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

Ye Chen; Quanming Xu; Xiaomin Yuan; Xinxin Li; Ting Zhu; Yanmei Ma; Ji-Long Chen

doi:10.18632/oncotarget.22738

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Research Papers:

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

Ye Chen _, Quanming Xu, Xiaomin Yuan, Xinxin Li, Ting Zhu, Yanmei Ma and Ji-Long Chen

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Oncotarget. 2017; 8:110337-110349. https://doi.org/10.18632/oncotarget.22738

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Abstract

Ye Chen1, Quanming Xu1,2, Xiaomin Yuan1,2, Xinxin Li1, Ting Zhu1, Yanmei Ma1 and Ji-Long Chen1,3

1Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

2College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

3CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China

Correspondence to:

Ye Chen, email: [email protected]

Ji-Long Chen, email: [email protected]

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.

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Research Papers:

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

Abstract