Multiple sequence alignment and phylogenetic analysis of complete genome of Chikungunya virus

Objective Chikungunya virus( CHIKV) has caused large outbreaks worldwide in recent years. The aim of the study was to understand the time,area,variation and genetic evolution of CHIKV prevalance,and lay the foundation for prevention and control of Chikungunya fever. Methods Sequences were assembled with the DNA-Star software package and compared with Clustal X to previously published CHIKV sequences in Gen Bank. Neighbor-joining trees were constructed using MEGA version 6. 06. Results All strains are highly related,with 97. 7%-100. 0% nucleotide sequence similarity,with 80. 3%-100. 0% amino acid similarity. Phylogenetic analysis demonstrated that the sequences were clustered into three genotypes. Viruses isolated in the same area and time were highly similar. Conclusions Although CHIKV strains vary,individual isolates are genetically conserved.