Abstract
Dengue viruses (DENV) are the most common mosquito-borne RNA virus with high variation and adaptation in tropical and subtropical regions. Exploration of codon usage bias of DENV can be significant to understand their genetic variation and adaptation. In the study, the codon usage pattern of dengue virus type 1 (DENV-1) was analyzed by using codonW, CUSP and SPSS. The extent of codon preference of DENV-1 is weak with a 50.57 mean value of ENC, indicating that the DENV-1 genome has low codon bias. Of the 18 optimal codons of DENV-1, 13 end in A/U, with A ending in the majority. The result shows that DENV-1 prefers A-ended codons, and their codon bias is influenced more by natural selection than by mutations selection, as revealed by ENC-plot and neutrality analysis. Furthermore, comparison of codon usage bias between DENV-1 and host showed that codon usage pattern of DENV-1 is more similar to Home sapiens instead of Aedes aegypti or A. albopictus. Our findings contributed to understanding of the evolution of the DENV-1. Key words: Dengue virus type 1, Codon bias, RSCU, ENC-plot, neutrality-plot.
Highlights
Dengue virus (DENV) is a single-stranded positive-sense RNA virus belonging to the Flavivirus genus
To determine whether codon bias exists in the genome of dengue virus type 1 (DENV-1), the effective codon usage (ENC) was measured
It can be considered that the codon preference of DENV-1 is weak, that is, the use of each codon is more uniform
Summary
Dengue virus (DENV) is a single-stranded positive-sense RNA virus belonging to the Flavivirus genus. Dengue fever is the most important viral-borne disease in clinical practice, with 96 million cases of apparent infection each year among nearly four billion people at risk in 128 countries (Bhatt et al, 2013). Since 1978, the first outbreak of dengue fever in China, it has occurred every few years and has become a serious public health threat in Southern China (Sun et al, 2014; Hu et al, 2017). The genome of DENV-1 has 10735bp, which contains a 10179bp single open reading frame encoding Capsid protein, Membrane glycoprotein precursor, Membrane glycoprotein, Envelope protein and seven non-structural (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) proteins (Perera and Kuhn, 2008; Byk and Gamarnik, 2016)
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