Development of diagnostic and point of care assays for a gammaherpesvirus infecting koalas

New insights into the range and transmission dynamics of a koala gammaherpesvirus, phascolarctid gammaherpesvirus 2

The recent classification of the koala to endangered across most of its range has emphasised the urgent need for enhanced disease surveillance. Little is known about the distribution and clinical significance of phascolarctid gammaherpesvirus 2 (PhaHV-2) outside the Australian states of Victoria and South Australia. PhaHV-2 may have significant impacts on koala wellbeing, justifying investigation into its distribution and impact. To better characterise virus distribution and factors associated with infection, we developed a novel quantitative polymerase chain reaction assay with a high sensitivity, specificity and throughput capacity, to facilitate rapid detection and quantification of PhaHV-2. We applied this assay to 157 predominantly clinically-derived, urogenital swab samples. Results indicated that the distribution of PhaHV-2 extends throughout the endangered New South Wales koala populations. Frequency of detection of PhaHV-2 was highest in South Australia (25%) and lowest in northern Qld (0%) and was more likely in older koalas than younger koalas. We corroborate previous findings of an association with presence of PhaHV-1 and find no evidence to support sex as a predictor for viral presence in clinically-derived samples. The capacity to rapidly detect mucosal shedding of PhaHV-2 will enable rapid isolation of affected individuals and aid further research into the pathophysiological impacts of this virus in koalas and the influence of co-infections.

Advancements in noninvasive koala monitoring through combining Chlamydia detection with a targeted koala genotyping assay

Wildlife diseases are major players in local and global extinctions. Effective disease surveillance, management and conservation strategies require accurate estimates of pathogen prevalence. Yet pathogen detection in wild animals remains challenging. Current gold standards often require samples collected through veterinary examination, but this method is costly, intensive, invasive, and requires specialised staff and equipment. Collection of non-invasive samples, such as scats, is an effective monitoring tool which can be deployed at large scale, as scats contain DNA of both host and pathogens. The koala (Phascolarctos cinereus) is listed as 'endangered' under the EPBC Act 1999, with chlamydial disease representing a major threat. Here, we present a new approach that combines restriction-enzyme associated sequencing and targeted-sequence-capture genotyping, namely DArTcap, to detect Chlamydia pecorum in koala scats. We found this method has similar accuracy to current gold standards (qPCR of swab samples), with a sensitivity of 91.7% and a specificity of 100%. This method can be incorporated into existing koala genetic studies using marker panels, where population attributes can be estimated alongside C. pecorum presence, using the same scat samples, with the option to add further markers of interest. Such a one-stop-shop panel would considerably reduce processing times and cost.

The Utility of the Koala Scat: A Scoping Review

The use of samples or scats to provide important ecological, genetic, disease and physiology details on free-range populations is gaining popularity as an alternative non-invasive methodology. Koala populations in SE Queensland and NSW have recently been listed as endangered and continue to face anthropomorphic and stochastic environmental impacts that could potentially lead to their extinction. This scoping review examines the current and potential utility of the koala scat to contribute data relevant to the assessment of koala conservation status and decision making. Although we demonstrate that there is great potential for this methodology in providing details for both individual wild animal and population biology (distribution, abundance, sex ratio, immigration/emigration, genetic diversity, evolutionary significant unit, disease epidemiology, nutrition, reproductive status and stress physiology), the calibre of this information is likely to be a function of the quality of the scat that is sampled.

Expanding the known distribution of phascolartid gammaherpesvirus 1 in koalas to populations across Queensland and New South Wales

Koala populations across the east coast of Australia are under threat of extinction with little known about the presence or distribution of a potential pathogen, phascolartid gammaherpesvirus 1 (PhaHV-1) across these threatened populations. Co-infections with PhaHV-1 and Chlamydia pecorum may be common and there is currently a limited understanding of the impact of these co-infections on koala health. To address these knowledge gaps, archived clinical and field-collected koala samples were examined by quantitative polymerase chain reaction to determine the distribution of PhaHV-1 in previously untested populations across New South Wales and Queensland. We detected PhaHV-1 in all regions surveyed with differences in detection rate between clinical samples from rescued koalas (26%) and field-collected samples from free-living koalas (8%). This may reflect increased viral shedding in koalas that have been admitted into care. We have corroborated previous work indicating greater detection of PhaHV-1 with increasing age in koalas and an association between PhaHV-1 and C. pecorum detection. Our work highlights the need for continued surveillance of PhaHV-1 in koala populations to inform management interventions, and targeted research to understand the pathogenesis of PhaHV-1 and determine the impact of infection and co-infection with C. pecorum.