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Jarosz AS, Halo JV. Transcription of Endogenous Retroviruses: Broad and Precise Mechanisms of Control. Viruses 2024; 16:1312. [PMID: 39205286 PMCID: PMC11359688 DOI: 10.3390/v16081312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Endogenous retroviruses (ERVs) are the remnants of retroviral germline infections and are highly abundant in the genomes of vertebrates. At one time considered to be nothing more than inert 'junk' within genomes, ERVs have been tolerated within host genomes over vast timescales, and their study continues to reveal complex co-evolutionary histories within their respective host species. For example, multiple instances have been characterized of ERVs having been 'borrowed' for normal physiology, from single copies to ones involved in various regulatory networks such as innate immunity and during early development. Within the cell, the accessibility of ERVs is normally tightly controlled by epigenetic mechanisms such as DNA methylation or histone modifications. However, these silencing mechanisms of ERVs are reversible, and epigenetic alterations to the chromatin landscape can thus lead to their aberrant expression, as is observed in abnormal cellular environments such as in tumors. In this review, we focus on ERV transcriptional control and draw parallels and distinctions concerning the loss of regulation in disease, as well as their precise regulation in early development.
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Affiliation(s)
- Abigail S. Jarosz
- Science and Mathematics Division, Lorrain County Community College, Lorrain, OH 44035, USA;
| | - Julia V. Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA
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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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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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Johnston SD, Hulse L, Keeley T, Mucci A, Seddon J, Maynard S. The Utility of the Koala Scat: A Scoping Review. BIOLOGY 2024; 13:523. [PMID: 39056716 PMCID: PMC11273466 DOI: 10.3390/biology13070523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
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.
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Affiliation(s)
- Stephen D. Johnston
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Lyndal Hulse
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
| | - Tamara Keeley
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Albano Mucci
- School of Environment, The University of Queensland, Gatton 4343, Australia; (L.H.); (T.K.); (A.M.)
| | - Jennifer Seddon
- School of Veterinary Science, The University of Queensland, Gatton 4343, Australia;
- Research Division, James Cook University, Townsville 4811, Australia
| | - Sam Maynard
- Saunders Havill Group, Bowen Hills 4006, Australia;
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Pramono D, Takeuchi D, Katsuki M, AbuEed L, Abdillah D, Kimura T, Kawasaki J, Miyake A, Nishigaki K. FeLIX is a restriction factor for mammalian retrovirus infection. J Virol 2024; 98:e0177123. [PMID: 38440982 PMCID: PMC11019853 DOI: 10.1128/jvi.01771-23] [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: 11/12/2023] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
Endogenous retroviruses (ERVs) are remnants of ancestral viral infections. Feline leukemia virus (FeLV) is an exogenous and endogenous retrovirus in domestic cats. It is classified into several subgroups (A, B, C, D, E, and T) based on viral receptor interference properties or receptor usage. ERV-derived molecules benefit animals, conferring resistance to infectious diseases. However, the soluble protein encoded by the defective envelope (env) gene of endogenous FeLV (enFeLV) functions as a co-factor in FeLV subgroup T infections. Therefore, whether the gene emerged to facilitate viral infection is unclear. Based on the properties of ERV-derived molecules, we hypothesized that the defective env genes possess antiviral activity that would be advantageous to the host because FeLV subgroup B (FeLV-B), a recombinant virus derived from enFeLV env, is restricted to viral transmission among domestic cats. When soluble truncated Env proteins from enFeLV were tested for their inhibitory effects against enFeLV and FeLV-B, they inhibited viral infection. Notably, this antiviral machinery was extended to infection with the Gibbon ape leukemia virus, Koala retrovirus A, and Hervey pteropid gammaretrovirus. Although these viruses used feline phosphate transporter 1 (fePit1) and phosphate transporter 2 as receptors, the inhibitory mechanism involved competitive receptor binding in a fePit1-dependent manner. The shift in receptor usage might have occurred to avoid the inhibitory effect. Overall, these findings highlight the possible emergence of soluble truncated Env proteins from enFeLV as a restriction factor against retroviral infection and will help in developing host immunity and antiviral defense by controlling retroviral spread.IMPORTANCERetroviruses are unique in using reverse transcriptase to convert RNA genomes into DNA, infecting germ cells, and transmitting to offspring. Numerous ancient retroviral sequences are known as endogenous retroviruses (ERVs). The soluble Env protein derived from ERVs functions as a co-factor that assists in FeLV-T infection. However, herein, we show that the soluble Env protein exhibits antiviral activity and provides resistance to mammalian retrovirus infection through competitive receptor binding. In particular, this finding may explain why FeLV-B transmission is not observed among domestic cats. ERV-derived molecules can benefit animals in an evolutionary arms race, highlighting the double-edged-sword nature of ERVs.
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MESH Headings
- Animals
- Cats
- Endogenous Retroviruses/genetics
- Endogenous Retroviruses/metabolism
- Gene Products, env/genetics
- Gene Products, env/metabolism
- Leukemia Virus, Feline/classification
- Leukemia Virus, Feline/genetics
- Leukemia Virus, Feline/metabolism
- Leukemia Virus, Gibbon Ape/genetics
- Leukemia Virus, Gibbon Ape/metabolism
- Leukemia, Feline/genetics
- Leukemia, Feline/metabolism
- Leukemia, Feline/virology
- Phosphate Transport Proteins/genetics
- Phosphate Transport Proteins/metabolism
- Receptors, Virus/metabolism
- Retroviridae Infections/metabolism
- Retroviridae Infections/virology
- Solubility
- Female
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Affiliation(s)
- Didik Pramono
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Dai Takeuchi
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Masato Katsuki
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Loai AbuEed
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Dimas Abdillah
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Tohru Kimura
- The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
| | - Junna Kawasaki
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Ariko Miyake
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
| | - Kazuo Nishigaki
- Laboratory of Molecular Immunology and Infectious Disease, The Joint Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi, Japan
- Research Institute for Cell Design Medical Science, Yamaguchi University, Yamaguchi, Japan
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Lillie M, Pettersson M, Jern P. Contrasting segregation patterns among endogenous retroviruses across the koala population. Commun Biol 2024; 7:350. [PMID: 38514810 PMCID: PMC10957985 DOI: 10.1038/s42003-024-06049-0] [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: 12/12/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the population. Here, we investigate geographic patterns of three focal ERV lineages of increasing estimated ages, from the koala retrovirus (KoRV) to phaCin-β and to phaCin-β-like, using the whole-genome sequencing of 430 koalas from the Koala Genome Survey. Thousands of ERV loci were found across the population, with contrasting patterns of polymorphism. Northern individuals had thousands of KoRV integrations and hundreds of phaCin-β ERVs. In contrast, southern individuals had higher phaCin-β frequencies, possibly reflecting more recent activity and a founder effect. Overall, our findings suggest high ERV burden in koalas, reflecting historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for conservation genetics in this endangered species.
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Affiliation(s)
- Mette Lillie
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-752 36, Uppsala, Sweden.
| | - Mats Pettersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden.
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Akter L, Hashem MA, Rakib TM, Rashid MHO, Hossain KA, Akhter R, Utsunomiya M, Kitab B, Hifumi T, Miyoshi N, Maetani F, Tsukiyama-Kohara K. Investigation of koala retrovirus in captive koalas with pneumonia and comparative analysis of subtype distribution. Arch Virol 2023; 168:298. [PMID: 38010495 DOI: 10.1007/s00705-023-05928-x] [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: 07/26/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
This study focused on the involvement of koala retrovirus (KoRV) in pneumonia in koalas. Three deceased pneumonic koalas from a Japanese zoo were examined in this study. Hematological and histopathological findings were assessed, and KoRV proviral DNA loads in the blood and tissues were compared with those of eight other KoRV-infected koalas from different zoos. Demographic data and routine blood profiles were collected, and blood and tissue samples were analyzed to rule out concurrent infections in pneumonic koalas. KoRV subtyping and measurement of the KoRV proviral DNA load were performed by polymerase chain reaction (PCR) using specific primers targeting the pol and env genes. The results showed that the koalas had histopathologically suppurative and fibrinous pneumonia. Chlamydiosis was not detected in any of the animals. PCR analysis revealed KoRV-A, -B, and -C infections in all koalas, except for animals K10-11, which lacked KoRV-B. Significant variations in the proviral DNA loads of these KoRV subtypes were observed in all tissues and disease groups. Most tissues showed reduced KoRV loads in koalas with pneumonia, except in the spleen, which had significantly higher loads of total KoRV (2.54 × 107/µg DNA) and KoRV-A (4.74 × 107/µg DNA), suggesting potential immunosuppression. This study revealed the intricate dynamics of KoRV in various tissues, indicating its potential role in koala pneumonia via immunosuppression and opportunistic infections. Analysis of the levels of KoRV proviral DNA in different tissues will shed light on viral replication and the resulting pathogenesis in future studies.
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Affiliation(s)
- Lipi Akter
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md Abul Hashem
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Tofazzal Md Rakib
- Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Md Haroon Or Rashid
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
| | - Kazi Anowar Hossain
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
| | - Rupaly Akhter
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
| | - Masashi Utsunomiya
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
| | - Bouchra Kitab
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan
| | - Tatsuro Hifumi
- Department of Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Noriaki Miyoshi
- Department of Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Fumie Maetani
- Hirakawa Zoological Park, Kagoshima, Japan
- Awaji Farm England Hill Zoo, Hyogo, Japan
| | - Kyoko Tsukiyama-Kohara
- Transboundary Animal Diseases Center, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto, Kagoshima, 8900065, Japan.
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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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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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