1
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Harding EF, Mercer LK, Yan GJH, Waters PD, White PA. Invasion and Amplification of Endogenous Retroviruses in Dasyuridae Marsupial Genomes. Mol Biol Evol 2024; 41:msae160. [PMID: 39101626 PMCID: PMC11334065 DOI: 10.1093/molbev/msae160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/05/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Retroviruses are an ancient viral family that have globally coevolved with vertebrates and impacted their evolution. In Australia, a continent that has been geographically isolated for millions of years, little is known about retroviruses in wildlife, despite the devastating impacts of a retrovirus on endangered koala populations. We therefore sought to identify and characterize Australian retroviruses through reconstruction of endogenous retroviruses from marsupial genomes, in particular the Tasmanian devil due to its high cancer incidence. We screened 19 marsupial genomes and identified over 80,000 endogenous retrovirus fragments which we classified into eight retrovirus clades. The retroviruses were similar to either Betaretrovirus (5/8) or Gammaretrovirus (3/8) retroviruses, but formed distinct phylogenetic clades compared to extant retroviruses. One of the clades (MEBrv 3) lost an envelope but retained retrotranspositional activity, subsequently amplifying throughout all Dasyuridae genomes. Overall, we provide insights into Australian retrovirus evolution and identify a highly active endogenous retrovirus within Dasyuridae genomes.
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Affiliation(s)
- Emma F Harding
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Lewis K Mercer
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Grace J H Yan
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Paul D Waters
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Sydney, Australia
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2
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Tarlinton R, Greenwood AD. Koala retrovirus and neoplasia: correlation and underlying mechanisms. Curr Opin Virol 2024; 67:101427. [PMID: 39047314 DOI: 10.1016/j.coviro.2024.101427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/27/2024]
Abstract
The koala retrovirus, KoRV, is one of the few models for understanding the health consequences of retroviral colonization of the germline. Such colonization events transition exogenous infectious retroviruses to Mendelian traits or endogenous retroviruses (ERVs). KoRV is currently in a transitional state from exogenous retrovirus to ERV, which in koalas (Phascolarctos cinereus) has been associated with strongly elevated levels of neoplasia. In this review, we describe what is currently known about the associations and underlying mechanisms of KoRV-induced neoplasia.
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Affiliation(s)
- Rachael Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany; School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
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3
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Hayward JA, Tian S, Tachedjian G. GALV-KoRV-related retroviruses in diverse Australian and African rodent species. Virus Evol 2024; 10:veae061. [PMID: 39175839 PMCID: PMC11341202 DOI: 10.1093/ve/veae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/12/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
The enigmatic origins and transmission events of the gibbon ape leukemia virus (GALV) and its close relative the koala retrovirus (KoRV) have been a source of enduring debate. Bats and rodents are each proposed as major reservoirs of interspecies transmission, with ongoing efforts to identify additional animal hosts of GALV-KoRV-related retroviruses. In this study, we identified nine rodent species as novel hosts of GALV-KoRV-related retroviruses. Included among these hosts are two African rodents, revealing the first appearance of this clade beyond the Australian and Southeast Asian region. One of these African rodents, Mastomys natalensis, carries an endogenous GALV-KoRV-related retrovirus that is fully intact and potentially still infectious. Our findings support the hypothesis that rodents are the major carriers of GALV-KoRV-related retroviruses.
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Affiliation(s)
- Joshua A Hayward
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
- Department of Microbiology, Monash University, Wellington Rd, Clayton, VIC 3168, Australia
| | - Shuoshuo Tian
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
| | - Gilda Tachedjian
- Life Sciences Discipline, Burnet Institute, 85 Commercial Rd, Melbourne, VIC 3004, Australia
- Department of Microbiology, Monash University, Wellington Rd, Clayton, VIC 3168, Australia
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, 792 Elizabeth St, Melbourne, VIC 3000, Australia
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4
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Jern P, Greenwood AD. Wildlife endogenous retroviruses: colonization, consequences, and cooption. Trends Genet 2024; 40:149-159. [PMID: 37985317 DOI: 10.1016/j.tig.2023.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/22/2023]
Abstract
Endogenous retroviruses (ERVs) are inherited genomic remains of past germline retroviral infections. Research on human ERVs has focused on medical implications of their dysregulation on various diseases. However, recent studies incorporating wildlife are yielding remarkable perspectives on long-term retrovirus-host interactions. These initial forays into broader taxonomic analysis, including sequencing of multiple individuals per species, show the incredible plasticity and variation of ERVs within and among wildlife species. This demonstrates that stochastic processes govern much of the vertebrate genome. In this review, we elaborate on discoveries pertaining to wildlife ERV origins and evolution, genome colonization, and consequences for host biology.
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Affiliation(s)
- Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany; School of Veterinary Medicine, Freie Unversität Berlin, Berlin, Germany.
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5
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Wright BR, Casteriano A, Muir YSS, Hulse L, Simpson SJ, Legione AR, Vaz PK, Devlin JM, Krockenberger MB, Higgins DP. Expanding the known distribution of phascolartid gammaherpesvirus 1 in koalas to populations across Queensland and New South Wales. Sci Rep 2024; 14:1223. [PMID: 38216613 PMCID: PMC10786818 DOI: 10.1038/s41598-023-50496-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/20/2023] [Indexed: 01/14/2024] Open
Abstract
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.
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Affiliation(s)
- Belinda R Wright
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia.
| | - Andrea Casteriano
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Yasmine S S Muir
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Lyndal Hulse
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sarah J Simpson
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Alistair R Legione
- Melbourne Veterinary School, Faculty of Science, Asia Pacific Centre for Animal Health, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paola K Vaz
- Melbourne Veterinary School, Faculty of Science, Asia Pacific Centre for Animal Health, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joanne M Devlin
- Melbourne Veterinary School, Faculty of Science, Asia Pacific Centre for Animal Health, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mark B Krockenberger
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Damien P Higgins
- Sydney School of Veterinary Science, University of Sydney, Camperdown, NSW, 2006, Australia
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6
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Wang J, Han GZ. Genome mining shows that retroviruses are pervasively invading vertebrate genomes. Nat Commun 2023; 14:4968. [PMID: 37591904 PMCID: PMC10435555 DOI: 10.1038/s41467-023-40732-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Endogenous retroviruses (ERVs) record past retroviral infections, providing molecular archives for interrogating the evolution of retroviruses and retrovirus-host interaction. However, the vast majority of ERVs are not active anymore due to various disruptive mutations, and ongoing retroviral invasion of vertebrate genomes has been rarely documented. Here we analyze genomics data from 2004 vertebrates for mining invading ERVs (ERVi). We find that at least 412 ERVi elements representing 217 viral operational taxonomic units are invading the genomes of 123 vertebrates, 18 of which have been assessed to be threatened species. Our results reveal an unexpected prevalence of ongoing retroviral invasion in vertebrates and expand the diversity of retroviruses recently circulating in the wild. We characterize the pattern and nature of ERVi in the historical and biogeographical context of their hosts, for instance, the generation of model organisms, sympatric speciation, and domestication. We suspect that these ERVi are relevant to conservation of threatened species, zoonoses in the wild, and emerging infectious diseases in humans.
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Affiliation(s)
- Jianhua Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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7
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Quigley BL, Timms P, Nyari S, McKay P, Hanger J, Phillips S. Reduction of Chlamydia pecorum and Koala Retrovirus subtype B expression in wild koalas vaccinated with novel peptide and peptide/recombinant protein formulations. Vaccine X 2023; 14:100329. [PMID: 37577264 PMCID: PMC10422670 DOI: 10.1016/j.jvacx.2023.100329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 06/05/2023] [Accepted: 06/05/2023] [Indexed: 08/15/2023] Open
Abstract
Koalas are an endangered species under threat of extinction from several factors, including infections agents. Chlamydia pecorum infection results in morbidity and mortality from ocular and urogenital diseases while Koala Retrovirus (KoRV) infection has been linked to increased rates of cancer and chlamydiosis. Both C. pecorum and KoRV are endemic in many wild Australian koala populations, with limited treatment options available. Fortunately, vaccines for these pathogens are under development and have generated effective immune responses in multiple trials. The current study aimed to improve vaccine formulations by testing a novel peptide version of the Chlamydia vaccine and a combination Chlamydia - KoRV vaccine. Utilising a monitored wild population in Southeast Queensland, this trial followed koalas given either a 'Chlamydia only' vaccine (utilising four peptides from the chlamydial Major Outer Membrane Protein, MOMP), a combination 'Chlamydia and KoRV' vaccine (comprised of the chlamydial peptides plus a KoRV recombinant envelope protein (rEnv)) or no treatment. Clinical observations, C. pecorum and KoRV gene expression, serum IgG, and mucosal immune gene expression were assessed over a 17-month period. Overall, both vaccine formulations resulted in a decrease in chlamydiosis mortality, with decreases in C. pecorum, CD4, CD8β and IL-17A gene expression observed. In addition, the combination vaccine group also showed an increase in anti-KoRV IgG production that corresponded to a decrease in detected KoRV-B expression. While these results are favourable, the chlamydial peptide vaccine did not appear to outperform the established recombinant chlamydial vaccine and suggests that a combination vaccine formulated with recombinant MOMP plus KoRV rEnv could capitalize on the demonstrated benefits of both for the betterment of koalas into the future.
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Affiliation(s)
- Bonnie L Quigley
- The Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, Australia
| | - Peter Timms
- The Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, Australia
| | - Sharon Nyari
- The Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, Australia
| | - Philippa McKay
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, QLD, Australia
| | - Jon Hanger
- Endeavour Veterinary Ecology, 1695 Pumicestone Rd, Toorbul, QLD, Australia
| | - Samuel Phillips
- The Centre for Bioinnovation, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, Australia
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8
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Eisenhofer R, Brice KL, Blyton MDJ, Bevins SE, Leigh K, Singh BK, Helgen KM, Hough I, Daniels CB, Speight N, Moore BD. Individuality and stability of the koala ( Phascolarctos cinereus) faecal microbiota through time. PeerJ 2023; 11:e14598. [PMID: 36710873 PMCID: PMC9879153 DOI: 10.7717/peerj.14598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie L. Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Michaela DJ Blyton
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, Queensland, Australia
| | - Scott E. Bevins
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kellie Leigh
- Science for Wildlife Ltd, Sydney, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia,Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Kristofer M. Helgen
- Australian Museum Research Institute, Sydney, New South Wales, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia,Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Ian Hough
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Christopher B. Daniels
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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9
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Blanchard AM, Emes RD, Greenwood AD, Holmes N, Loose MW, McEwen GK, Meers J, Speight N, Tarlinton RE. Genome Reference Assembly for Bottlenecked Southern Australian Koalas. Genome Biol Evol 2022; 15:6948355. [PMID: 36542479 PMCID: PMC9887267 DOI: 10.1093/gbe/evac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viability. In addition, the recent colonization of the koala genome by KoRV provides a unique opportunity to study the process of retroviral adaptation to vertebrate genomes and the impact this has on speciation, genome structure, and function. The genome build described here is from an animal from the bottlenecked Southern population free of endogenous and exogenous KoRV. It provides a more contiguous genome build than the previous koala reference derived from an animal from a more outbred Northern population and is the first koala genome from a KoRV polymerase-free animal.
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Affiliation(s)
| | - Richard David Emes
- School of Veterinary Medicine and Science, University of Nottingham, Leicestershire, United Kingdom
| | | | - Nadine Holmes
- School of Life Sciences, University of Nottingham, United Kingdom
| | | | | | - Joanne Meers
- School of Veterinary Science, University of Queensland, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Australia
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10
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Diversity and transmission of koala retrovirus: a case study in three captive koala populations. Sci Rep 2022; 12:15787. [PMID: 36138048 PMCID: PMC9499970 DOI: 10.1038/s41598-022-18939-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/22/2022] [Indexed: 11/21/2022] Open
Abstract
Koala retrovirus is a recently endogenized retrovirus associated with the onset of neoplasia and infectious disease in koalas. There are currently twelve described KoRV subtypes (KoRV-A to I, K–M), most of which were identified through recently implemented deep sequencing methods which reveal an animals’ overall KoRV profile. This approach has primarily been carried out on wild koala populations around Australia, with few investigations into the whole-population KoRV profile of captive koala colonies to date. This study conducted deep sequencing on 64 captive koalas of known pedigree, housed in three institutions from New South Wales and South-East Queensland, to provide a detailed analysis of KoRV genetic diversity and transmission. The final dataset included 93 unique KoRV sequences and the first detection of KoRV-E within Australian koala populations. Our analysis suggests that exogenous transmission of KoRV-A, B, D, I and K primarily occurs between dam and joey. Detection of KoRV-D in a neonate sample raises the possibility of this transmission occurring in utero. Overall, the prevalence and abundance of KoRV subtypes was found to vary considerably between captive populations, likely due to their different histories of animal acquisition. Together these findings highlight the importance of KoRV profiling for captive koalas, in particular females, who play a primary role in KoRV exogenous transmission.
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11
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Hashem MA, Kayesh MEH, Maetani F, Goto A, Nagata N, Kasori A, Imanishi T, Tsukiyama-Kohara K. Subtype distribution and expression of the koala retrovirus in the Japanese zoo koala population. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 102:105297. [PMID: 35533919 DOI: 10.1016/j.meegid.2022.105297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/26/2022] [Accepted: 05/01/2022] [Indexed: 10/18/2022]
Abstract
We investigated the proviral copies and RNA expression in koala retrovirus (KoRV)-infected koalas. To ascertain any variation in viral load by institution, age, sex, or body condition score, we quantified KoRV proviral DNA and RNA loads in captive koalas (n = 37) reared in Japanese zoos. All koalas were positive for KoRV genes (pol, LTRs, and env of KoRV-A) in genomic DNA (gDNA), and 91.89% were positive for the pol gene in RNA. In contrast, the distribution rates of KoRV-B, KoRV-C, KoRV-D, and KoRV-F env genes in gDNA were 94.59%, 27.03%, 67.57%, and 54.05%, respectively. A wide inter-individual variation and/or a significant inter-institutional difference in proviral DNA (p < 0.0001) and RNA (p < 0.001) amounts (copies/103 koala β-actin copies) were observed in Awaji Farm England Hill Zoo koalas, which were obtained from southern koala populations, suggesting exogenous incorporation of KoRV in these koalas. Significant (p < 0.05) age differences were noted in KoRV RNA load (p < 0.05) and median total RNA load (p < 0.001), with loads higher in younger koalas (joeys and juveniles). Thus, the current study provides the distribution of KoRV subtypes in Japanese zoo koala populations and identifies several additional risk factors (sex, age, and body condition) associated with KoRV expression.
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Affiliation(s)
- Md Abul Hashem
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan; Department of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan; Department of Health Chattogram City Corporation, Chattogram 4000, Bangladesh
| | - Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan; Department of Microbiology and Public Health, Patuakhali Science and Technology University, Babuganj, Barishal 8210, Bangladesh
| | | | | | | | | | | | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan; Department of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.
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12
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Expansion of a retrovirus lineage in the koala genome. Proc Natl Acad Sci U S A 2022; 119:e2201844119. [PMID: 35696585 PMCID: PMC9231498 DOI: 10.1073/pnas.2201844119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, diversity, and prevalence provide insights into the historical dynamics of retrovirus-host interactions. In bioinformatic analyses of koala (Phascolarctos cinereus) whole-genome sequences, we identify a recently expanded ERV lineage (phaCin-β) that is related to the New World squirrel monkey retrovirus. This ERV expansion shares many parallels with the ongoing koala retrovirus (KoRV) invasion of the koala genome, including highly similar and mostly intact sequences, and polymorphic ERV loci in the sampled koala population. The recent phaCin-β ERV colonization of the koala genome appears to predate the current KoRV invasion, but polymorphic ERVs and divergence comparisons between these two lineages predict a currently uncharacterized, possibly still extant, phaCin-β retrovirus. The genomics approach to ERV-guided discovery of novel retroviruses in host species provides a strong incentive to search for phaCin-β retroviruses in the Australasian fauna.
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13
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Tarlinton RE, Legione AR, Sarker N, Fabijan J, Meers J, McMichael L, Simmons G, Owen H, Seddon JM, Dick G, Ryder JS, Hemmatzedah F, Trott DJ, Speight N, Holmes N, Loose M, Emes RD. Differential and defective transcription of koala retrovirus indicates the complexity of host and virus evolution. J Gen Virol 2022; 103. [PMID: 35762858 DOI: 10.1099/jgv.0.001749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
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.
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Affiliation(s)
- R E Tarlinton
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - A R Legione
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Australia
| | - N Sarker
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - J Fabijan
- Longleat Safari Park, Durrel Wildlife Conservation Trust, UK
| | - J Meers
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - L McMichael
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - G Simmons
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - H Owen
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - J M Seddon
- School of Veterinary Science, The University of Queensland, Brisbane, Australia
| | - G Dick
- Longleat Safari Park, Durrel Wildlife Conservation Trust, UK
| | - J S Ryder
- Garston Veterinary Group, Somerset, UK
| | - F Hemmatzedah
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - D J Trott
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - N Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, Australia
| | - N Holmes
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - M Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - R D Emes
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
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14
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Blyton MDJ, Pyne M, Young P, Chappell K. Koala retrovirus load and non-A subtypes are associated with secondary disease among wild northern koalas. PLoS Pathog 2022; 18:e1010513. [PMID: 35588407 PMCID: PMC9119473 DOI: 10.1371/journal.ppat.1010513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/08/2022] [Indexed: 01/17/2023] Open
Abstract
Koala Retrovirus (KoRV) has been associated with neoplasia in the vulnerable koala (Phascolarctos cinereus). However, there are conflicting findings regarding its association with secondary disease. We undertook a large-scale assessment of how the different KoRV subtypes and viral load are associated with Chlamydia pecorum infection and a range of disease pathologies in 151 wild koalas admitted for care to Currumbin Wildlife Hospital, Australia. Viral load (KoRV pol copies per ml of plasma) was the best predictor of more disease pathologies than any other KoRV variable. The predicted probability of a koala having disease symptoms increased from 25% to over 85% across the observed range of KoRV load, while the predicted probability of C. pecorum infection increased from 40% to over 80%. We found a negative correlation between the proportion of env deep sequencing reads that were endogenous KoRV-A and total KoRV load. This is consistent with suppression of endogenous KoRV-A, while the exogenous KoRV subtypes obtain high infection levels. Additionally, we reveal evidence that the exogenous subtypes are directly associated with secondary disease, with the proportion of reads that were the endogenous KoRV-A sequence a negative predictor of overall disease probability after the effect of KoRV load was accounted for. Further, koalas that were positive for KoRV-D or KoRV-D/F were more likely to have urogenital C. pecorum infection or low body condition score, respectively, irrespective of KoRV load. By contrast, our findings do not support previous findings that KoRV-B in particular is associated with Chlamydial disease. Based on these findings we suggest that koala research and conservation programs should target understanding what drives individual differences in KoRV load and limiting exogenous subtype diversity within populations, rather than seeking to eliminate any particular subtype.
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Affiliation(s)
- Michaela D. J. Blyton
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, Australia
| | - Michael Pyne
- Currumbin Wildlife Hospital and Foundation, Currumbin, Queensland, Australia
| | - Paul Young
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, Australia
| | - Keith Chappell
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland, Australia
- The University of Queensland, Australian Institute of Bioengineering and Nanotechnology, St Lucia, Queensland, Australia
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15
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Koala retrovirus genetic diversity and transmission dynamics within captive koala populations. Proc Natl Acad Sci U S A 2021; 118:2024021118. [PMID: 34493581 DOI: 10.1073/pnas.2024021118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
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.
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16
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Stephenson T, Speight N, Low WY, Woolford L, Tearle R, Hemmatzadeh F. Molecular Diagnosis of Koala Retrovirus (KoRV) in South Australian Koalas ( Phascolarctos cinereus). Animals (Basel) 2021; 11:ani11051477. [PMID: 34065572 PMCID: PMC8161083 DOI: 10.3390/ani11051477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/06/2021] [Accepted: 05/16/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Koala retrovirus (KoRV) is a significant threat to koalas across Australia. Koalas in northern koala populations (from New South Wales and Queensland) have KoRV inserted into their DNA and inherited to their offspring. Southern koala populations (from Victoria and South Australia) have KoRV infection spread through close contact of koalas. As such, there are koalas within South Australia that are not infected with KoRV. Accurate diagnosis of the infection of each koala is therefore fundamental for disease studies. Previous studies have shown differences in prevalence of different KoRV genes in the Mount Lofty Ranges Koala population; therefore, clarification is necessary. This study uses a large cohort (n = 216) and defines the diagnostic regions of the KoRV genome within the South Australian population. Using multiple molecular techniques, it demonstrates strong evidence for two clear groupings of koalas: KoRV positive and KoRV negative. Within this study, a population of 41% were shown to be KoRV positive and 57% were KoRV negative, with 2% inconclusive. This differentiation is of great importance when examining the clinical importance of KoRV infection within southern koalas. Abstract 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.
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Affiliation(s)
- Tamsyn Stephenson
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
- Correspondence:
| | - Natasha Speight
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
| | - Wai Yee Low
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (W.Y.L.); (R.T.)
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
- Veterinary Diagnostics Laboratory, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia
| | - Rick Tearle
- The Davies Livestock Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (W.Y.L.); (R.T.)
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy 5371, Australia; (N.S.); (L.W.); (F.H.)
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17
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Kayesh MEH, Hashem MA, Tsukiyama-Kohara K. Toll-Like Receptor and Cytokine Responses to Infection with Endogenous and Exogenous Koala Retrovirus, and Vaccination as a Control Strategy. Curr Issues Mol Biol 2021; 43:52-64. [PMID: 33946297 PMCID: PMC8928999 DOI: 10.3390/cimb43010005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
Koala populations are currently declining and under threat from koala retrovirus (KoRV) infection both in the wild and in captivity. KoRV is assumed to cause immunosuppression and neoplastic diseases, favoring chlamydiosis in koalas. Currently, 10 KoRV subtypes have been identified, including an endogenous subtype (KoRV-A) and nine exogenous subtypes (KoRV-B to KoRV-J). The host’s immune response acts as a safeguard against pathogens. Therefore, a proper understanding of the immune response mechanisms against infection is of great importance for the host’s survival, as well as for the development of therapeutic and prophylactic interventions. A vaccine is an important protective as well as being a therapeutic tool against infectious disease, and several studies have shown promise for the development of an effective vaccine against KoRV. Moreover, CRISPR/Cas9-based genome editing has opened a new window for gene therapy, and it appears to be a potential therapeutic tool in many viral infections, which could also be investigated for the treatment of KoRV infection. Here, we discuss the recent advances made in the understanding of the immune response in KoRV infection, as well as the progress towards vaccine development against KoRV infection in koalas.
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Affiliation(s)
- Mohammad Enamul Hoque Kayesh
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Department of Microbiology and Public Health, Faculty of Animal Science and Veterinary Medicine, Patuakhali Science and Technology University, Barishal 8210, Bangladesh
| | - Md Abul Hashem
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Department of Health, Chattogram City Corporation, Chattogram 4000, Bangladesh
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan; (M.E.H.K.); (M.A.H.)
- Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: ; Tel.: +81-99-285-3589
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