Expansion of a retrovirus lineage in the koala genome

Retroviruses have left their legacy in host genomes over millions of years as endogenous retroviruses (ERVs), and their structure, diversity, and prevalence provide insights into the historical dynamics of retrovirus-host interactions. In bioinformatic analyses of koala (Phascolarctos cinereus) whole-genome sequences, we identify a recently expanded ERV lineage (phaCin-beta) that is related to the New World squirrel monkey retrovirus. This ERV expansion shares many parallels with the ongoing koala retrovirus (KoRV) invasion of the koala genome, including highly similar and mostly intact sequences, and polymorphic ERV loci in the sampled koala population. The recent phaCin-beta ERV colonization of the koala genome appears to predate the current KoRV invasion, but polymorphic ERVs and divergence comparisons between these two lineages predict a currently uncharacterized, possibly still extant, phaCin-beta retrovirus. The genomics approach to ERV-guided discovery of novel retroviruses in host species provides a strong incentive to search for phaCin-beta retroviruses in the Australasian fauna.

Automated summary

Endogenous retroviruses (ERVs) have been preserved in host genomes for millions of years, providing insights into the interaction between retroviruses and hosts. The identification of a recently expanded ERV lineage called phaCin-beta in koalas suggests the presence of a possibly still existing phaCin-beta retrovirus. The use of genomics approaches to search for novel retroviruses in host species is highly valuable.