Analysis of a rabies cross-species transmission suggests a role for sub-viral populations in successful maintenance within new host reservoirs.

Cross species transmission (CST) events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of RABV within the fox population. Utilisation of Bayesian inferences to investigate whole genome sequences from a cohort of fox and dog brain tissues from Turkey sampled demonstrated that the initial CST occurred in 1997 (+/- 136 year). Furthermore, these data indicate that the most likely source was from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was detected for virus adaptation to foxes, at consensus sequence level; therefore, the deep sequence data was analysed to investigate the influence of sub-consensus populations on virus adaptation. Viral heterogeneity was measured in all RABV samples; viruses in the epizootic stage had increased heterogeneity, in relation to those in the later enzootic stage, suggesting this could be a mechanism contributing to viral adaptation in new hosts. The dynamics of majority and minority variants are consistent with genetic drift, rather than positive selection. The expansion of sub-consensus viral populations in the new host species is hypothesised to enable the virus to overcome barriers, which otherwise would inhibit the successful onward maintenance in the new host.