Bethany Jackson

Evidence of multiple introductions of beak and feather disease virus into the Pacific islands of Nouvelle-Caledonie (New Caledonia).

Beak and feather disease virus (BFDV) is a circular ssDNA virus that causes psittacine beak and feather disease and has almost global presence. Here, we report for the first time the presence of in Nouvelle-Calédonie (New Caledonia). One hundred and sixty-eight exotic and 79 endemic birds were sampled in Nouvelle-Calédonie, 26 were found to be positive for BFDV. We characterized the full genomes of 26 isolates and phylogenetic analysis placed nine of the isolates into the BFDV-J strain, with the remaining 17 isolates from Deplanches Rainbow Lorikeet (Trichoglossus haematodus deplanchii) forming a novel strain, BFDV-P. Of more concern was the discovery of an infected bird from the vulnerable and endemic New Caledonian Parakeet (Cyanoramphus saisseti). Our results reveal that there have been at least two introductions of BFDV into Nouvelle-Calédonie.

Multiple Cryptosporidium genotypes detected in wild black rats (Rattus rattus) from northern Australia

As part of a broader investigation into the potential role of black rats (Rattus rattus) as disease vectors into native small mammal populations of northern Australia, blood and faecal samples from wild black rats were screened by molecular methods, for piroplasms (Babesia and Theileria), trypanosomes and the enteric parasite Cryptosporidium. While piroplasms and trypanosomes were not detected in the blood of these animals, the overall prevalence of Cryptosporidium 18S rDNA in faecal samples was 8.2% (7/85). Co-occurrence of multiple genotypes was observed in 57.1% of the infected individuals (4/7); cloning and re-sequencing resulted in 14 sequences which broadly grouped with Cryptosporidium sp. rat-genotypes II and III. A novel rat-derived Cryptosporidium sp. genotype at the actin locus was also obtained from five animals. The relatively low infection rate detected, and the epidemiological data on cryptosporidiosis, do not conclusively support a current threat to native Australian mammals from black rats carrying Cryptosporidium. However, this observation is based on sampling limited isolates, in limited regions. Further studies, also including sampling of native mammals, are required on larger sample sizes and from wider geographic areas, to determine the significance of these findings, including the public health importance of Cryptosporidium spp. from rodents.

Preliminary surveillance for beak and feather disease virus in wild parrots of New Caledonia: implications of a reservoir species for Ouvea Parakeets

Abstract Beak and feather disease virus (BFDV) is a recognised key threat for the conservation of parrots globally, causing morbidity and mortality of individuals in susceptible species. We present findings from a survey in 2012 to investigate the presence of BFDV in wild New Caledonian parrots, including the endangered Ouvea Parakeet (Eunymphicus uvaeensis.) Blood and feather samples from seven Ouvea Parakeets and 13 New Caledonian Rainbow Lorikeets (Trichoglossus haematodus deplanchii), and feathers from 15 New Caledonian Rainbow Lorikeets, five Horned Parakeets (Eunymphicus cornutus) and six New Caledonian Parakeets (Cyanoramphus saisseti) obtained from passive sampling, were tested by polymerase chain reaction (PCR) for BFDV. We identified a BFDV prevalence of 25% (95% CI 11–45%) in wild New Caledonian Rainbow Lorikeets, suggesting this species may act as a reservoir for persistence of BFDV in the wild, placing other parrots in New Caledonia at risk. All other parrot species tested negative for BFDV. New Caledonian Rainbow Lorikeets were introduced to Ouvéa Island in the 1970s, potentially bringing BFDV with them. As Ouvea Parakeets are restricted to this small island, we strongly recommend surveillance screening for BFDV in this species to guide future biosecurity and conservation efforts, and further understand the risk posed by BFDV to threatened parrots.

High prevalence of Trypanosoma vegrandis in bats from Western Australia

Abstract The present study describes the first report of Trypanosoma vegrandis in bats using morphology and sequence analysis of the 18S rRNA gene. The PCR prevalence of T. vegrandis in bats was 81.8% (18/22). The high prevalence of T. vegrandis in the present study suggests that bats may play an important role in the epidemiology of T. vegrandis in Australia. T. vegrandis appears to be geographically dispersed, has a wide distribution in Australia and low levels of host specificity.

Clinical beak and feather disease virus infection in wild juvenile eastern rosellas of New Zealand; biosecurity implications for wildlife care facilities

Abstract CASE HISTORY: Four juvenile eastern rosellas (Platycercus eximius) were admitted to two separate wildlife care facilities in the Auckland region by members of the public. They had missing or dystrophic wing and tail feathers that rendered them flightless, suggestive of beak and feather disease virus (BFDV) infection. Two were subject to euthanasia after failing to re-grow their feathers, with samples taken for histopathology and PCR analysis. Blood samples were obtained from the other two birds at the time of examination, however these individuals were lost to follow up. PATHOLOGICAL AND MOLECULAR FINDINGS: Basophilic inclusion bodies were observed in histological sections of the feather bulb, typical of BFDV infection, from the two euthanised individuals. Blood from all four birds tested positive by PCR for BFDV, and analysis of the recovered full BFDV genomes identified them as belonging to the BFDV-A strain. DIAGNOSIS: Beak and feather disease virus infection. CLINICAL RELEVANCE: This report highlights the clinical impacts of BFDV in juvenile eastern rosellas that may result in their admission to wildlife care facilities, creating a biosecurity risk in institutions that may host other native parrots intended for release. The environmental stability of BFDV and resistance to disinfection requires strict quarantine procedures to prevent contamination and spread within a facility. It is recommended that high-risk species such as wild eastern rosella be excluded from facilities that may also house native parrots.

Discovery and Partial Genomic Characterisation of a Novel Nidovirus Associated with Respiratory Disease in Wild Shingleback Lizards (Tiliqua rugosa).

A respiratory disease syndrome has been observed in large numbers of wild shingleback lizards (Tiliqua rugosa) admitted to wildlife care facilities in the Perth metropolitan region of Western Australia. Mortality rates are reportedly high without supportive treatment and care. Here we used next generation sequencing techniques to screen affected and unaffected individuals admitted to Kanyana Wildlife Rehabilitation Centre in Perth between April and December 2015, with the resultant discovery of a novel nidovirus significantly associated with cases of respiratory disease according to a case definition based on clinical signs. Interestingly this virus was also found in 12% of apparently healthy individuals, which may reflect testing during the incubation period or a carrier status, or it may be that this agent is not causative in the disease process. This is the first report of a nidovirus in lizards globally. In addition to detection of this virus, characterisation of a 23,832 nt segment of the viral genome revealed the presence of characteristic nidoviral genomic elements providing phylogenetic support for the inclusion of this virus in a novel genus alongside Ball Python nidovirus, within the Torovirinae sub-family of the Coronaviridae. This study highlights the importance of next generation sequencing technologies to detect and describe emerging infectious diseases in wildlife species, as well as the importance of rehabilitation centres to enhance early detection mechanisms through passive and targeted health surveillance. Further development of diagnostic tools from these findings will aid in detection and control of this agent across Australia, and potentially in wild lizard populations globally.

Genomic characterization of a novel poxvirus from a flying fox: evidence for a new genus?

The carcass of an Australian little red flying fox (Pteropus scapulatus) which died following entrapment on a fence was submitted to the laboratory for Australian bat lyssavirus exclusion testing, which was negative. During post-mortem, multiple nodules were noted on the wing membranes, and therefore degenerate PCR primers targeting the poxvirus DNA polymerase gene were used to screen for poxviruses. The poxvirus PCR screen was positive and sequencing of the PCR product demonstrated very low, but significant, similarity with the DNA polymerase gene from members of the Poxviridae family. Next-generation sequencing of DNA extracted from the lesions returned a contig of 132 353 nucleotides (nt), which was further extended to produce a near full-length viral genome of 133 492 nt. Analysis of the genome revealed it to be AT-rich with inverted terminal repeats of at least 1314 nt and to contain 143 predicted genes. The genome contains a surprisingly large number (29) of genes not found in other poxviruses, one of which appears to be a homologue of the mammalian TNF-related apoptosis-inducing ligand (TRAIL) gene. Phylogenetic analysis indicates that the poxvirus described here is not closely related to any other poxvirus isolated from bats or other species, and that it likely should be placed in a new genus.

Ovariectomy as treatment for ovarian bacterial granulomas in a Duvaucel's gecko (Hoplodactylus duvaucelii)

CASE HISTORY: An adult female Duvaucels gecko (Hoplodactylus duvaucelii) from a threatened species breeding programme presented due to a prolonged gestation period and distended abdomen. CLINICAL AND PATHOLOGICAL FINDINGS: The gecko was in lean body condition with an irregularly shaped, firm mass in the coelomic cavity. Radiographically there was a diffuse radio-opacity within the coelomic cavity with cranial displacement of the right lung field. Ultrasonography revealed a round homogenous abdominal mass of medium echogenicity with an echogenic capsule. Haematology showed a leucocytosis with a moderate left shift in heterophils and toxic changes. Bilateral ovariectomy was performed to remove two ovarian granulomas and Salmonella enterica subspecies houtenae (IV) was cultured from the ovarian tissue. The gecko recovered well from the surgery, regained weight and remained in good health 3 years following the surgery. DIAGNOSIS: Pre-ovulatory stasis and ovarian granulomas associated with infection with Salmonella enterica subsp. houtenae. CLINICAL RELEVANCE: The surgery described in this case resulted in recovery of the gecko, which despite its loss of reproductive capability is of value as an education animal. This is the first report of pre-ovulatory stasis and ovarian granulomas associated with infection with Salmonella enterica in a Duvaucels gecko and is also the first reported case of pre-ovulatory stasis in a viviparous lizard species. The case adds to knowledge regarding potential reproductive pathology in lizards, which is particularly important information for managers of captive lizard breeding programmes.

Exudative cloacitis in the kakapo (Strigops habroptilus) potentially linked to Escherichia coli infection.

AIM: To investigate the initiating causes of cloacitis (inflammation of the cloaca) in kakapo (Strigops habroptilus). METHODS: Metagenomics using unbiased RNA or DNA sequencing was applied to faecal material from an 11-year-old female kakapo with exudative cloacitis, and a pool of eight birds (male and female aged 1–20 years) with no current signs or history of the disease. Faecal material from the diseased bird was collected pre- and post-treatment. For RNA sequencing, extracted RNA/DNA was subject to DNase, and the remaining RNA reverse transcribed to cDNA and subject to multiple displacement amplification prior to sequencing. RESULTS: No significant alignment to any known avian virus sequence was obtained from any faecal samples. However significant BLAST alignments to five bacteriophages known to infect enterobacteria were obtained. Strong evidence was obtained for the presence of the bacteriophage Escherichia phage TL-2011b, a bacteriophage known to occur in Escherichia coli causing outbreaks of foodborne disease in humans, in the sample from the diseased bird, but not the non-diseased pool. Differences in E. coli community structure between the diseased bird and the non-diseased pool were also apparent. CONCLUSIONS: Escherichia coli infection of human origin is suggested as a possible cause of exudative cloacitis, although confirmatory work is required to test this hypothesis.

Molecular characterisation and genetic variation of Elephant Endotheliotropic Herpesvirus infection in captive young Asian elephants in Thailand

Elephant Endotheliotropic Herpesvirus (EEHV) is emerging as a new threat for elephant conservation, since being identified as the cause of severe, often fatal, haemorrhagic disease in young Asian elephants. To describe positive cases and the molecular relatedness of virus detected in elephants in Thailand, we re-examined all available of EEHV samples occurring in young elephants in Thailand between 2006 and 2014 (n=24). Results indicated 75% (18/24) of suspected cases were positive for EEHV by semi-nested PCR. Further gene analysis identified these positive cases as EEHV1A (72%, 13/18 cases), EEHV1B (11%, 2/18) and EEHV4 (17%, 3/18). This study is the first to phylogenetically analyse and provide an overview of most of the known EEHV cases that have occurred in Thailand. Positive individuals ranged in age from one to nine years, with no sex association detected, and occurred across geographical locations throughout the country. All individuals, except one, were captive-born. No history of direct contact among the cases was recorded, and this together with the fact that various subtype clusters of virus were found, implied that none of the positive cases were epidemiologically related. These results concur with the hypothesis that EEHV1 is likely to be an ancient endogenous pathogen in Asian elephants. It is recommended that active surveillance and routine monitoring for EEHV should be undertaken in all elephant range countries, to gain a better understanding of the epidemiology, transmission and prevention of this disease.