Selection of RNA aptamers targeting the 3’ untranslated region of the West Nile Virus genome

West Nile Virus (WNV) is a positive polarity, single-stranded RNA virus that causes West Nile fever, for which no cure has been found to date. WNV, like other RNA viruses, needs to compact all the information to complete the viral cycle into a very small genome. Beyond the information that is stored in the primary structure, the genome of RNA viruses bear functional structural domains that perform multiple essential functions for the viral cycle. In WNV, several of these functional domains are found in the 3'UTR region. Based on the importance of these functional domains, in this work, RNA aptamers have been studied as a possible therapeutic agent. Aptamers are oligonucleotides with the ability to efficiently bind to a molecule, not taking into account only the sequence of the target but also its structural motifs. In this work, various aptamers directed against the 3'UTR region of WNV, which could potentially inhibit processes of the WNV viral cycle, have been analysed and selected by in silico analysis. We have also studied certain characteristics of the SL-I structural element of the WNV 3’UTR, which shows a high chance of interacting with host molecules. This work will lead further studies towards the generation of antiviral aptamers against WNV and a deeper understanding of WNV interaction with the host cell.