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. 2018 Aug 14;19(8):2397.
doi: 10.3390/ijms19082397.

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Xu Zhang  1 , Yuchen Cai  2 , Xiaofeng Zhai  3 , Jie Liu  4 , Wen Zhao  5 , Senlin Ji  6 , Shuo Su  7 , Jiyong Zhou  8
Affiliations

Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses

Xu Zhang et al. Int J Mol Sci. .

Abstract

Rabies virus (RABV) and other lyssaviruses can cause rabies and rabies-like diseases, which are a persistent public health threat to humans and other mammals. Lyssaviruses exhibit distinct characteristics in terms of geographical distribution and host specificity, indicative of a long-standing diversification to adapt to the environment. However, the evolutionary diversity of lyssaviruses, in terms of codon usage, is still unclear. We found that RABV has the lowest codon usage bias among lyssaviruses strains, evidenced by its high mean effective number of codons (ENC) (53.84 ± 0.35). Moreover, natural selection is the driving force in shaping the codon usage pattern of these strains. In summary, our study sheds light on the codon usage patterns of lyssaviruses, which can aid in the development of control strategies and experimental research.

Keywords: RABV; codon usage bias; lyssaviruses; natural selection.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Species-specific comparative analysis of ENC (effective number of codons) values of each lyssavirus coding sequences. C means complete genome. Green, red, blue, orange, black and grey represent LBV (Lagos bat virus), DUVV (Duvenhage virus), ABLV (Australian bat lyssavirus), EBLV-1 (European bat lyssavirus 1), MOKV (Mokola virus) and RABV (rabies virus), respectively.
Figure 2
Figure 2
Principal component analysis. Species-specific PCA plots were constructed for whole genome and individual lyssavirus coding sequences. (A) Whole genome; (B) N; (C) P; (D) M; (E) G; (F) L. The color coding is the same as that of (A).
Figure 3
Figure 3
ENC-GC3 plot. (A) Whole genome; (B) N; (C) P; (D) M; (E) G; (F) L. The color coding is the same as that of (A).
Figure 4
Figure 4
PR2 plot analysis. (A) LBV; (B) DUVV; (C) ABLV; (D) EBLV-1; (E) MOKV; (F) RABV. W means whole genome. Black, red, orange, blue, purple and green represent whole genome, N gene, P gene, M gene, G gene and L gene, respectively.
Figure 5
Figure 5
Neutrality plot analysis. (A) Whole genome; (B) N; (C) P; (D) M; (E) G; (F) L. The colour coding is the same as that of (A).
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