Low prevalence of flying fox gammaretroviruses suggests exogenous transmission among Pteropus species in Australia

Abstract Retroviruses in Australian Pteropus species (flying foxes) remain poorly understood, creating gaps in knowledge regarding their impact on wildlife health and risks to human and ecological health. This study aimed to address this gap using a quantitative polymerase chain reaction (qPCR) assay that targeted selected flying fox gammaretroviruses in 962 packed blood cell samples. This is, to our knowledge, the first study to examine the prevalence of these viruses in all four species of Australian Pteropus. Proviral prevalence was generally low (Pteropus alecto 8.1%; Pteropus conspicillatus 7.9%; Pteropus scapulatus 3.8%; Pteropus poliocephalus 2.7%). Species was the only significant predictor of viral prevalence after accounting for age, sex and seasonality. Pteropus poliocephalus showed significantly lower prevalence than P. alecto (odds ratio = 0.31, 95% confidence interval: 0.15–0.64, p = 0.002). To contextualize these findings, we screened publicly available genomic and sequencing datasets, which revealed only short, low-identity matches to the flying fox gammaretroviruses sequence. Although short-read shotgun sequencing has limited sensitivity, competitive mapping, genomic screening and qPCR screening results support the hypothesis that these are low-prevalence exogenous gammaretroviruses circulating in Australian flying foxes.