Rabbits In Australia Research Articles

The impact of integrating rabbit haemorrhagic disease virus (K5) release with pindone baiting on wild rabbit populations.

Several conventional and recently available tools are available for an integrated control of European rabbits in Australia. We quantified the impact of the release of rabbit haemorrhagic disease virus K5 (RHDV K5, hereafter K5) and pindone (2-pivalyl-1,3-indandione)baiting at 13 sites within Cudlee Creek fire scar in the Adelaide Hills, South Australia. K5 release was followed by pindone baiting between December 2021 and March 2022; the application of both control methods followed industry best practice. We counted rabbits using spotlights before and after the application of both control methods. Fly samples and livers from dead rabbits were collected to track K5 transmission within and between sites, and to detect the natural circulation of rabbit haemorrhagic disease virus 2 (RHDV2). K5 release had minimal impact on rabbit populations, with treated populations increasing by a mean of 65.5% at 14 days post-release and 27.9% at 77 days post-K5 release across all sites, comparable to the changes at control sites. K5 detection in flies up to 77 days post its release, and its detection in rabbit livers, demonstrates that it can survive and transmit in the environment for prolonged periods and that it can lethally infect some rabbits. This limited impact of K5 is consistent with previous studies and may be explained by pre-existing RHDV/RHDV2 immunity in the target populations or the presence of young rabbits with natural innate RHDV immunity. The detection of K5 in flies from control sites demonstrates that it was vectored beyond its release location. A reduction in rabbit counts post-pindone baiting was observed at most treatment sites, with a mean population reduction of 36.6% across all sites. Landholders need to carefully and strategically plan their integrated rabbit control programmes. Not all combinations of controls, even if theoretically logical, achieve meaningful outcomes for rabbit management.

Quantifying resistance to myxomatosis in wild rabbits produces novel evolutionary insights.

Wild rabbits in Australia developed genetic resistance to the myxoma virus, which was introduced as a biological control agent. However, little is known about the rate at which this evolutionary change occurred. We collated data from challenge trials that estimated rabbit resistance to myxomatosis in Australia and expressed resistance on a continuous scale, enabling trends in its development to be assessed over 45 years up to 1995. Resistance initially increased rapidly, followed by a plateau lasting ten years, before a second rapid increase occurred associated with the introduction of European rabbit fleas as myxoma virus vectors. By contrast, in the United Kingdom, where rabbit flea vectors were already present when the myxoma virus initially spread, resistance developed more slowly. No estimates of rabbit resistance to myxomatosis have been made for almost 30 years, despite other highly lethal rabbit pathogens becoming established worldwide. Continued testing of wild-caught rabbits in Australia to determine current levels of resistance to myxomatosis is recommended to assess its current effectiveness for managing pest rabbits. Given the economic and environmental significance of invasive rabbits, it would be remiss to manage such biological resources and ecosystem services poorly.

Comparative Epidemiology of Rabbit Haemorrhagic Disease Virus Strains from Viral Sequence Data.

Since their introduction in 1859, European rabbits (Oryctolagus cuniculus) have had a devastating impact on agricultural production and biodiversity in Australia, with competition and land degradation by rabbits being one of the key threats to agricultural and biodiversity values in Australia. Biocontrol agents, with the most important being the rabbit haemorrhagic disease virus 1 (RHDV1), constitute the most important landscape-scale control strategies for rabbits in Australia. Monitoring field strain dynamics is complex and labour-intensive. Here, using phylodynamic models to analyse the available RHDV molecular data, we aimed to: investigate the epidemiology of various strains, use molecular data to date the emergence of new variants and evaluate whether different strains are outcompeting one another. We determined that the two main pathogenic lagoviruses variants in Australia (RHDV1 and RHDV2) have had similar dynamics since their release, although over different timeframes (substantially shorter for RHDV2). We also found a strong geographic difference in their activities and evidence of overall competition between the two viruses.

Using genetic analysis to determine the distribution, prevalence and diversity of Eimeria species in pest rabbits (Oryctolagus cuniculus) in Australia.

To genetically assess the Australian distribution and frequency of Eimeria species in wild rabbits, with a primary focus on Eimeria intestinalis and Eimeria flavescens as possible additional agents of rabbit biocontrol, the distal colon and faecal samples from wild rabbits sourced from 26 Australian locations with mean annual rainfalls of between 252mm and 925mm were analysed using amplicon sequencing of the ITS1 region. Contrary to previous microscopy studies which had only detected E. flavescens on mainland Australia at Wellstead in south-west Western Australia, we detected this species at all 23 effectively sampled sites. The more pathogenic E. intestinalis was only found at 52.2% of sites. Three unique Eimeria genotypes were detected that did not align to the 11 published sequences using a pairwise-match threshold of 90%, and may represent unsequenced known species or novel species. One genotype we termed E. Au19SH and was detected at 20 sites, E. Au19CO was detected at eight sites, and E. Au19CN was detected in one rabbit at Crows Nest (Qld). Site diversity ranged from only five Eimeria species at Boboyan (ACT) to 13 unique sequences at Cargo (NSW). Eimeria diversity in individual rabbits ranged from 11 unique sequences in a rabbit at Wellstead (WA) and a rabbit at Cargo (NSW), to one in 17 rabbits and zero in six rabbits. The three rabbit age classes averaged 4.3 Eimeria species per rabbit. No relationship was found between the number of Eimeria species detected and mean annual rainfall. As Eimeria species were found to be fairly ubiquitous at most sites they appear to be an unlikely additional candidate to assist the control of pest rabbits in Australia.

Divergent Evolutionary Pathways of Myxoma Virus in Australia: Virulence Phenotypes in Susceptible and Partially Resistant Rabbits Indicate Possible Selection for Transmissibility.

ABSTRACTTo characterize the ongoing evolution of myxoma virus in Australian rabbits, we used experimental infections of laboratory rabbits to determine the virulence and disease phenotypes of recent virus isolates. The viruses, collected between 2012 and 2015, fell into three lineages, one of which, lineage c, experienced a punctuated increase in evolutionary rate. All viruses were capable of causing acute death with aspects of neutropenic septicemia, characterized by minimal signs of myxomatosis, the occurrence of pulmonary edema and bacteria invasions throughout internal organs, but with no inflammatory response. For the viruses of highest virulence all rabbits usually died at this point. In more attenuated viruses, some rabbits died acutely, while others developed an amyxomatous phenotype. Rabbits that survived for longer periods developed greatly swollen cutaneous tissues with very high virus titers. This was particularly true of lineage c viruses. Unexpectedly, we identified a line of laboratory rabbits with some innate resistance to myxomatosis and used these in direct comparisons with the fully susceptible rabbit line. Importantly, the same disease phenotype occurred in both susceptible and resistant rabbits, although virulence was shifted toward more attenuated grades in resistant animals. We propose that selection against inflammation at cutaneous sites prolongs virus replication and enhances transmission, leading to the amyxomatous phenotype. In some virus backgrounds this creates an immunosuppressive state that predisposes to high virulence and acute death. The alterations in disease pathogenesis, particularly the overwhelming bacterial invasions that characterize the modern viruses, suggest that their virulence grades are not directly comparable with earlier studies.IMPORTANCE The evolution of the myxoma virus (MYXV) following its release as a biological control for European rabbits in Australia is the textbook example of the coevolution of virus virulence and host resistance. However, most of our knowledge of MYXV evolution only covers the first few decades of its spread in Australia and often with little direct connection between how changes in virus phenotype relate to those in the underlying virus genotype. By conducting detailed experimental infections of recent isolates of MYXV in different lines of laboratory rabbits, we examined the ongoing evolution of MYXV disease phenotypes. Our results reveal a wide range of phenotypes, including an amyxomatous type, as well as the impact of invasive bacteria, that in part depended on the level of rabbit host resistance. These results provide a unique insight into the complex virus and host factors that combine to shape disease phenotype and viral evolution.

Pathogen profiling of Australian rabbits by metatranscriptomic sequencing.

Australia is known for its long history of using biocontrol agents, such as myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead, we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia, we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from several Clostridia species, Pasteurella multocida, Pseudomonas spp., and Eimeria stiedae, in liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing disease and mortality. In addition, we identified Hepatitis E virus and Cyniclomyces yeast in some samples, both of which are not usually associated with severe disease. In one-third of the sequenced total liver RNAs, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of up-regulated host immune responses, while immune response pathways were not up-regulated when E. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.

Immunological Cross-Protection between Different Rabbit Hemorrhagic Disease Viruses-Implications for Rabbit Biocontrol and Vaccine Development.

The use of rabbit hemorrhagic disease virus (RHDV) as a biocontrol agent to control feral rabbit populations in Australia, in combination with circulating endemic strains, provides a unique environment to observe the interactions between different lagoviruses competing for the same host. Following the arrival of RHDV2 (GI.2) in Australia, it became necessary to investigate the potential for immunological cross-protection between different variants, and the implications of this for biocontrol programs and vaccine development. Laboratory rabbits of various immune status—(1) rabbits with no detectable immunity against RHDV; (2) rabbits with experimentally acquired immunity after laboratory challenge; (3) rabbits immunised with a GI.2-specific or a multivalent RHDV inactivated virus prototype vaccine; or (4) rabbits with naturally acquired immunity—were challenged with one of three different RHDV variants (GI.1c, GI.1a or GI.2). The degree of cross-protection observed in immune rabbits was associated with the variant used for challenge, infectious dose of the virus and age, or time since acquisition of the immunity, at challenge. The immune status of feral rabbit populations should be determined prior to intentional RHDV release because of the high survival proportions in rabbits with pre-existing immunity. In addition, to protect domestic rabbits in Australia, a multivalent RHDV vaccine should be considered because of the limited cross-protection observed in rabbits given monovalent vaccines.

Good intentions with adverse outcomes when conservation and pest management guidelines are ignored: A case study in rabbit biocontrol

AbstractTo mitigate the negative impacts of invasive rabbits in Australia, land managers are permitted to release the biocontrol virus, rabbit hemorrhagic disease virus (RHDV), to reduce rabbit numbers. However, it is strongly recommended that RHDV is not released when young rabbits are present in the population as infection in this cohort is sublethal and induces life‐long virus immunity. The recruitment of these rabbits into the breeding population may make the population harder to control in future, potentially leading to increasing rather than decreased population size. To investigate whether the recommended release guidelines are followed, we obtained data on the supply and release of RHDV by land managers. We then used generalized additive models to investigate Australia‐wide and state‐specific annual and long‐term temporal trends in the supply and release of RHDV. Half of all RHDV supply (47%) and three quarters of reported releases (74%) Australia‐wide occurred during the anticipated major rabbit breeding seasons and when the risk of immunizing young rabbits is greatest. We found evidence of both RHDV supply and release during the anticipated major rabbit breeding seasons in almost all states for which data existed. RHDV supply increased with below average annual rainfall. This may indicate a tendency for land managers to notice, and want to control, rabbits and their impacts more following drier years when both rabbits and their impacts are potentially more damaging. Our study raises concerns regarding the inappropriate release of RHDV by land managers and whether its supply should be restricted to ensure ongoing and effective management of invasive rabbits. More broadly, our study serves as a warning to other conservation and pest management activities reliant on land managers or citizens following implementation guidelines. In some cases, good intentions may have adverse outcomes.

The animal welfare impacts of a gas explosive device used for the management of wild rabbits in Australia

Context Destruction of rabbit warrens to prevent re-invasion is an important component of integrated rabbit management. Ripping, and less commonly blasting with explosives, are used to destroy warren systems and to kill any rabbits remaining in warrens, usually after the population has already been reduced. However, the use of these methods can sometimes be constrained by vegetation, topography, presence of culturally significant sites or important habitats, or they may be inefficient or expensive due to the low density of warrens. Gas explosive devices provide an alternative method in these situations; however, little is known about their animal welfare impacts. The R3 Unit is a gas explosive device used in Australia. It pumps a calibrated mixture of propane and oxygen into a warren and then ignites the mixture, causing a blast wave to travel through the warren. Aims To determine the animal welfare impacts of the R3 Unit gas explosive device and to assess its effectiveness at achieving a rapid death in wild rabbits. Methods Trials of the R3 Unit were initially conducted in artificial warrens to determine the relationship between blast pressure, warren size and structure. We then assessed the extent of injury and probability of death of rabbits in both artificial and natural warrens. Key results As blast pressure increases within a warren, probability of death also increases. Blast pressures exceeding 56 psi will render rabbits unconscious, but a blast pressure of at least 67 psi is required to kill rabbits quickly and humanely. Sublethal blasts at lower pressures result in significant injuries that lead to severe suffering. Conclusions The R3 Unit can humanely kill rabbits when the blast pressure is sufficient to cause immediate unconsciousness and death (without regaining consciousness). To achieve adequate blast pressure, warrens must be small, with a diameter no more than 4 m, and all entrances must be sealed. Implications The R3 Unit can provide an effective alternative to warren ripping and blasting in certain situations. However, to ensure the device is used correctly to minimise animal welfare impacts, operators must be trained in its use and follow best practice procedures.

Distribution and Genetic Diversity of Hepatitis E Virus in Wild and Domestic Rabbits in Australia.

In 2020, Hepatitis E virus (HEV) was detected for the first time in Australian rabbits. To improve our understanding of the genetic diversity and distribution of the virus, 1635 rabbit liver samples from locations across Australia were screened via RT-qPCR for HEV. HEV genomes were amplified and sequenced from 48 positive samples. Furthermore, we tested 380 serum samples from 11 locations across Australia for antibodies against HEV. HEV was detected in rabbits from all states and territories, except the Northern Territory. Seroprevalence varied between locations (from 0% to 22%), demonstrating that HEV is widely distributed in rabbit populations across Australia. Phylogenetic analyses showed that Australian HEV sequences are genetically diverse and that HEV was likely introduced into Australia independently on several occasions. In summary, this study broadens our understanding of the genetic diversity of rabbit HEV globally and shows that the virus is endemic in both domestic and wild rabbit populations in Australia.

Rabbits and leaf-cutting ants: the Brazilian plan to use the myxoma virus (MYXV) against rabbit plagues in Australia, 1896-1952

This article analyzes the singularity of historical, scientific, and political processes from the discovery of the disease caused by the myxoma virus (MYXV) that came to be known as infectious myxomatosis to the application of this virus against a plague of rabbits in Australia. This narrative focuses on research by Henrique de Beaurepaire Aragão, a researcher at the Oswaldo Cruz Institute, and later efforts by the scientist Jean Macnamara to promote studies and implement MYXV in Australia. The scientists' research notes were consulted, along with official documents recording the experiments and periodicals. In this process, the historical development of virology and biological controls as a field of study was also considered.

EFFECT OF AUTOGENOUS, NON-VASCULARIZED PERIOSTEUM TRANSPLANTATION ON ALLOGRAFT BONE GRAFTING FOR LARGE CORTICAL LOAD-BEARING BONE DEFECT – A RABBIT MODEL

Segmental bone allografts are widely used in managing large cortical bone defects. To improve host-graft union, the effect of allograft on a large cortical tibial bone defect augmented with a non-vascularized periosteal flap was studied. Twelve mature Australian white rabbits (Oryctolagus cuniculus) were divided into intervention groups and a control group. Bone defects in the intervention groups were treated with segmental allografts wrapped with a non-vascularized periosteal flap. The control group was treated with allograft transplantation alone. Healing was evaluated at the end of the 2nd, 4th, and 6th weeks with plain radiographs, CT scan, and histology. In the intervention groups, the bony union was achieved at both ends of the allografts at the 4th to 6th weeks. Solid callus encasing the whole allograft segments at the end of the 6th week. In the control group, the union did not occur at both ends of the allograft segments even up to the end of the 6th week. No callus formation surrounding the allograft segments. Fragmentation and telescoping of the allograft segment into the medullary cavity of the host were observed. The use of autogenous, non-vascularized periosteal flap modified the healing process of allograft and maintained the integrity of the allograft.

Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses.

The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably in recent years. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the evolutionary interactions among these lagovirus variants, we monitored their geographical distribution and relative incidence over time in a continental-scale competition study. Within 3 years of the incursion of rabbit haemorrhagic disease virus 2 (RHDV2, denoted genotype GI.1bP-GI.2 [polymerase genotype]P-[capsid genotype]) into Australia, two novel recombinant lagovirus variants emerged: RHDV2-4e (genotype GI.4eP-GI.2) in New South Wales and RHDV2-4c (genotype GI.4cP-GI.2) in Victoria. Although both novel recombinants contain non-structural genes related to those from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that the determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the RHDV2-4c recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both the new RHDV2-4e and -4c recombinant variants replaced the previous dominant parental RHDV2 (genotype GI.1bP-GI.2) in their respective geographical areas, despite sharing an identical or near-identical (i.e. single amino acid change) VP60 major capsid protein with the parental virus. This suggests that the observed replacement by these recombinants was not driven by antigenic variation in VP60, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the RHDV2-4e recombination event in early to mid-2015, while the five RHDV2-4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a 2-year period highlights the high frequency of these events, detectable only through intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.

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.

Viruses for Landscape-Scale Therapy: Biological Control of Rabbits in Australia.

Viral diseases, whether of animals or humans, are normally considered as problems to be managed. However, in Australia, two viruses have been used as landscape-scale therapeutics to control European rabbits (Oryctolagus cuniculus), the preeminent invasive vertebrate pest species. Rabbits have caused major environmental and agricultural losses and contributed to extinction of native species. It was not until the introduction of Myxoma virus that effective control of this pest was obtained at a continental scale. Subsequent coevolution of rabbit and virus saw a gradual reduction in the effectiveness of biological control that was partially ameliorated by the introduction of the European rabbit flea to act as an additional vector for the virus. In 1995, a completely different virus, Rabbit hemorrhagic disease virus (RHDV), escaped from testing and spread through the Australian rabbit population and again significantly reduced rabbit numbers and environmental impacts. The evolutionary pressures on this virus appear to be producing quite different outcomes to those that occurred with myxoma virus and the emergence and invasion of a novel genotype of RHDV in 2014 have further augmented control. Molecular studies on myxoma virus have demonstrated multiple proteins that manipulate the host innate and adaptive immune response; however the molecular basis of virus attenuation and reversion to virulence are not yet understood.

Comparison of three serological tests for the detection of Coxiella burnetii specific antibodies in European wild rabbits

BackgroundCoxiella burnetii causes Q fever, a zoonotic bacterial disease with a multi-host cycle and reservoirs in wild and domestic animal species. Q fever has a significant impact on the Australian public health and economy but its ecology and contributing reservoir species remain poorly understood. In Europe, rabbits (Oryctolagus cuniculus) were identified as a major reservoir of C. burnetii and it is possible that they play a similar role in Australia. In absence of commercial kit available for rabbit, the Thermo Fisher - PrioCHECK™ Ruminant Q fever Ab Plate Kit was adapted to successfully screen rabbits population in Europe. However, this assay is not accessible in Australia and we assessed the equivalency of two commercially available kits in Australia – IDEXX - CHEKIT Q Fever Antibody ELISA kit and IDVet - ID Screen® Q Fever Indirect Multi-species with the Thermo Fisher kit (reference kit).ResultsA total of 94 rabbit sera were screened by all three ELISA kits using the same confirmed positive and negative controls. While the IDEXX kit failed to agree the other two assays (concordance correlation coefficient, rb < 0.77), IDVet kit showed satisfactory equivalency with Thermo Fisher (rb = 0.927).ConclusionIDvet kit provides the best alternative for Thermo Fisher in the detection of C. burnetii specific antibodies in rabbits in Australia. Further trials are required to confirm these preliminary results due to the low seroprevalence of Coxiella burnetii observed in the study sera.

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia.

BackgroundEuropean brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares. As their spatial distribution in Australia partially overlaps, we conducted a comparative microbiome study to determine how the composition of gastrointestinal microbiota varies between these species, since this may indicate species differences in diet, physiology, and other internal and external factors.MethodsWe analysed the faecal microbiome of nine wild hares and twelve wild rabbits from a sympatric periurban reserve in Canberra, Australia, using a 16S rRNA amplicon-based sequencing approach. Additionally, we compared the concordance between results from Illumina and Nanopore sequencing platforms.ResultsWe identified significantly more variation in faecal microbiome composition between individual rabbits compared to hares, despite both species occupying a similar habitat. The faecal microbiome in both species was dominated by the phyla Firmicutes and Bacteroidetes, typical of many vertebrates. Many phyla, including Actinobacteria, Proteobacteria and Patescibacteria, were shared between rabbits and hares. In contrast, bacteria from phylum Verrucomicrobia were present only in rabbits, while phyla Lentisphaerae and Synergistetes were represented only in hares. We did not identify phylum Spirochaetes in Australian hares; this phylum was previously shown to be present at high relative abundance in European hare faecal samples. These differences in the composition of faecal microbiota may be indicative of less discriminate foraging behaviour in rabbits, which in turn may enable them to adapt quicker to new environments, and may reflect the severe environmental impacts that this species has in Australia.

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.

The moral residue of conservation.

Should conservationists use lethal management to control introduced wildlife populations? Should they kill individual animals to protect endangered species? Are trade-offs that prioritize some values at the expense of others morally appropriate? These sorts of ethical questions are common in conservation. In debating such questions, conservationists often seem to presume 1 of 2 possible answers: the act in question is right or it is wrong. But morality in conservation is considerably more complex than this simple binary suggests. A robust conservation ethic requires a vocabulary that gives voice to the uncertainty and unease that arise when what seems to be the best available course of action also seems to involve a measure of wrongdoing. The philosophical literature on moral residue and moral dilemmas supplies this vocabulary. Moral dilemmas arise when one must neglect certain moral requirements to fulfill others. Under such circumstances, even the best possible decision leaves a moral residue, which is experienced emotionally as some form of grief. Examples of conservation scenarios that leave a moral residue include management of introduced rabbits in Australia, trophy hunting in Africa, and forest management trade-offs in the Pacific Northwest. Moral residue is integral to the moral experience of conservationists today, and grief is an appropriate response to many decisions conservationists must make. Article impact statement: Defensible conservation decisions may neglect moral requirements, leaving a moral residue; conservationists should respond with grief.

Emerging RHDV2 suppresses the impact of endemic and novel strains of RHDV on wild rabbit populations

Abstract Multi‐strain, host‐disease dynamics describe a system where multiple strains of a pathogen compete for susceptible individuals of a single host. The theoretical properties of these systems have been well studied, but there are few empirical studies in wildlife hosts. We examined the impacts of two novel strains of rabbit haemorrhagic disease virus (RHDV) recently introduced into Australia, one inadvertently (RHDV2) and one deliberately for rabbit biocontrol (RHDV‐K5), by analysing long‐term monitoring data for introduced European rabbits Oryctolagus cuniculus from 18 sites throughout Australia. We examined population‐level impacts using rabbit spotlight counts pre‐ and post‐arrival of the two strains. We also analysed serological data to determine potential interactions among the introduced and existing field strains of RHDV, as well as a pre‐existing benign strain of calicivirus (RCV‐A1). Serological analyses suggested that RHDV2 arrived in Australia during spring 2014 and spread rapidly through the Australian rabbit population within 2 years. Following the establishment of RHDV2, rabbit abundance was reduced by an average of 60%, with impacts most pronounced in South and Western Australia. In contrast, the deliberate release of RHDV‐K5 had little impact on rabbit populations. Although RHDV2 has spread rapidly throughout Australia, our serological analyses do not support the observation that RHDV2 is rapidly replacing existing field strains of RHDV, as was previously reported in Australia and Europe. Nevertheless, RHDV2 has negatively impacted the ability of RHDV and RCV‐A1 to spread within rabbit populations, most likely due to its ability to infect juvenile rabbits, thereby removing them from the pool of susceptible individuals available to be infected by competing strains. Synthesis and applications. The impact of the release of a novel strain of rabbit haemorrhagic disease virus (RHDV‐K5) for rabbit biocontrol in Australia has been suppressed by the emergence of a competing strain, RHDV2. Hence, the success of further releases of similar RHDV strains for rabbit biocontrol appears doubtful. Despite this, RHDV2 has suppressed rabbit abundances by an average of 60%, with impacts most pronounced in South and Western Australia. Whether the incursion of RHDV2 leads to the competitive exclusion of other endemic RHDV strains remains to be resolved. However, the existence of partial cross‐immunity could allow some level of coexistence between RHDV2 and RHDV strains, at least in the medium term.