[Analysis on the preference of synonymous codon in VP1 nucleotide sequence of the EV71 based on RSCU method]

Based on RSCU method and by analyzing the preference of codon usage in VP1 nucleotide sequences of EV71 isolated in Chinese mainland and Taiwan region from 1998 to 2008, it is clear that there is an obvious time discrimination in RSCU calculated from EV71 VP1 strain between two different regions of China and it is more obvious in Taiwan region, therefore, according to the diversity of RSCU, the years can be divided into 2 intervals in Chinese mainland and 4 intervals in Taiwan region, especially, the number of intervals in one region have a positive co-relation with the activity of variation of the EV71 in the same region. The change of the preference of codon usage in VP1 nucleotide sequences of EV71 can significantly embody the Variation of the EV71, so we can make use of the analysis on preference of codon usage in VP1 nucleotide sequences of EV71 to predict the possible variation trend of the EV71.