The detection of polymorphism of RecKoRV Loci within the Victorian koala population
Koala Retrovirus (KoRV) is known to be the most recently acquired endogenous retrovirus and is still settling to its genomic parasitic lifestyle. KoRV has both infectious and endogenous (integrated into the host genome) forms. One hundred percent of the Koalas in northern Australia are positive for...
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| Format: | Thesis (University of Nottingham only) |
| Language: | English |
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2023
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| Online Access: | https://eprints.nottingham.ac.uk/74076/ |
| _version_ | 1848800840603664384 |
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| author | Dudeja, Sukanya |
| author_facet | Dudeja, Sukanya |
| author_sort | Dudeja, Sukanya |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Koala Retrovirus (KoRV) is known to be the most recently acquired endogenous retrovirus and is still settling to its genomic parasitic lifestyle. KoRV has both infectious and endogenous (integrated into the host genome) forms. One hundred percent of the Koalas in northern Australia are positive for the virus. A higher proviral copy number per cell has been observed in Northern koalas due to
endogenized KoRV compared to that in the south. The Koalas in southern Australia show a variability in the prevalence rate of the exogenous virus and a lower rate of KoRV induced disease. Southern Australian koalas earlier considered to be disease free or only having the exogenous counterparts of the virus, demonstrate a defective variant of KoRV known as Recombinant KoRV(RecKoRV). RecKoRV is formed due to the recombination between Phascolarctid Endogenous Retroelement (PhER) and KoRV. The presence of RecKoRV variants particularly in the founder population on the French island calls into question the existence of KoRV free animals. The difference in the KoRV profiles between the northern and the southern animals raises the possibility that these replication defective transcripts may be interfering with full length transcripts of the replication competent KoRV. The presence of RecKoRV variants particularly in
the founder population and in the Victorian animals indicate that all southern animals have these variants. The aim of this study is to look at the polymorphism of the RecKoRV loci using integration site-specific PCRs to explore whether these are fixed or variable in the Victorian koala population. RT-PCRs were performed on koala samples collected from the Cape Otway region in Victoria, Australia to check for the prevalence of KoRV. RecKoRV Insertion site-specific PCRs were optimized and performed on a second set of samples which were collected from different regions in Victoria Australia and were negative for KoRV to detect the polymorphism of different RecKoRV loci. The design of these PCRs proved problematic with non-specific amplification, possibly due to the repetitive nature of the LTRs of retroviruses. Techniques such as inverse PCR may be necessary to analyze the insertion site variation of these RecKoRV loci. |
| first_indexed | 2025-11-14T20:57:57Z |
| format | Thesis (University of Nottingham only) |
| id | nottingham-74076 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-14T20:57:57Z |
| publishDate | 2023 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-740762025-02-28T12:27:27Z https://eprints.nottingham.ac.uk/74076/ The detection of polymorphism of RecKoRV Loci within the Victorian koala population Dudeja, Sukanya Koala Retrovirus (KoRV) is known to be the most recently acquired endogenous retrovirus and is still settling to its genomic parasitic lifestyle. KoRV has both infectious and endogenous (integrated into the host genome) forms. One hundred percent of the Koalas in northern Australia are positive for the virus. A higher proviral copy number per cell has been observed in Northern koalas due to endogenized KoRV compared to that in the south. The Koalas in southern Australia show a variability in the prevalence rate of the exogenous virus and a lower rate of KoRV induced disease. Southern Australian koalas earlier considered to be disease free or only having the exogenous counterparts of the virus, demonstrate a defective variant of KoRV known as Recombinant KoRV(RecKoRV). RecKoRV is formed due to the recombination between Phascolarctid Endogenous Retroelement (PhER) and KoRV. The presence of RecKoRV variants particularly in the founder population on the French island calls into question the existence of KoRV free animals. The difference in the KoRV profiles between the northern and the southern animals raises the possibility that these replication defective transcripts may be interfering with full length transcripts of the replication competent KoRV. The presence of RecKoRV variants particularly in the founder population and in the Victorian animals indicate that all southern animals have these variants. The aim of this study is to look at the polymorphism of the RecKoRV loci using integration site-specific PCRs to explore whether these are fixed or variable in the Victorian koala population. RT-PCRs were performed on koala samples collected from the Cape Otway region in Victoria, Australia to check for the prevalence of KoRV. RecKoRV Insertion site-specific PCRs were optimized and performed on a second set of samples which were collected from different regions in Victoria Australia and were negative for KoRV to detect the polymorphism of different RecKoRV loci. The design of these PCRs proved problematic with non-specific amplification, possibly due to the repetitive nature of the LTRs of retroviruses. Techniques such as inverse PCR may be necessary to analyze the insertion site variation of these RecKoRV loci. 2023-07-19 Thesis (University of Nottingham only) NonPeerReviewed application/pdf en arr https://eprints.nottingham.ac.uk/74076/1/MRes_Sukanya%20Dudeja_20418933.pdf Dudeja, Sukanya (2023) The detection of polymorphism of RecKoRV Loci within the Victorian koala population. MRes thesis, University of Nottingham. Retroviruses; Polymorphism; Koalas |
| spellingShingle | Retroviruses; Polymorphism; Koalas Dudeja, Sukanya The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title | The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title_full | The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title_fullStr | The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title_full_unstemmed | The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title_short | The detection of polymorphism of RecKoRV Loci within the Victorian koala population |
| title_sort | detection of polymorphism of reckorv loci within the victorian koala population |
| topic | Retroviruses; Polymorphism; Koalas |
| url | https://eprints.nottingham.ac.uk/74076/ |