colonies enables long-term viral persistence [20,21]. Using virus sequence data obtained from domestic animals that succumbed to rabies over a 14-year period, we (i) identified the time scale of evolutionary relationships between VBRVs from Costa Rica and other North, Central and South American countries, (ii) reconstructed the histories of international and inter-continental viral dispersals through Central America, and (iii) examined whether the dynamics of viral lineage residence in Costa Rica were better explained by endemic circulation of resident viruses or extinction–recolonization dynamics
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