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 is closely related to a non-pathogenic virus of rabbits (RCV). Tissue tropism differs between the two viruses, with the benign RCV primarily replicating in the duodenum and the highly virulent RHDV 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 29 new RHDV and RCV full length genomes were sequenced using Illumina MiSeq technology. Sequences were combined with published sequences (n=128) for evolutionary analysis. As several RHDVb/RCV recombinants were included in the dataset, phylogenetic analysis was carried out separately for the non-structural protein genes and the capsid protein gene, VP60, which are located either side of the recombination breakpoint. 

Virus strains with confirmed liver tropism clustered together in phylogenetic analyses of VP60, although some of these strains are not highly virulent. For example, a moderately pathogenic RCV isolate from Michigan (MRCV) that replicates in the liver clustered with RHDV in the VP60 phylogeny, but with the non-pathogenic RCVs in the phylogenetic analysis of the non-structural protein genes. Nineteen conserved amino acid changes in the non-structural protein sequences distinguish the benign viruses from their pathogenic relatives, nine of these changes occurring in the p16 protein. These findings suggest a key role for VP60 in tissue tropism, with additional genes contributing to the change in virulence. Future investigations into the function of the non-structural proteins, particularly the as yet uncharacterised p16 protein, and their role in virus virulence is clearly warranted.