Tracing ancient viral footprints: a comprehensive study of endogenous viral elements in Bombus species

Endogenous Viral Elements (EVEs) are viral sequences integrated into the host germline and passed to offspring. Most virus types can integrate, often with the help of host retroelements, especially for non-retroviral RNA viruses. It is known that EVEs are widespread across insect species and related to an extensive range of virus taxa, many of which might share similar evolutionary origins. Bombus bees are essential pollinators that have been experiencing worldwide colony declines in recent decades. Therefore, uncovering genetic elements and pathways to better understand host–pathogen interactions is crucial in conserving biodiversity. Non-retroviral Integrated RNA Virus Sequences (NIRVS) were widespread in Bombus genomes, without a clear correlation between genome size and the number of EVEs. Most of the EVEs were single-copy, ranging from 111 to 3,729 bp with an average of 504 bp. Most of them share similarities with unclassified viruses and known viruses belonging to the families Partitiviridae and Virgaviridae, as well as the order Martellivirales. We observed that over 25% of the NIRVS contain conserved domains, with larger ones having a higher probability of functional annotation. Most NIRVS with conserved domains contained Polymerase-related motifs, the most represented group of domains among Bombus species. A comprehensive analysis of the NIRVS sharing pattern suggests that they are more likely to be inherited from a common ancestor than to result from integration events after speciation. Also, viral elements are widely conserved amongst species. Furthermore, we investigated transcriptional activity and the potential of the NIRVS to function as a priming agent for antiviral responses against exogenous viruses. On that note, most NIRVS in Bombus are transcriptionally active, and some share 15 nt of contiguity with exogenous bee viruses and could potentially be used as templates for piRNA production. The integration of non-retroviral RNA viruses into bumblebee genomes is ancient and represents a dynamic evolutionary process in which many viral elements are conserved, shared, and may be functionally active in Bombus bees.