Molecular epidemiology of R abbit H aemorrhagic D isease V irus in A ustralia: when one became many

Abstract

R abbit H aemorrhagic D isease V irus ( RHDV ) was introduced into A ustralia in 1995 as a biological control agent against the wild E uropean rabbit ( O ryctolagus cuniculus ). We evaluated its evolution over a 16‐year period (1995–2011) by examining 50 isolates collected throughout A ustralia, as well as the original inoculum strains. Phylogenetic analysis of capsid protein VP 60 sequences of the A ustralian isolates, compared with those sampled globally, revealed that they form a monophyletic group with the inoculum strains ( CAPM V‐351 and RHDV 351 INOC ). Strikingly, despite more than 3000 rereleases of RHDV 351 INOC since 1995, only a single viral lineage has sustained its transmission in the long‐term, indicative of a major competitive advantage. In addition, we find evidence for widespread viral gene flow, in which multiple lineages entered individual geographic locations, resulting in a marked turnover of viral lineages with time, as well as a continual increase in viral genetic diversity. The rate of RHDV evolution recorded in A ustralia −4.0 (3.3–4.7) × 10 −3 nucleotide substitutions per site per year – was higher than previously observed in RHDV , and evidence for adaptive evolution was obtained at two VP 60 residues. Finally, more intensive study of a single rabbit population (Turretfield) in S outh A ustralia provided no evidence for viral persistence between outbreaks, with genetic diversity instead generated by continual strain importation.

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