Most studies of viral emergence lack detailed knowledge on which strains were founders for the outbreak or when these events occurred. Hence, the human-mediated introduction of Rabbit Haemorrhagic Disease Virus (RHDV) into Australia and New Zealand during the 1990s as a biocontrol agent against feral rabbits is exceptional in that the founder viruses of both epidemics share a common origin and the timing of their releases are known. This provides a unique opportunity to understand the patterns of evolution and spread following viral emergence in naïve host populations.
In this study, we first investigated the composition of original viral stocks of RHDV that were imported and released into Australia through next generation sequencing. This revealed heterogeneity that was mostly purged during early passaging in rabbits. More importantly, conflicts were identified between the sequences of the founder viruses determined here and those previously published that may have affected previous estimates of evolutionary rates in this lineage. Therefore, along with data from 28 new field isolates, we use a genome-wide phylogenetic approach to reconstruct the evolutionary history of RHDV in Australia and New Zealand. Within Australia, a major phylogenetic division between viruses sampled from the east and west of the country was identified, with both regions likely seeded by viruses from South Australia, the state where the virus was first released. Furthermore, despite their common origins, marked differences in evolutionary rates were observed between the Australian and New Zealand RHDV, and which led to conflicting conclusions about population growth rates. Finally, an analysis of mutational patterns suggested that evolutionary rates have been elevated in the Australian viruses, at least in part due to the presence of low fitness deleterious variants that have yet to be selectively purged.