Academic literature on the topic 'Koala retrovirus'

ABSTRACT A novel retrovirus, morphologically consistent with mammalian C-type retroviruses, was detected by electron microscopy in mitogen-stimulated peripheral blood mononuclear cell cultures from 163 koalas and in lymphoma tissue from 3 koalas. PCR amplified provirus from the blood and tissues of 17 wild and captive koalas, and reverse transcriptase-PCR demonstrated viral mRNA, viral genomic RNA, and reverse transcriptase activity in koala serum and cell culture supernatants. Comparison of viral sequences derived from genomic DNA and mRNA showed identity indicative of a single retroviral species—here designated koala retrovirus (KoRV). Southern blot analysis of koala tissue genomic DNA using labelled KoRV probes demonstrated banding consistent with an endogenous retrovirus. Complete and apparently truncated proviruses were detected in DNA of both clinically normal koalas and those with hematopoietic disease. KoRV-related viruses were not detected in other marsupials, and phylogenetic analysis showed that KoRV paradoxically clusters with gibbon ape leukemia virus (GALV). The strong similarity between GALV and KoRV suggests that these viruses are closely related and that recent cross-host transmission has occurred. The complete proviral DNA sequence of KoRV is reported.

Koala retrovirus, a recent discovery in Australian koalas, is endogenised in 100% of northern koalas but has lower prevalence in southern populations, with lower proviral and viral loads, and an undetermined level of endogenisation. KoRV has been associated with lymphoid neoplasia, e.g., lymphoma. Recent studies have revealed high complexity in southern koala retroviral infections, with a need to clarify what constitutes positive and negative cases. This study aimed to define KoRV infection status in Mount Lofty Ranges koalas in South Australia using RNA-seq and proviral analysis (n = 216). The basis for positivity of KoRV was deemed the presence of central regions of the KoRV genome (gag 2, pol, env 1, and env 2) and based on this, 41% (89/216) koalas were positive, 57% (124/216) negative, and 2% inconclusive. These genes showed higher expression in lymph node tissue from KoRV positive koalas with lymphoma compared with other KoRV positive koalas, which showed lower, fragmented expression. Terminal regions (LTRs, partial gag, and partial env) were present in SA koalas regardless of KoRV status, with almost all (99.5%, 215/216) koalas positive for gag 1 by proviral PCR. Further investigation is needed to understand the differences in KoRV infection in southern koala populations.

Endogenous retroviruses (ERVs) are proviral sequences that result from colonization of the host germ line by exogenous retroviruses. The majority of ERVs represent defective retroviral copies. However, for most ERVs, endogenization occurred millions of years ago, obscuring the stages by which ERVs become defective and the changes in both virus and host important to the process. The koala retrovirus, KoRV, only recently began invading the germ line of the koala (Phascolarctos cinereus), permitting analysis of retroviral endogenization on a prospective basis. Here, we report that recombination with host genomic elements disrupts retroviruses during the earliest stages of germ-line invasion. One type of recombinant, designated recKoRV1, was formed by recombination of KoRV with an older degraded retroelement. Many genomic copies of recKoRV1 were detected across koalas. The prevalence of recKoRV1 was higher in northern than in southern Australian koalas, as is the case for KoRV, with differences in recKoRV1 prevalence, but not KoRV prevalence, between inland and coastal New South Wales. At least 15 additional different recombination events between KoRV and the older endogenous retroelement generated distinct recKoRVs with different geographic distributions. All of the identified recombinant viruses appear to have arisen independently and have highly disrupted ORFs, which suggests that recombination with existing degraded endogenous retroelements may be a means by which replication-competent ERVs that enter the germ line are degraded.

ABSTRACT Recently, a new endogenous koala gammaretrovirus, designated KoRV, was isolated from koalas. The KoRV genome shares 78% nucleotide identity with another gammaretrovirus, gibbon ape leukemia virus (GALV). KoRV is endogenous in koalas, while GALV is exogenous, suggesting that KoRV predates GALV and that gibbons and koalas acquired the virus at different times from a common source. We have determined that subtle adaptive differences between the KoRV and GALV envelope genes account for differences in their receptor utilization properties. KoRV represents a unique example of a gammaretrovirus whose envelope has evolved to allow for its expanded host range and zoonotic potential.

ABSTRACT The iconic Australian marsupial, the koala (Phascolarctos cinereus), has suffered dramatic population declines as a result of habitat loss and fragmentation, disease, vehicle collision mortality, dog attacks, bushfires and climate change. In 2012, koalas were officially declared vulnerable by the Australian government and listed as a threatened species. In response, research into diseases affecting koalas has expanded rapidly. The two major pathogens affecting koalas are Chlamydia pecorum, leading to chlamydial disease and koala retrovirus (KoRV). In the last eight years, these pathogens and their diseases have received focused study regarding their sources, genetics, prevalence, disease presentation and transmission. This has led to vast improvements in pathogen detection and treatment, including the ongoing development of vaccines for each as a management and control strategy. This review will summarize and highlight the important advances made in understanding and combating C. pecorum and KoRV in koalas, since they were declared a threatened species. With complementary advances having also been made from the koala genome sequence and in our understanding of the koala immune system, we are primed to make a significant positive impact on koala health into the future.

Koala populations are currently in rapid decline across Australia, with infectious diseases being a contributing cause. The koala retrovirus (KoRV) is a gammaretrovirus present in both captive and wild koala colonies that presents an additional challenge for koala conservation in addition to habitat loss, climate change, and other factors. Currently, nine different subtypes (A to I) have been identified; however, KoRV genetic diversity analyses have been limited. KoRV is thought to be exogenously transmitted between individuals, with KoRV-A also being endogenous and transmitted through the germline. The mechanisms of exogenous KoRV transmission are yet to be extensively investigated. Here, deep sequencing was employed on 109 captive koalas of known pedigree, housed in two institutions from Southeast Queensland, to provide a detailed analysis of KoRV transmission dynamics and genetic diversity. The final dataset included 421 unique KoRV sequences, along with the finding of an additional subtype (KoRV-K). Our analysis suggests that exogenous transmission of KoRV occurs primarily between dam and joey, with evidence provided for multiple subtypes, including nonendogenized KoRV-A. No evidence of sexual transmission was observed, with mating partners found to share a similar number of sequences as unrelated koala pairs. Importantly, both distinct captive colonies showed similar trends. These findings indicate that breeding strategies or antiretroviral treatment of females could be employed as effective management approaches in combating KoRV transmission.

Toll-like receptors (TLRs), evolutionarily conserved pattern recognition receptors, play an important role in innate immunity by recognizing microbial pathogen-associated molecular patterns. Koala retrovirus (KoRV), a major koala pathogen, exists in both endogenous (KoRV-A) and exogenous forms (KoRV-B to J). However, the expression profile of TLRs in koalas infected with KoRV-A and other subtypes is yet to characterize. Here, we investigated TLR expression profiles in koalas with a range of subtype infection profiles (KoRV-A only vs. KoRV-A with KoRV-B and/or -C). To this end, we cloned partial sequences for TLRs (TLR2–10 and TLR13), developed real-time PCR assays, and determined TLRs mRNA expression patterns in koala PBMCs and/or tissues. All the reported TLRs for koala were expressed in PBMCs, and variations in TLR expression were observed in koalas infected with exogenous subtypes (KoRV-B and KoRV-C) compared to the endogenous subtype (KoRV-A) only, which indicates the implications of TLRs in KoRV infection. TLRs were also found to be differentially expressed in koala tissues. This is the first report of TLR expression profiles in koala, which provides insights into koala’s immune response to KoRV infection that could be utilized for the future exploitation of TLR modulators in the maintenance of koala health.

Background.Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized.Results.To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized.Conclusions.Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

Koalas are a vulnerable iconic species, for which disease is a significant threat to populations around Australia. Lymphoid neoplasia and immunomodulation in koalas have been associated with an important pathogen, koala retrovirus (KoRV). The prevalence and transmission of KoRV differs in northern koalas, from Queensland and New South Wales, compared to southern koalas, from Victoria and South Australia. Northern koalas inherit and horizontally transmit KoRV via endogenous and exogenous mechanisms, respectively with all koalas infected. Southern koalas are hypothesised to only have exogenous transmission, and within these populations the prevalence is less. Both proviral load (inserted viral genome into host DNA) and viral load (extracellular RNA viral genome) are significantly higher in northern koalas in comparison to southern koalas, representing active transcription in a greater number of cells. Mechanisms for KoRV-associated oncogenesis are still unknown, along with the prevalence of lymphoid neoplasia in the Mount Lofty Ranges population, South Australia. Increased susceptibility of disease has been inferred from studies exploring KoRV coinfection with Chlamydia pecorum, a bacterium which causes both ocular and urogenital disease in koalas. KoRV and C. pecorum are well-studied key pathogens of koalas, although the significance of another infectious agent Phascolarctid gammaherpesviruses, is unknown. Avian and human studies have shown increased incidence of neoplasia when coinfected with a retrovirus and gammaherpesvirus, but there is no current evidence for this in koalas. Association of diseases is based on a confident diagnosis of infectious agents, for which koalas in South Australia have shown variations in proviral analysis creating complexity in the diagnosis of KoRV. The KoRV viral genome consists of three genes, gag, pol and env, flanked by long terminal repeats, LTRs. The pol gene qPCR has been a standard diagnostic tool, but more investigation across multiple genome targets has shown variance in SA koala PCR and qPCR results. In this study, PCR and qPCR methods were used against two targets in the gag gene, one in the pol gene and two in the env gene. Koalas for which all proviral targets were positive were designated KoRV positive and koalas for which one gag target, pol target and env targets were negative were designated KoRV negative. There were 41.2% (89/216) KoRV positive, 56.9% (123/216) KoRV negative koalas and only 1.9% (4/216) deemed inconclusive. Viral gene expression analysed by qPCR was found to be present in 10/10 KoRV positive koalas, and absent in 5/5 KoRV negative koalas. RNAseq analysis revealed transcription of sequences homologous to terminal regions of the KoRV genome in all koalas, verified by the presence of one gag gene target in almost all (215/216) koalas tested by PCR. The presence of these regions in South Australian koalas without the presence of the full KoRV genome, suggests an endogenised retroviral element, potentially within the koala genome prior to KoRV. Lymphomic koalas showed high expression of KoRV and higher proviral loads compared to KoRV positive koalas without lymphoma. Lymphoma was found in 1.2% (3/240) of koalas and these cases were collated with previous South Australian lymphoma cases for classification. All cases had abdominal involvement, were intermediate to large cell and of non-T cell origin. RNAseq data was compared from lymphomic lymph nodes, lymph nodes from KoRV positive and lymph nodes of KoRV negative koalas. High KoRV transcription was found in lymphomic tissue, 1207 genes showed differential expression between KoRV positive koalas diagnosed with lymphoma and KoRV negative koalas and 939 genes between KoRV positive koalas diagnosed with lymphoma and KoRV positive koalas. Oncogenes MYB, MYCL and FLT3 were significantly upregulated and possible candidates in the incitement of oncogenesis. Dysregulation in IL10, and pathways associated with NF-kB also support the role of immunosuppression in lymphoma pathogenesis. Based on theories of KoRV-associated immunosuppression leading to opportunistic infections and augmentation of disease with pathogens, coinfections and comorbidities were investigated in 247 necropsied koalas. KoRV was not found to be associated with C. pecorum or disease severity. However, C. pecorum was associated with another recently discovered infectious agent, Phascolarctid gammaherpesvirus (PhaHV), and in this cohort PhaHV was associated with the presence of paraovarian cysts, regardless of chlamydial status, similar to Victorian koalas. Also, KoRV and PhaHV-2 coinfection was associated with neoplasia and warrants further investigation. Disease and infectious agents were negatively correlated with victims of road traffic accidents showing the potential importance of this group of koalas. Novel pathologies were found in this koala necropsy cohort. Pulmonary actinomycosis, a new presentation of respiratory disease of koalas, with a subset of these koalas presenting with secondary hypertrophic osteopathy, a second novel pathology in koalas. Fifteen koalas were found to have pyogranulomatous lobar pneumonia, predominantly affecting the left caudal lung lobe. Histological examination showed Splendore Hoeppli phenomenon with associated Gram-positive or Gram-variable, non-acid fast, filamentous bacteria. The pathogen was identified as a novel Actinomyces sp. and through 16S rRNA gene sequencing was closest to A. timonensis. Collaboration with other wildlife veterinarians found that two of the study koalas also presented with another undescribed pathology in koalas, hypertrophic osteopathy, found secondary to the pulmonary lesions. These discoveries highlight the necessity for ongoing necropsy studies in koalas to increase the knowledge of disease presentations in this iconic species. Overall, this thesis aimed to examine the association of disease with several pathogens, with particular focus on the association between KoRV and lymphoma. Advancements were made in recommendations for KoRV diagnosis in South Australia, gene dysregulation in KoRVassociated lymphoma, interactions with other key pathogens; C. pecorum and PhaHV, and the report of novel disease presentations. The increased knowledge of infectious disease and interaction of disease in South Australian koalas can help management strategies protecting the health and welfare of these koalas. Also, identification of dysregulated genes has increased the knowledge of oncogenesis by koala retrovirus.
Thesis (Ph.D.) -- University of Adelaide, School of Animal and Veterinary Sciences, 2021