Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host

Host shift events play an important role in epizootics as adaptation to new hosts can\udprofoundly affect the spread of the disease and the measures needed to control it. During\udthe late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus\ud(RABV) within the fox population. Utilisation of Bayesian inferences to investigate whole\udgenome sequences from a cohort of fox and dog brain tissues from Turkey demonstrated\udthat the epizootic occurred in 1997 (+/- 1 year). Furthermore, these data indicate that the\udepizootic was most likely due to a host shift from locally infected domestic dogs, rather\udthan an incursion of a novel fox or dog RABV. No evidence was detected for virus\udadaptation to foxes at consensus sequence level; therefore, the deep sequence data was\udanalysed 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 after\udthe 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 majority\udand minority variants are consistent with genetic drift, rather than positive selection. The transient expansion of sub-consensus viral populations in the new host species likely\udrepresents the virus adapting to a new environment, perhaps due to increased replication\udwithin the CNS resulting in a larger population of viruses, or reflecting the lack of host\udconstraints present in the new host reservoir