A high frequency of detection of koala retrovirus fragments 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 recombination with another retrovirus (such as Phascolarctos endogenous retrovirus). KoRV spread and endogenization in Australia were thought to be ongoing in a north to south direction given the low prevalence of the virus in southern koala populations, based on molecular detection of the <i>pol</i> gene. However, recKoRV has highlighted that fragments of KoRV with the <i>pol</i> region missing are present within southern koalas. In this study, a new 5'-region-based KoRV PCR assay was developed, capable of detecting both intact KoRV and all known variants of recKoRV. Using this assay, 319 archived DNA samples from 287 Victorian koalas were retested to investigate KoRV endogenization. We found 98.3% (282/287) of these samples were positive for the KoRV-5' fragment, the majority of which were KoRV-<i>pol</i> 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 low virus prevalence, and provides new epidemiological and practical management implications.