Free, H. B. | Search bioRxiv

bioRxiv2025

Novel Endogenous Retrovirus in the Slow Loris

Endogenous retroviruses (ERVs) are the result of an exogenous infectious retrovirus becoming integrated within the host genome through infection of germline cells. The majority of ERV research has been conducted on humans and other great apes and research of them within other primates can provide unique insights. Screening the genome of two endangered slow lorises Nycticebus bengalensis and N. coucang with a previously identified LTR, a novel ERV was identified within their genomes with varying levels of completeness and numerous solo LTRs. Phylogenetic analysis of the genes of this ERV indicates that it is a betaretrovirus most closely related to HERV-K. Despite being closely related to HERV-K, the ERV does not appear to be within humans and is only found in Asian lorises and absent in all other primates. Due to the staggering similarity of viral insertions of this ERV between the two species of slow lorises, indicates that the current N. coucang genome may actually be a hybrid of the two species or a N. bengalensis from a different population as the reference genome. This study highlights that studying ERVs in more distant primates provides information about the genomes and evolution of these species as well as viral evolution.

genomics↗

bioRxiv2024

Novel Endogenous Retroviruses in Anura

Endogenous retroviruses (ERVs) represent remnants of past retroviral infections and have had a pivotal role in vertebrate evolution, contributing toward the generation of novel genes and regulatory elements. The majority of ERV research to date has had a mammalian focus; Anurans (the order of amphibians consisting of frogs and toads) are comparable in genome size and number of extant species and yet very few ERVs have been described in this order. Under the current classification, alpharetroviruses appear to be avian-specific; here we screened 47 publicly available Anuran genomes for alpharetroviruses using a bioinformatic pipeline. Both truncated and full-length ERV elements were identified through this screening process which were represented by multiple loci. Ten families of novel Anuran ERVs (AnERV1-10) with intact viral genes were identified in 11 anuran species, some of which are shared between multiple species. Furthermore, based on conserved domain and phylogenetic analysis, all ten novel ERV families appeared in recombined states. This included two families with alpharetrovirus classified Env proteins, although the majority had epsilonretrovirus classified Pol and gammaretrovirus classified Env proteins. These findings extend the pattern of recombination presented in two other Anuran ERVs and adds to the complex evolutionary history of retroviruses. These results suggest that analysis of other vertebrate groups beyond the mammals would provide new information on the presence and state of ERVs, providing further evidence of the modes of ERV evolution within host genomes and their role in the diversification of the vertebrate tree of life.

genomics↗