Retroviruses that colonize the host germline can be passed on as inherited genetic variants. The koala (Phascolarctos cinereus) is currently experiencing germline colonization by two retroviruses, the koala retrovirus (KoRV) and phaCin-ß. We analyzed the integration site segregation and diversity of endogenous KoRV, phaCin-ß, and the related phaCin-ß-like in large koala pedigrees from the San Diego Zoo Wildlife Alliance (SDZWA) and seven European Zoos (EUZ). The use of multigenerational pedigrees and the inclusion of life history and health information for each individual koala revealed elimination of retroviruses from proto-oncogenes and the generation and spread of new germline integrations. For the 55 triads examined, 21 unique integrations were identified in koalas but were absent in their parents. Retroviral integrations associated with leukemia, fertility and longevity were used to estimate genetic risk scores and develop a longevity breeding index to minimize neoplasia

Retroviruses that colonize host germline DNA can be passed on as inherited genetic variants. The koala (Phascolarctos cinereus) is currently experiencing germline colonization by two retroviruses, the koala retrovirus (KoRV) and phaCin-ß. Germline and somatic integrations, particularly of KoRV, are linked to high koala cancer rates, disruption of gene function with integrations occurring frequently in or near active proto-oncogenes. The process and consequences of KoRV germline colonization have generally been studied without host family lineage information. We analyzed the integration site segregation and diversity of endogenous KoRV, phaCin-ß, and phaCin-ß-like (an older heritable virus related to phaCin-ß) in large koala pedigrees from the San Diego Zoo Wildlife Alliance (SDZWA) and seven European Zoos (EUZ). The entire living population of the SDZWA and cryopreserved tissues of koalas (n=91) representing 46 triads and four generations were whole-genome Illumina sequenced at an average of 50-fold coverage. In addition, 20 koala individuals, representing 9 triads and three generations, of EUZ were enriched for KoRV integration sites and PacBio sequenced. SDZWA koalas were most genetically similar to Northern Australian koalas, with clear evidence of translocations to EUZ. The use of multigenerational pedigrees and the inclusion of life history and health information for each individual koala revealed germline integrated retroviruses eliminated from the living population, as proto-oncogene integrations, and the generation and spread of new germline integrations. For the 55 triads examined, 21 unique integrations were identified in koalas but were absent in their parents. These findings were supported by high sequence coverage. In six cases, these new integrations were confirmed in subsequent offspring. Retroviral integrations associated with leukemia, fertility and longevity were used to estimate genetic risk scores and develop a longevity breeding index to minimize neoplasia risk in the captive koala breeding population. A koala with a high estimated leukemia genetic risk score subsequently died of leukemia as predicted.