Analysis of the codon usage pattern in Middle East Respiratory Syndrome Coronavirus - PubMed (original) (raw)

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

Ye Chen et al. Oncotarget. 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.

Keywords: MERS-CoV; codon usage pattern; mutation bias; natural selection.

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Conflict of interest statement

CONFLICTS OF INTEREST Competing financial interests: The authors declare no competing financial interests.

Figures

Figure 1

Figure 1. The relative abundance values of the 16 dinucleotides

The different colours represent the different dinucleotides. The red dotted line indicates that the relative abundance value of a dinucleotide is 1.

Figure 2

Figure 2. The plots of ENC values against GC3s values for MERS-CoV and MERS-CoV related strains

All the points corresponding to human, camel isolated MERS-CoV strains and bat and hedgehog(erinaceus) isolated CoV were labelled in circle, square, triangle, and rhombus, respectively.

Figure 3

Figure 3

(A) The neutral analysis of GC3s against GC12s. (B) The evolutionary analysis of the GC3s and GC12s values. The solid line represents the regression line.

Figure 4

Figure 4. CA of MERS-CoV human/camel isolates

Each viral gene is displayed in a 3-dimensional representation. The X, Y and Z-axes have arbitrary scales generated by the CA and the weight of each codon in these axes varies in different segments. The codon usage trends with time of the viral isolates are indicated by different colours. The different hosts of the MRES-CoV isolates are indicated by different shapes. (A), (B), (C), (D) and (E) represents the 3D graph of the M, N, ORF1ab, S and the complete genome, respectively, using the CA data.

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