The trajectory of KoRV-A Evolution Indicates Initial Integration into the Koala Germline Genome Near Coffs Harbour [Adelaide DNA-seq]

Koala Retrovirus-A is a gamma-retrovirus sweeping wild koalas via a combination of horizontal and vertical transfer, contributing substantial genomic diversity across and even within koala populations. While studies have estimated KoRV-A's integration into the koala genome occurred 120–50,000 years ago, the origin and spread patterns of its endogenization remain unclear. Here, we analyze KoRV-A germline insertions using whole-genome sequencing data from 405 wild koalas, encompassing nearly the full koala habitat range. We map a trajectory of KoRV-A evolution and propose that KoRV-A first entered the koala germline genome near Coffs Harbour. As KoRV-A spread, replication-competitive subtypes emerged, two of which recombined with an ancient endogenous retrovirus, PhER, resulting in distinct recombination variants across northern and southern koala populations. Additionally, we identified a geographic barrier north of Sydney, which has slowed the southward spread of KoRV-A into Sydney and beyond. To investigate the evolution of KoRV-A, we performed short-read DNA-seq and RNA-seq on six Adelaide koalas. These data was combined with DNA-seq and RNA-seq from our previous studies (Yu et al., 2019 and Yu et al., 2024) and the Koala Genome Survey.