Statistical Model for Bioinformatics Analysis of Synonymous Codon Usage Bias in Dengue Type 2 Virus

Dengue virus serotype 2 (DENV-2) infection seldom occurred in mainland China in the past three decades. After about ten years' silence, DENV-2 reemerged in south China in 2010. Previous reports have suggested that the negative selection, RNA recombination were the most driving forces for DENV evolution. However, the pattern of DENV codon usage was lacking and its role in evolution remains unknown. In this report, we analyzed the synonymous codon usage pattern of DENV-2 coding region. Results show all preferred codons in DENV-2 are ended with A/G nucleotide, which constitute the majority of nucleotide composition in DENV-2 coding region. Mutation pressure rather than nature selection is the main power driving the synonymous codon usage bias. The complementary pattern of codon usage bias between DENV-2 and human cell suggests an important involvement of host cell in the codon usage bias. There is nothing special for DENV-2 isolated in 2010 as to codon usage bias. These bioinformatics analyses of synonymous codon usage bias in DENV-2 provide more information for better understanding DENV evolution and pathogenicity.