Retroviruses have two ways in which they can spread; horizontal transfer between individuals, or vertical transmission from parent to child. The latter requires integration of the viral genome into the host’s germline; ensuring that it is inherited. These germline viral copies are referred to as endogenous retroviruses (ERVs) and are generally seen as evolutionary remnants of past viral infection and restricted to the vertebrate genomes. The current assumption is that ERVs tend to horizontally transfer between individuals, and that intact copies of ERVs in the genome are derived from recent infections.
However, when we searched for similar elements outside vertebrates based on the homology to their evolutionary cousins, namely, gypsy LTR retrotransposons, we found that they are ubiquitously present in metazoan genomes, including ancient animals such as cnidarians, ctenophores and tunicates. Phylogenetic analysis revealed that ERVs have been co-evolving with the host organisms throughout the metazoan evolution. Thus, contrary to the previous assumption, ERVs have been actively transmitting primarily through vertical transfer. We discuss possible mechanisms through which ERVs spread in this way, and how host organisms may restrict their activities.