Australian Rabbit Populations Research Articles

Genomic insights into a population of introduced European rabbits Oryctolagus cuniculus in Australia and the development of genetic resistance to rabbit hemorrhagic disease virus.

The European rabbit (Oryctolagus cuniculus) is one of the most devastating invasive species in Australia. Since the 1950s, myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV) have been used to manage overabundant rabbit populations. Resistance to MYXV was observed within a few years of the release. More recently, resistance to lethal RHDV infection has also been reported, undermining the efficiency of landscape-scale rabbit control. Previous studies suggest that genetic resistance to lethal RHDV infection may differ locally between populations, yet the mechanisms of genetic resistance remain poorly understood. Here, we used genotyping by sequencing (GBS) data representing a reduced representation of the genome, to investigate Australian rabbit populations. Our aims were to understand the relationship between populations and identify possible genomic signatures of selection for RHDV resistance. One population we investigated had previously been reported to show levels of resistance to lethal RHDV infection. This population was compared to three other populations with lower or no previously reported RHDV resistance. We identified a set of novel candidate genes that could be involved in host-pathogen interactions such as virus binding and infection processes. These genes did not overlap with previous studies on RHDV resistance carried out in different rabbit populations, suggesting that multiple mechanisms are feasible. These findings provide useful insights into the different potential mechanisms of genetic resistance to RHDV virus which will inform future functional studies in this area.

Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics.

Since its introduction to control overabundant invasive European rabbits (Oryctolagus cuniculus), the highly virulent rabbit haemorrhagic disease virus (RHDV) has caused regular annual disease outbreaks in Australian rabbit populations. Although initially reducing rabbit abundance by 60%, continent-wide, experimental evidence has since indicated increased genetic resistance in wild rabbits that have experienced RHDV-driven selection. To identify genetic adaptations, which explain the increased resistance to this biocontrol virus, we investigated genome-wide SNP (single nucleotide polymorphism) allele frequency changes in a South Australian rabbit population that was sampled in 1996 (pre-RHD genomes) and after 16years of RHDV outbreaks. We identified several SNPs with changed allele frequencies within or close to genes potentially important for increased RHD resistance. The identified genes are known to be involved in virus infections and immune reactions or had previously been identified as being differentially expressed in healthy versus acutely RHDV-infected rabbits. Furthermore, we show in a simulation study that the allele/genotype frequency changes cannot be explained by drift alone and that several candidate genes had also been identified as being associated with surviving RHD in a different Australian rabbit population. Our unique data set allowed us to identify candidate genes for RHDV resistance that have evolved under natural conditions, and over a time span that would not have been feasible in an experimental setting. Moreover, it provides a rare example of host genetic adaptations to virus-driven selection in response to a suddenly emerging infectious disease.

Retrospective serological analysis reveals presence of the emerging lagovirus RHDV2 in Australia in wild rabbits at least five months prior to its first detection.

The lagovirus rabbit haemorrhagic disease virus (RHDV) has been circulating in Australia since the mid-1990s when it was released to control overabundant rabbit populations. In recent years, the viral diversity of different RHDVs in Australia has increased, and currently four different types of RHDV are known to be circulating. To allow for ongoing epidemiological studies and impact assessments of these viruses on Australian wild rabbit populations, it is essential that serological tools are updated. To this end, reference sera were produced against all four virulent RHDVs (RHDV, RHDV2 and two different strains of RHDVa) known to be present in Australia and tested in a series of available immunological assays originally developed for the prototype RHDV, to assess patterns of cross-reactivity and the usefulness of these assays to detect lagovirus antibodies, either in a generic or specific manner. Enzyme-linked immunosorbent assays (ELISAs) developed to detect antibody isotypes IgM, IgA and IgG were sufficiently cross-reactive to detect antibodies raised against all four virulent lagoviruses. For the more specific detection of antibodies to the antigenically more different RHDV2, a competition ELISA was adapted using RHDV2-specific monoclonal antibodies in combination with Australian viral antigen. Archival serum banks from a long-term rabbit monitoring site where rabbits were sampled quarterly over a period of 6years were re-screened using this assay and revealed serological evidence for the arrival of RHDV2 in this population at least 5months prior to its initial detection in Australia in a dead rabbit in May 2015. The serological methods and reference reagents described here will provide valuable tools to study presence, prevalence and impact of RHDV2 on Australian rabbit populations; however, the discrimination of different antigenic variants of RHDVs as well as mixed infections at the serological level remains challenging.

Genetic perspectives on the historical introduction of the European rabbit (Oryctolagus cuniculus) to Australia

The introduced European rabbit (Oryctolagus cuniculus) is one of Australia’s most damaging invasive alien species, both in terms of ecological and economic impact. Biological control of rabbits using the myxoma and rabbit haemorrhagic disease viruses has been undertaken in Australia since the mid-1950s, and locally varying genetic resistance to these biocontrol viruses has been reported. The efficacy of biocontrol agents may be influenced, among several factors, by the genetic background of rabbit populations. Therefore, understanding the invasion process of rabbits in Australia, and their resultant population structure, remains crucial for enhancing future rabbit management strategies. Using reduced-representation sequencing techniques we genotyped 18 Australian rabbit populations at 7617 SNP loci and show that Australia’s invasive rabbits form three broad geographic clusters representing different ancestral lineages, along with a number of highly localised, strongly differentiated lineages. This molecular data supports a history of multiple independent rabbit introductions across the continent followed by regional dispersal, and the resulting patchwork genetic structure may contribute to variation across the country in rabbit resistance to the viral biocontrols. Our study highlights the importance of using genome-wide molecular information to better understand the historical establishment process of invasive species as this may ultimately influence genetic variabilty, disease resistance and the efficacy of biocontrol agents.

Rabbit haemorrhagic disease: virus persistence and adaptation in Australia

In Australia, the rabbit haemorrhagic disease virus (RHDV) has been used since 1996 to reduce numbers of introduced European rabbits (Oryctolagus cuniculus) which have a devastating impact on the native Australian environment. RHDV causes regular, short disease outbreaks, but little is known about how the virus persists and survives between epidemics. We examined the initial spread of RHDV to show that even upon its initial spread, the virus circulated continuously on a regional scale rather than persisting at a local population level and that Australian rabbit populations are highly interconnected by virus-carrying flying vectors. Sequencing data obtained from a single rabbit population showed that the viruses that caused an epidemic each year seldom bore close genetic resemblance to those present in previous years. Together, these data suggest that RHDV survives in the Australian environment through its ability to spread amongst rabbit subpopulations. This is consistent with modelling results that indicated that in a large interconnected rabbit meta-population, RHDV should maintain high virulence, cause short, strong disease outbreaks but show low persistence in any given subpopulation. This new epidemiological framework is important for understanding virus–host co-evolution and future disease management options of pest species to secure Australia's remaining natural biodiversity.

Recovery of South Australian rabbit populations from the impact of rabbit haemorrhagic disease

Context Recovery of Australian rabbit populations from the impact of rabbit haemorrhagic disease virus (RHDV) contrasts with more prolonged suppression of wild rabbits in Europe, and has been widely discussed in the scientific community, but not yet documented in formal scientific literature. The underlying causes of recovery remain unclear, but resistance to RHDV infection has been reported in laboratory studies of wild-caught rabbits. Aims We document numerical changes in two South Australian wild rabbit populations that were initially suppressed by RHDV, and examine serological data to evaluate several alternative hypotheses for the cause of recovery. Methods Rabbit numbers were assessed from spotlight transect counts and dung mass transects between 1991 and 2011, and age and RHDV antibody sero-prevalence were estimated from rabbits shot in late summer. Key results Rabbit numbers were heavily suppressed by RHDV between 1995 and 2002, then increased 5- to 10-fold between 2003 and 2010. During the period of increase, annual RHDV infection rates remained stable or increased slightly, average age of rabbits remained stable and annual rainfall was below average. Conclusions Rabbit populations recovered but neither avoidance of RHDV infection, gradual accumulation of long-lived RHD-immune rabbits, nor high pasture productivity were contributing factors. This leaves increased annual survival from RHDV infection as the most likely cause of recovery. Implications Previously documented evidence of resistance to RHDV infection may be of little consequence to post-RHD recovery in rabbit numbers, unless the factors that influence the probability of infection also shape the course of infection and affect survival of infected rabbits.

Efficacy of a competitive enzyme-linked immunosorbent assay (cELISA) for estimating prevalence of immunity to rabbit haemorrhagic disease virus (RHDV) in populations of Australian wild rabbits (Oryctolagus cuniculus)

This study examines the efficacy of a cELISA in estimating the prevalence of immunity to rabbit haemorrhagic disease virus (RHDV) in wild rabbits in Australia. Rabbits (n = 343) captured from six locations in Victoria and Queensland were experimentally challenged with a lethal oral dose (1500 50%-lethal doses, LD50) of RHDV. Death or survival to challenge was used to determine the performance characteristics of the test. The diagnostic specificity, sensitivity and accuracy were highly variable between sites, making it difficult to select a representative cut-off value for all sites that achieved a reasonable level of accuracy for the prediction of surviving and non-surviving rabbits. Estimates of prevalence of immunity were biased owing to effects of site of capture (time of capture) and age structure of the population. Using predictive equations, the best estimates of survival were ±10% but these results came from a limited range of sites, all of which had survival in the range 49–70%. The cELISA will determine whether the RHDV is present in rabbit populations but it should be used with caution when estimating the prevalence of immunity to RHDV. The cELISA may thus be limited in its application for examining the epidemiology of RHDV in Australian rabbit populations.