Recent studies have revealed the presence of large numbers of endogenous viral elements, or EVEs, in eukaryotic genomes. Surprisingly perhaps was the discovery of RNA EVEs, from viruses whose replication cycle does not require chromosomal integration. To date, numerous examples of these non-retroviral EVEs have been identified.
In light of previous reports of EVEs present in the Aedes aegypti genome, we used a host-centred bioinformatics approach to undertake a more thorough analysis of the A. aegypti genome for RNA EVEs. BLAST analyses were performed on the genome using a dataset comprising 239 dsRNA viral proteins, 515 ssRNA(+) viral proteins and 296 ssRNA(-) viral proteins. In addition we also used 281 protein sequences from 112 ssRNA(-) viruses, recently identified in arthropods. Potential EVEs were translated and a reciprocal tBLASTn screen was undertaken against the non-redundant GenBank database to eliminate non-viral hits.
In total, 220 EVEs related to RNA viral sequences were identified with significant homology (E value ≤ 1x10-10), to viruses from the Rhabdoviridae (124 EVEs), Flaviviridae (56), Chuviridae (19), Orthomyxoviridae (7), Closteroviridae (1), Mesoniviridae (1), Bunyaviridae (3), and Reoviridae (3) families. Three EVEs were related to the unclassified Negev viruses, 2 others to unclassified dsRNA viruses and one to an unclassified ssRNA(-) virus.
Of the 56 flaviviral EVEs identified, interestingly 54 belonged to a single insect-specific flavivirus, whose genome could be almost completely reconstructed (89%), with 63% of the structural proteins and 97% of the non-structural proteins present. Some of these EVEs were also duplicated in tandem arrays within the genome.
This study may represent the largest number of non-retroviral EVEs found so far in any one genome. As more and more diverse viral genomes, genera and families are discovered, more EVEs will be identified, which can only widen our understanding of both viral evolution and viral-host co-evolution.