The evolutionary history and dynamics of bat rabies virus

Rabies virus (RABV) is endemic in terrestrial mammals throughout the world and in bats on the American continent. We performed the most extensive phylogenetic analyses of bat RABV sequences undertaken to date using a variety of genes. Our study supported previous suggestions that viral sequences are grouped according to the behaviour of the host species. However, there was more genetic and geographical diversity within each phylogenetic group than previously recognised, including evidence for new groups. Furthermore, three clades of Latin American bat RABV that were distinct from the previously identified “group IV” bat RABV clade and more closely related to North American bat RABV clades, were identified. Strikingly, phylogenetic trees for the G (glycoprotein) gene had a significantly different evolutionary history to those inferred for the N (nucleoprotein) and P (phosphoprotein) genes, and an analysis of these competing topologies revealed that it is not possible on current data to resolve whether bat RABV arose from terrestrial mammal RABV, or vice-versa. Finally, using coalescent approaches, we estimated that RABV had similar rates of population growth and nucleotide substitution (∼2.5–4 × 10−4 substitutions per site, per year) in both bats and terrestrial mammals, despite underlying differences in epidemiology.