Comprehensive analysis of the codon usage patterns of polyprotein of Zika virus

Zika virus (ZIKV) is a mosquito-borne virus in the family Flaviviridae, and the massive outbreak of ZIKV has endangered public health. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. In this study, 90 ZIKV isolates were used for a comprehensive analysis on the codon usage patterns. The overall codon usage among ZIKV strains is similar and slightly biased. The value of effective number of codons (ENC) showed that the overall extent of codon usage bias in ZIKV is relatively low. Nucleotide analysis showed that the overall codon usage is biased toward A- and G-ending codons. The phylogenetic analysis indicated that their independent evolutionary origins from a common ancestor. The RSCU analysis showed that the codon usage pattern of ZIKV is more similar to that of Homo sapiens. Correlation analysis, Correspondence analysis, ENC-GC_3S plot, and PR2 plot indicated that the codon usage patterns of the viruses are not only influenced by mutational pressure but also by natural selection, but neutrality plot analysis showed that the latter plays a major role. These results built the base for further research on the molecular evolution of ZIKV.