A High Frequency of Detection of Recombinant Koala Retrovirus (recKoRV) in Victorian Koalas Suggests Historic Integration of KoRV

Recombinant koala retrovirus (recKoRV) is a recently discovered variant of koala retrovirus (KoRV), which likely emerged due to the insertion of another retrovirus (likely Phascolartus endogenous retrovirus) into the backbone of KoRV. KoRV endogenisation was thought to be ongoing in Victoria based on the low prevalence of the virus based on molecular detection of the pol gene, however recKoRV was not incorporated into the previous KoRV diagnostic test results. In this study, a new 5'-region-based PCR assay was developed, capable of detecting both intact KoRV and recKoRV. Using this assay, 319 archived DNA samples from 287 Victorian koalas were retested to investigate KoRV endogenisation. We found a 98.3% (282/287) of these samples were positive for the KoRV-5' fragment, the majority of which were KoRV-pol negative (222/287) on prior testing. Our findings demonstrate extensive KoRV integration into the Victorian koala populations, suggestive of a historic presence of KoRV in Victorian koalas. This finding makes biological sense relative to the translocation history of Victorian koalas, compared to the prior paradigm of ongoing endogenisation, and provides new epidemiological and practical management implications.