Koala retrovirus load and non-A subtypes are associated with secondary disease among wild northern koalas

Koala Retrovirus (KoRV) has been associated with neoplasia in the vulnerable koala (Phascolarctos cinereus). However, there are conflicting findings regarding its association with secondary disease. We undertook a large-scale assessment of how the different KoRV subtypes and viral load are associated with Chlamydia pecorum infection and a range of disease pathologies in 151 wild koalas admitted for care to Currumbin Wildlife Hospital, Australia. Viral load (KoRV pol copies per ml of plasma) was the best predictor of more disease pathologies than any other KoRV variable. The predicted probability of a koala having disease symptoms increased from 25% to over 85% across the observed range of KoRV load, while the predicted probability of C. pecorum infection increased from 40% to over 80%. We found a negative correlation between the proportion of env deep sequencing reads that were endogenous KoRV-A and total KoRV load. This is consistent with suppression of endogenous KoRV-A, while the exogenous KoRV subtypes obtain high infection levels. Additionally, we reveal evidence that the exogenous subtypes are directly associated with secondary disease, with the proportion of reads that were the endogenous KoRV-A sequence a negative predictor of overall disease probability after the effect of KoRV load was accounted for. Further, koalas that were positive for KoRV-D or KoRV-D/F were more likely to have urogenital C. pecorum infection or low body condition score, respectively, irrespective of KoRV load. By contrast, our findings do not support previous findings that KoRV-B in particular is associated with Chlamydial disease. Based on these findings we suggest that koala research and conservation programs should target understanding what drives individual differences in KoRV load and limiting exogenous subtype diversity within populations, rather than seeking to eliminate any particular subtype.Author summary: With the koala now listed as vulnerable in Australia and local population declines of greater than 80% in part due to disease, it is now critically important to establish the role koala retrovirus (KoRV) plays in disease to guide future conservation efforts. While KoRV has previously been linked to increased rates of cancer in koalas, it is less clear whether it also increases the koalas’ susceptibility to other infections. We assessed how KoRV is associated with Chlamydia and a range of other diseases. We found that the amount of KoRV circulating in the blood was strongly associated with disease. KoRV exists as both a heritable virus in the koala’s genome and as an infectious virus. We found that the infectious forms of the virus are associated with higher levels of KoRV in the blood and directly with disease. These findings highlight the major role KoRV is likely to play in the high rate of disease in northern koala populations, which is contributing to their decline. We suggest that koala research and conservation should target understanding what drives differences among koalas in the amount of KoRV circulating in the blood and on limiting the spread of different KoRV subtypes between populations.