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J Gen Virol. 2019 Jul 22. doi: 10.1099/jgv.0.001304. [Epub ahead of print]

Genetic diversity of Koala retrovirus env gene subtypes: insights into northern and southern koala populations.

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2Laboratory Sciences & Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh.
1School of Veterinary Science, The University of Queensland, Queensland, Australia.
3School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.
4School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK.
5School of Biological Sciences, The University of Queensland, Queensland, Australia.
6School of Animal, Rural and. Environmental Sciences, Nottingham Trent University, Nottingham NG1 4FQ, UK.
7Advanced Data Analysis Centre (ADAC), University of Nottingham, Nottingham, UK.


Koala retrovirus (KoRV) is a recently endogenized retrovirus associated with neoplasia and immunosuppression in koala populations. The virus is known to display sequence variability and to be present at varying prevalence in different populations, with animals in southern Australia displaying lower prevalence and viral loads than northern animals. This study used a PCR and next-generation sequencing strategy to examine the diversity of the KoRV env gene in both proviral DNA and viral RNA forms in two distinct populations representative of the 'northern' and 'southern' koala genotypes. The current study demonstrated that the full range of KoRV subtypes is present across both populations, and in both healthy and sick animals. KoRV-A was the predominant proviral subtype in both populations, but there was marked diversity of DNA and RNA subtypes within individuals. Many of the northern animals displayed a higher RNA viral diversity than evident in their proviral DNA, indicating relatively higher replication efficiency of non-KoRV-A subtypes. The southern animals displayed a lower absolute copy number of KoRV than the northern animals as reported previously and a higher preponderance of KoRV-A in individual animals. These discrepancies in viral replication and diversity remain unexplained but may indicate relative protection of the southern population from KoRV replication due to either viral or host factors and may represent an important protective effect for the host in KoRV's ongoing entry into the koala genome.


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