Analysis of single nucleotide polymorphism of Yersinia pestis in Qinghai Province
HE Jian
JIN Juan
LI Sheng
BAI Jixiang
JIN Yong
ZHANG Li
YANG Xiaoyan
XIN Youquan
Abstract：Objective To study the genotype and regional distribution of single nucleotide polymorphism(SNP)of Yersinia pestis in Qinghai Province.Methods A toal of 250 strains of Y.pestis isolated from hosts and vectors in different regions from 1954 to 2020 were selected as experimental strains,the DNA of Y.pestis was extracted by using the traditional phenol-chloroform mixed extraction method.The Illumina HiSeq 2000 platform was used to sequence the whole gene of 250 strains.According to the SNPs analysis method of the whole genome of Y.pestis in the literature,based on 133 domestic and foreign strains of Y.pestis and Y.pseudotuberculosis IP32953,2 298 SNP loci were compared.MEGA 6.0 software was used to construct phylogenetic relationships for the 250 strains and 32 reference strains of Qinghai Province.Results A total of 250 strains were distributed in 8 cities/states and 31 counties/districts in Qinghai Province.There were 66 strains in Haixi Prefecture,70 strains in Haibei Prefecture,28 strains in Hainan Prefecture,62 strains in Yushu Prefecture,and 24 strains in Huangnan Prefecture,Golog Prefecture,Xining City,and Haidong City.Based on the clustering of 2 298 SNPs sites,the 250 strains of Y.pestis from Qinghai Province were distributed in 5 subclades;6 strains(2.0％)from 0.PE clade,235 strains(94.0％)from 1.IN clade,4 strains(1.6％)from 2.ANT clade,1 strain(0.4％)from 2.MED clade,and 4 strains of 3.ANT branch(1.6％).Conclusion There is a high diversity of SNP genotypes in plague natural foci of Qinghai Province,and the regional distribution characteristics are obvious.
Keywords：Yersinia pestissingle nucleotide polymorphism(SNP)SNP genotypingQinghai Province
Publication Date：2025-02-19
Online Publishing Date：2025-08-15(First online date of this platform, not the publication date of the document)
Pages：4( 103-106 )