Rabbit haemorrhagic disease virus (RHDV) is used in Australia to control the European rabbit, a major agricultural and ecological pest. RHDV causes acute fatal haemorrhagic disease and shares a common ancestor with closely related non-pathogenic viruses of rabbits (RCVs). Tissue tropism differs between the two viruses, with the benign RCVs primarily replicating in the duodenum and the highly virulent RHDVs targeting the liver. The genetic similarity of these two viruses with contrasting phenotypes makes them an ideal model system to study the evolution of RHDV virulence, with a particular focus on genes or specific mutations responsible for tissue tropism and virulence.
A total of 43 RCV and 11 RHDV full-length genomes were sequenced using Illumina MiSeq technology. Sequences were combined with published sequences (n=146) for evolutionary analysis, which included inferences of phylogenetics, recombination, evolutionary rate and background selection pressures.
The Australian non-pathogenic RCVs showed greater diversity (85-100% nucleotide identity) across the complete genome when compared to the Australian RHDVs (92-100%), while also displaying a higher rate of evolutionary change than RHDV (at 5.32x10-3 nucleotide substitutions/site/year). Separate phylogenetic analysis of the capsid protein gene and the non-structural protein genes showed that clustering of either region of the genome was not associated with virulence or tissue tropism. This suggests that a few mutations have lead to a change in tissue tropism and pathogenicity, and that virulence (and liver tissue tropism) has emerged independently at least twice. Alignment of all RHDV and RCV protein sequences allowed identification of four sites in the non-structural proteins and five sites in the capsid protein that distinguished pathogenic RHDV sequences from non-pathogenic RCV sequences and therefore may play a role in virulence. Future experimental research into the role of these mutations in the evolution of virulence is clearly warranted.