Analysis of sequence and secondary structure conservation of MERS-CoV 5’-UTR.
GenBank at NCBI is the NIH genetic sequence database that has compiled complete MERS-CoV genomes. 252 complete viral genomes were isolated from humans in 11 countries including Saudi Arabia, United Arab Emirates, Jodan, Quatar, Oman, Egypt, United Kingdom, USA, South Korea, Thailand, and China. 74 complete genomes were isolated from camels in Saudi Arabia and 132 from dromedary camels in United Arab Emirates. The initial alignment of sequence was performed using EMBL-EBI Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo/). The most complete sequence for 5’-UTR were further analyzed using LocARNA program (11, 12)(http://rna.informatik.uni-freiburg.de/) to determine the conservation of both sequence and secondary structure of viral RNA. LocARNA performs simultaneous alignment and folding of multiple RNAs. It implements the state-of-the-art light-weight alignment algorithm with ensemble-based sparsification to improve the accuracy of analysis.