O型口蹄疫病毒VP1基因区序列系统发育树分型

从GenBank和世界口蹄疫参考实验室基因库(WRLFMD)下载O型FMDV全VP1序列共210条,其中23条为已知基因型序列,其他为未知基因型序列.利用分子生物学软件DNA Star中的ClustalW和TreeView工具,以已知基因型的VP1区序列构建系统发育树,验证分型结果与已知基因型是否一致.然后以已知基因型序列作为参照,将未知基因型序列与已知基因型序列一起构建系统发育树,以已知基因型序列在系统发育树中所处的位置,来判断未知基因型序列的归属,从而明确它们归属于何种基因型.结果表明,采用此种分型方法获得Cathay型74条、SEA型24条、EA型4条、WA型4条、Euro-SA型21条、ME-SA型68条、ISA-1型3条、ISA-2型2条,未能分型序列10条.

Genotyping of Type O Foot-and-mouth disease virus by Phylogenetic Analysis of VP1 Gene Sequences

Studying and genotyping the type O FMDV by phylogenetic analysis of the VP1 gene sequences.A total of 210 VP1 sequences of type O FMDV were downloaded from GenBank and FMDWRL website.The 23 of them had been typed into 8 genotypes and the others remained unknown.The ClustalW and the TreeView computer programs were used for similarity comparison and phylogenetic tree construction of the 23 VP1 gene sequences to confirm the computing methodology.Next the unknown sequences were genotyped by phylogenetic analysis together with the 23 known reference sequences.Based on the phylogenetic analysis,200 out of the 210 sequences were grouped into 8 established topotypes(genotypes),e.g.74 as topotype Cathy,24 as SEA,4 as EA,4 as WA,21 as Euro-SA,67 as ME-SA,3 as ISA-1 and 2 as ISA-2.The remaining 10 sequences failled to fit into any topotyes based on the phylogenetic analysis of the VP1 gene sequences,genotype unknown type O FMDV sequences could be classified into the existing topotypes.