Comparative study of Middle East respiratory syndrome coronavirus using bioinformatics techniques

Abstract

In this study, we collected 141 coding sequences of MERS-CoV from the National Center for Biotechnology and Information (NCBI), including the sequences isolated in Korea in 2015. We conducted the phylogenetic analysis using the Maximum Likelihood method to examine the overall variation patterns among the target sequences, and then, we divided the target sequences into 4 different groups according to occurred countries and host species. Using the codon analyzer named SimFluVar program, we analyzed the codon variation patterns in the wobble position among 4 groups. In order to investigate the effect of codon variations that can change the phenotype of target genes, we compared the transversional substitutions between the Korean-origin sequences and other groups. As a result, we found that the Korea-origin sequences showed very minor differences with those collected from the Saudi Arabia in 2015, whereas other groups which were collected from USA and UK in 2013 and 2014 showed more complicated differences. We also compared the Korea-origin sequences with those of camel-origin sequences, and we found that the substitution pattern was somewhat different with that of human-origin viruses.