The Global Phylogeography of Lyssaviruses - Challenging the 'Out of Africa' Hypothesis

Abstract

Rabies virus kills tens of thousands of people globally each year, especially in resource-limited countries. Yet, there are genetically- and antigenically-related lyssaviruses, all capable of causing the disease rabies, circulating globally among bats without causing conspicuous disease outbreaks. The species richness and greater genetic diversity of African lyssaviruses, along with the lack of antibody cross-reactivity among them, has led to the hypothesis that Africa is the origin of lyssaviruses. This hypothesis was tested using a probabilistic phylogeographical approach. The nucleoprotein gene sequences from 153 representatives of 16 lyssavirus species, collected between 1956 and 2015, were used to develop a phylogenetic tree which incorporated relevant geographic and temporal data relating to the viruses. In addition, complete genome sequences from all 16 (putative) species were analysed. The most probable ancestral distribution for the internal nodes was inferred using three different approaches and was confirmed by analysis of complete genomes. These results support a Palearctic origin for lyssaviruses (posterior probability = 0.85), challenging the 'out of Africa' hypothesis, and suggest three independent transmission events to the Afrotropical region, representing the three phylogroups that form the three major lyssavirus clades.

Fig 1. Evolutionary relationships between lyssaviruses.

The time-scaled phylogeny was generated from 153 nucleoprotein gene sequences and inferred with a Lognormal relaxed-clock Bayesian analysis using BEAST. Branch colours correspond to ecozones shown on the inset map. Support values corresponding to Bayesian posterior probabilities (above branches) and states probabilities from the different assigned ecozones (below branches) are indicated for key nodes. The time scale in years is shown. Phylogroups 3 (green, top) and 2 (blue) are shaded and key nodes discussed in the text labelled A-D. Virus names are Mokola virus (MOKV); Australian bat lyssavirus (ABLV); European bat lyssavirus-1 (EBLV-1); European bat lyssavirus-2 (EBLV-2), Irkut (IRKV), Aravan (ARAV), Khujand (KHUV); West Caucasian Bat Virus (WCBV); Lagos bat virus (LBV); Duvenhage virus (DUVV); Shimoni bat virus (SHIBV); Bokeloh bat lyssavirus (BBLV); Ikoma virus (IKOV); Lleida virus (LLEBV); Gannoruwa bat lyssavirus (GBLV); Rabies virus (RABV).

Fig 2. Ancestral state reconstruction using complete genomes of the 16 Lyssavirus species.

The reconstruction was based on the Maximum Likelihood tree and using the parsimony (A) and likelihood (B) models in Mesquite v.3.0.4. Coloured pie-charts represent proportions generated from the different assigned states of the character (see colour legends). Grey terminal pie-chart in likelihood analysis indicated a polymorphic state that was coded as uncertain in the data matrix for RABV species. Support values are indicated above branches and correspond to bootstrap and posterior probabilities, respectively. Virus names are detailed in Fig 1.