Analysis on the sequence of the whole genome of an isolated enterovirus 71 strain

An enterovirus 71 (EV71) strain Query was isolated from a patient specimen in 2015. In order to known about its genetic evolution, this study amplified gene fragment of the isolated stain by RT-PCT and carried out sequencing of the total genome. The homology and genetic evolution of the gene sequence of the virus strain in the study were analyzed. The results showed that the isolated EV71 strain in this study had higher homology of nucleotide sequence and amino acid sequence with other virus strains, which was 80%-97% and 88% to 92%, respectively, but it had lower homology with Cox.A16 (homology of nucleotide sequence and amino acid sequence of Cox.A16 was 81% and 79%, respectively). Compare of homologous sequence at the encoding region VP1 demonstrated that the experimental isolated strain EV71 had higher homology of amino acid sequence at VP1 region with other virus strains. Genetic evolution of nucleotide sequence at VP1 region of the identified strain and other EV71 strains was analyzed, and the results demonstrated gene sequence at VP1 region and 5'UTR region of the isolated strain and SDLY017 strain was at the same branch, both of which belonged to C4a, a subtype of type C4.