Abstract
Endogenous viruses are viral genomes that became integrated into the germline genome of their hosts and vertically inherited, from generation to generation, in host populations. Recent advances in genome sequencing have triggered the discovery of many non-retroviral endogenous viruses, showing that all types of eukaryotic viruses can become endogenous. This article first explains some of the methods that are used to systematically detect endogenous viruses in eukaryotic genomes and provides a detailed account of the various ways through which these viruses can shape the evolution of their host's genomes. It then shows how the discovery of endogenous viruses can shed new light on our knowledge of the origin and evolution of current viruses, as well as on the ecology of virus-host interactions. Finally, several research directions are proposed, and it is argued that an approach coupling paleovirology and virology can reveal the full complexity of the interactions between endogenous viruses, current viruses and their hosts.
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