Host shift events play an important role in epizootics as adaptation to new hosts canudprofoundly affect the spread of the disease and the measures needed to control it. Duringudthe late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virusud(RABV) within the fox population. Utilisation of Bayesian inferences to investigate wholeudgenome sequences from a cohort of fox and dog brain tissues from Turkey demonstratedudthat the epizootic occurred in 1997 (+/- 1 year). Furthermore, these data indicate that theudepizootic was most likely due to a host shift from locally infected domestic dogs, ratherudthan an incursion of a novel fox or dog RABV. No evidence was detected for virusudadaptation to foxes at consensus sequence level; therefore, the deep sequence data wasudanalysed to investigate the influence of sub-consensus populations on host shift events.udViral heterogeneity was measured in all RABV samples; viruses in the early phase afterudthe host shift had increased heterogeneity, in relation to those in the later stage, possibly indicating a role in establishing transmission within a new host. The dynamics of majorityudand minority variants are consistent with genetic drift, rather than positive selection. The transient expansion of sub-consensus viral populations in the new host species likelyudrepresents the virus adapting to a new environment, perhaps due to increased replicationudwithin the CNS resulting in a larger population of viruses, or reflecting the lack of hostudconstraints present in the new host reservoir.
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