Koala retrovirus, known as KoRV, is a condition strongly associated with diseases that cause infertility and blindness.
University of Queensland researcher Michaela Blyton said uncovering such patterns helps in learning how the disease is evolving and spreading, and how it can be contained through antiviral medication or koala breeding programs.
Her research has previously established the link between KoRV and chlamydia, cystitis and conjunctivitis, suggesting the virus weakens the animal's immune system.
The latest study with associate professor Keith Chappell found KoRV is only present in the genome of koalas from Queensland and NSW, while those in Victoria and South Australia appear to be free of the numerous subvariants.
The discovery strengthens the theory that the virus could be contributing to heightened disease levels in northern koala populations, Dr Blyton said.
"It might mean that in the short term, koala relocations in the north are limited so we're not introducing new virus subtypes into healthy populations," she said.
Dr Blyton said the findings are a step towards nullifying the impact of the disease, and "for now this is great news for a species facing threats on multiple fronts".
Koala numbers have fallen over the past decade due to land clearing, disease, and weather events induced by climate change.
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