Genome Wide Folding Structure Selection in Ebola Virus

Ebola is a virus with five subtypes and causes a severe, often fatal form of hemorrhagic fever disease in human and/or nonhuman primates; currently there is no approved vaccine or medicine is available for Ebola. It is known that mRNA stem-loops can affect and regulate various gene expression steps, and consequently affect viral fitness. In this work, we performed a large scale analysis to detect selection for local folding strength in 465 Ebola virus genomes, from five subtypes. We recognized positions that undergo selection for strong/weak folding by comparison to randomized models, for each subtype. In addition, we compared the significantly preserved intervals of different subtypes to discover shared positions, which may play important role in the viral life cycle, promoting development of future anti-viral therapeutic approaches and vaccines. Our analysis suggests that up to ~ 2.5% of positions in the viral genomes sequences undergo evolutionary selection for strong/weak folding, and 2-17% of them show significant preservation inside the subtype, and 15% of those are shared by at least two subtypes.