Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus.

// Ye Chen 1 , Quanming Xu 1, 2 , Xiaomin Yuan 1, 2 , Xinxin Li 1 , Ting Zhu 1 , Yanmei Ma 1 and Ji-Long Chen 1, 3 1 Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China 2 College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China 3 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China Correspondence to: Ye Chen, email: fafuchenye@163.com Ji-Long Chen, email: chenjl@im.ac.cn Keywords: MERS-CoV; codon usage pattern; mutation bias; natural selection Received: September 19, 2017      Accepted: October 27, 2017      Published: November 27, 2017 ABSTRACT Middle East Respiratory Syndrome Coronavirus (MERS-CoV), which first broken out in Jeddah in 2012, causes a severe acute respiratory illness with a high mortality rate. To better understand the molecular characteristics of isolated MERS-CoV genomes, we first analysed the codon usage pattern of the zoonotic MERS-CoV strains comprehensively to gain an insight into the mechanism of cross-species transmission. We found that MERS human/camel isolates showed a low codon usage bias. Both mutation and nature selection pressure have contributed to this low codon usage bias, with the former being the main determining factor. We also observed that gene function, evolution time and the different host species of the virus all contributed to the bias of MERS-CoV, to some extent. Additionally, the codon usage pattern of MERS-CoV isolates is different from other related Nidovirales viruses isolated from bats and hedgehogs. In the future, more epidemiological surveys are required to examine the factors that resulted in the emergence and outbreak of this virus.