Abundance, diversity and activity of endogenous retroviruses in the slow loris.

Abstract

Endogenous retroviruses (ERVs) constitute a significant fraction of vertebrate genomes and serve as genomic records of past retroviral infections, while also influencing host biology through regulatory co-option and, in some cases, ongoing retrotransposition. Despite extensive examination of ERVs in haplorrhine primates, equivalent analyses in strepsirrhines remain absent, leaving a substantial gap in our understanding of ERV diversity and evolutionary dynamics across the primate order. Here, we present the first comprehensive characterisation of ERVs in a strepsirrhine primate, identifying 15 Loris Endogenous Retrovirus (LERV) families encompassing 34 subfamilies and over 6,000 insertions in the Nycticebus coucang reference genome. Phylogenetic analyses resolved LERVs into three retroviral genera: betaretroviruses (LERV1-4), type-D betaretroviruses (LERV5-9), and gammaretroviruses (LERV10-15). LERV2a shows multiple hallmarks of recent or potentially ongoing retrotransposition, including a median insertion age of zero, a high proportion of identical LTR pairs, dN/dS ratios comparable to the active retrovirus HTLV, and insertional polymorphism between two conspecific genomes. Comparative genomic screening across Lorisidae revealed that LERV subfamily distribution broadly mirrors estimated insertion ages, with progressively fewer subfamilies detected in more distantly related species. These findings establish a detailed foundation for understanding retroviral evolution in Strepsirrhini and reveal that ongoing retroviral activity is not restricted to haplorrhine primates.