Screening Envelope Genes Across Primate Genomes Reveals Evolution and Diversity Patterns of Endogenous Retroviruses

Endogenous Retroviruses (ERVs) are integrated into the host DNA as result of ancient germ line infections, majorly by extinct exogenous retroviruses. In fact, vertebrates’ genomes contain thousands of ERV copies, providing “fossil” records for the ancestral retroviral diversity and its evolution within the host. Like exogenous retroviruses, ERV proviral sequence consists of gag, pro, pol , and env genes flanked by long terminal repeats (LTRs). Among them, the characterization of env gene changes over time allows both to understand ERVs evolutionary trajectory and possible physiological and pathological domestication. To this aim, we reconstructed 32 Env sequences representing the prototypes of these ancestral proteins in Class I, Class II, and Class III HERVs. These reconstructed Envs were then employed in diverse methods comprising similarity search, phylogenetic analysis, and examination of recombination events occurred within primates’ genomes that were applied to 43 primate species across the Catarrhini and Platyrrhini parvorders. Through a comprehensive pipeline we reconstitute a phylogenetic distribution of ERV based specifically on the env genes, showing that the ERVs have been prevalent and widely distributed across the primate lineage. We observed for the first time the presence of the HML groups in the Platyrrhini parvorder, possibly indicating initiation of spread of HML supergroup before the split between New World Monkeys (NWM) and Old World Monkeys (OWM) i.e. even before 40 mya. Importantly, we confirmed notable interclass and intra-class env recombination events showing the phenomenon of “ env snatching” among primates’ ERVs. As a result, we demonstrate that tracing the diversity patterns of ERVs’ env provides relevant insights into the retroviral evolutionary history of ERVs in Catarrhini and Platyrrhini parvorders. Overall, our findings reveal that env recombination contributes to the diversification of ERVs, thereby broadening our comprehension of retroviral and primate evolution.