Genome codon bias analysis of dengue virus type 1

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.