Evolutionary Dynamics of Endogenous Feline Leukemia Virus in the Felis Genus Through the Lens of Genomics

Feline leukemia virus (Gammaretrovirus felleu) causes variable pathologies, partially modulated by its endogenous form (enFeLV). Although enFeLV is found in genomes of all species of the Felis genus, the limitations of transposable element sequencing have hindered a comprehensive characterization. In this study, we examined 17 felid genomes for enFeLV copies, confirming that enFeLV is restricted to the Felis genus. From the long-read genomes of Felis catus, Felis nigripes, and Felis chaus, we identified 73 solo LTRs, 64 copies with genic segments, and 4 atypical copies. These were annotated and characterized using recombination assessment, phylogenetic analysis, insertion dating, and Fisher's exact tests. All enFeLV copies shared a single origin, with insertions occurring within the last 3.5 million years, except for predicted recombinants. Copy distribution, dating, and the phylogenetic position of F. chaus copies reinforce the hypothesis of a recent introgression of enFeLV into this species. Furthermore, 41 copies exhibit identical LTR pairs and 14 retain intact open reading frames spanning the viral genome. Uneven evolutionary pressures across the enFeLV genome were evidenced by discrepancies between tree topologies of individual genes and the preferential loss of pol. We conclude that enFeLV has undergone a complex post-endogenization evolutionary history and urge additional studies of other endogenous retroviruses.