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Our paper by Garcia et al. about a novel detection method for endogenous virus-like elements (EVE) and the discovery of an EVE/host fusion gene is published in Virus Evolution!

The hidden diversity of ancient bornaviral sequences from X and P genes in vertebrate genomes 
Bea Clarise B Garcia, Yahiro Mukai, Keizo Tomonaga, Masayuki Horie*

Endogenous viral elements (EVEs) are heritable virus-derived gene sequences in eukaryotic genomes, which are generated by the integration of viral sequences. Many EVEs were integrated into host genomes more than several million years ago, and therefore they can be precious sources to understand ancient viruses as "molecular fossils" of past viral infections. Furthermore, some EVEs are also known to have physiological functions in the host organisms, providing insights into genetic novelty as well as co-evolution between viruses and their hosts.

To date, EVE detection has relied solely on sequence similarity searches, such as tBLASTn, which uses modern viral sequences as queries. Thus, EVEs that do not have significant sequence similarity to modern viruses cannot be detected, even if they are present in the eukaryotic genomes.

We have previously performed comprehensive detection of EVEs derived from bornaviruses, which are RNA viruses (endogenous bornavirus-like sequences: EBL sequences). The endogenization of EBLs was reported to occur reverse-transcription and integration of viral mRNA by LINE-1, a retrotransposon in the host cells. Bornaviruses have six genes, N, X, P, M, G, and L. Of these, EBL sequences derived from the N, M, G, and L genes are relatively abundant, whereas EBLs derived from the X/P gene are very rare. Why are only EBLs derived from the X/P gene rarely found? We hypothesized that many X/P gene-derived EBL sequences exist but cannot be detected because there is no significant sequence similarity between them and the X/P genes of existing viruses due to the rapid evolution of X/P genes.

In this study, we developed a new method for detecting EBL sequences by focusing on the "read-through transcription" that occurs during mRNA expression of bornaviurses. As a result, we show a series of evidnece that many X/P-derived EBL sequences exist in the genomes of bats and rodents. Furthermore, we found that an X/P-derived EBL in the miniopterid bat genomes and the bat gene ZNF451 are expressed as a fusion gene.

The EVE search strategy developed in this study and the findings are useful for future EVE research and will contribute to our understanding of