Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution.

Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously thought to be either virus-free or to have only exogenous variants of KoRV with low rates of KoRV-induced disease. In contrast, animals in the northern part of their range universally have both endogenous and exogenous KoRV with very high rates of KoRV-induced disease such as lymphoma. In this study we use a combination of sequencing technologies, Illumina RNA sequencing of 'southern' (south Australian) and 'northern' (SE QLD) koalas and CRISPR enrichment and nanopore sequencing of DNA of 'southern' (South Australian and Victorian animals) to retrieve full-length loci and intregration sites of KoRV variants. We demonstrate that koalas that tested negative to the KoRV pol gene qPCR, used to detect replication-competent KoRV, are not in fact KoRV-free but harbour defective, presumably endogenous, 'RecKoRV' variants that are not fixed between animals. This indicates that these populations have historically been exposed to KoRV and raises questions as to whether these variants have arisen by chance or whether they provide a protective effect from the infectious forms of KoRV. This latter explanation would offer the intriguing prospect of being able to monitor and selectively breed for disease resistance to protect the wild koala population from KoRV-induced disease.

Chlamydia psittaci: a suspected cause of reproductive loss in three Victorian horses.

Chlamydia psittaci was detected by PCR in the lung and equine foetal membranes of two aborted equine foetuses and one weak foal from two different studs in Victoria, Australia. The abortions occurred in September 2019 in two mares sharing a paddock northeast of Melbourne. The weak foal was born in October 2019 in a similar geographical region and died soon after birth despite receiving veterinary care. The detection of C. psittaci DNA in the lung and equine foetal membranes of the aborted or weak foals and the absence of any other factors that are commonly associated with abortion or neonatal death suggest that this pathogen may be the cause of the reproductive loss. The detection of C. psittaci in these cases is consistent with the recent detection of C. psittaci in association with equine abortion in New South Wales. These cases in Victoria show that C. psittaci, and the zoonotic risk it poses, should be considered in association with equine reproductive loss in other areas of Australia.

Bovine digital dermatitis in Victoria, Australia.

AIMS: The objectives of this study were to estimate the prevalence of digital dermatitis (DD) in Victoria, Australia, and to investigate which organisms are consistent with typical DD lesions. The prevalence and causative pathogens of DD are not clear yet in Australia and this paper is one of the first to explore these questions in this country. METHODS: Examination and sampling of limbs was undertaken at three knackeries in Victoria, Australia. Limbs were classified as normal (N), active DD-lesion (A), dried or chronic DD-lesion (D) or suspected case of DD (S). A total of 823 cows were examined. Six skin biopsies were taken at each knackery, from which DNA was extracted for diversity profiling. Histochemical staining of samples was performed on eight of the skin biopsies. RESULTS: DD was detected in 29.8% of all cows. The prevalence of DD was significantly higher in dairy cows (32.2%) than in beef cows (10.8%). The differential abundance of Treponema-species was significantly increased in dried lesions, compared with the normal skin biopsies. Actinobacteria, Proteobacteria, Firmicutes and Tenericutes were found to be significantly different in abundance in the DD lesions compared with normal skin biopsies. Silver staining of samples showed only mild inflammation and in two samples organisms with morphology consistent with Spirochaetes were detected. CONCLUSIONS: The calculated prevalence indicates that DD is present in Victoria, Australia. The results of diversity profiling showed that the presence of Treponema-species was significantly different between the samples of DD lesions and normal skin.

Detection and Differentiation of Two Koala Gammaherpesviruses by Use of High-Resolution Melt (HRM) Analysis Reveals Differences in Viral Prevalence and Clinical Associations in a Large Study of Free-Ranging Koalas.

The iconic koala (Phascolarctos cinereus) is host to two divergent gammaherpesviruses, phascolarctid gammaherpesviruses 1 and 2 (PhaHV-1 and -2), but the clinical significance of the individual viruses is unknown and current diagnostic methods are unsuitable for differentiating between the viruses in large-scale studies. To address this, we modified a pan-herpesvirus nested PCR to incorporate high-resolution melt analysis. We applied this assay in a molecular epidemiological study of 810 koalas from disparate populations across Victoria, Australia, including isolated island populations. Animal and clinical data recorded at sampling were analyzed and compared to infection status. Between populations, the prevalence of PhaHV-1 and -2 varied significantly, ranging from 1% to 55%. Adult and older animals were 5 to 13 times more likely to be positive for PhaHV-1 than juveniles (P < 0.001), whereas PhaHV-2 detection did not change with age, suggesting differences in how these two viruses are acquired over the life of the animal. PhaHV-1 detection was uniquely associated with the detection of koala retrovirus, particularly in females (P = 0.008). Both viruses were significantly associated (P < 0.05) with the presence of genital tract abnormalities (uterine/ovarian cysts and testicular malformation), reduced fertility in females, urinary incontinence, and detection of Chlamydia pecorum, although the strength of these associations varied by sex and virus. Understanding the clinical significance of these viruses and how they interact with other pathogens will inform future management of threatened koala populations.

Localised Mycobacterium ulcerans infection in four dogs.

Localised infection caused by Mycobacterium ulcerans is described in two Kelpies, a Whippet and a Koolie domiciled on the Bellarine Peninsula, Victoria, Australia. The diagnosis was confirmed using real-time polymerase chain reaction (PCR) targeting the M. ulcerans-specific insertion sequence (IS2404) in DNA extracted from swabs of ulcerated lesions in all cases. Where available, molecular typing confirmed that three of the dogs were infected with a strain of M. ulcerans that was indistinguishable from a disease-causing strain in people and other animals in Victoria. One dog was still undergoing treatment at the time of writing, but the remaining three dogs were successfully treated with a combination of surgical debridement and medical therapy in one case, and medical therapy alone in the other two. Investigation of the home environs of three of the dogs using real-time PCR revealed low amounts of M. ulcerans DNA in various environmental samples. Mycobacterium ulcerans infection should be included in the differential diagnoses of any ulcerated skin lesions in dogs that live in or visit endemic areas of Victoria and Queensland.