Characterization of codon usage pattern and evolutionary changes of Human Enterovirus 71 in China

Enterovirus 71 (EV71) is a common etiological agent of hand, foot and mouth disease (HFMD) in children, which caused large outbreaks in mainland China in 2008. However, the genetic information of EV71 strains circulating in China is limited. Here, we performed a systematic evolutionary and codon usage bias analysis of EV71. The result shows that the overall extent of codon usage bias in EV71 is low (ENc = 56.696), and natural selection, mutation pressure, nucleotide compositions and host shape the codon usage patterns of EV71, with natural selection being more important than the others. We also found EV71 breaking out in large scale in 2008, the codon usage pattern of the virus isolated from China has change a lot compare the previous isolates, and after 2008, three different codon usage patterns were popularized in China. In the end, we've confirmed that C2 isolates has outbreak in China before 2000 through codon usage analysis for the first time. In conclusion, our results provide useful insights into the evolutionary relationships of EV 71.