徐州市本土新冠病毒流行趋势及基因组特征分析
Analysis of Epidemic Trend and Genomic Characteristics of SARS-CoV-2 in Xuzhou,China
魏丹 1杜阳光 1杜昱 1邢菲菲 1冯欢欢 1童晶1
作者信息
- 1. 徐州市疾病预防控制中心,徐州 221006
- 折叠
摘要
为了解徐州市新型冠状病毒(SARS-CoV-2)的型别流行趋势,从基因组水平分析其分子学特征及氨基酸突变差异,本文选取了徐州市2023年1-5月共117份本土COVID-19患者标本进行全基因组测序.测序标本中"≥80"年龄组患者所占比例最高,男性患病比例总体高于女性,患病群体呈现年轻化趋势.将测序结果上传Pangolin和Nextclade网站得到病毒型别及变异位点信息.测序分型均为奥密克戎变异株:BA.5.2及其亚分支30株,BF.7及其亚分支58株,XBB及其亚分支29株.BF.7及其亚分支为1-3月徐州市主导流行株,XBB及其亚分支为4-5月徐州市主导流行株.17株不同型别的SARS-CoV-2共检测到125处氨基酸突变位点,S蛋白区氨基酸突变位点数量最多(52处).XBB及其亚分支与其它分支比较,存在着3处不同方向的氨基酸突变,13处独有氨基酸突变,7处氨基酸突变缺失.系统进化树显示:BA.5.2及其亚分支、BF.7.14及其亚分支、XBB及其亚分支分成了三簇,与Pangolin网站分型结果基本吻合.使用高通量测序技术对SARS-CoV-2进行追踪溯源及分子特征分析,对徐州市疫情研判、防疫政策的制定和变异株的监测意义重大.
Abstract
In order to understand the epidemic trend of SARS-CoV-2 types in Xuzhou,China and to analyze the molecular characteristics and amino acid mutation differences on the genomic level,a total of 117 samples from local COVID-19 cases in Xuzhou,China from January to May 2023 were selected for whole genome sequencing.The proportion of cases in the"≥80"age group is the highest among sequencing samples,and the overall proportion of male cases is higher than female cases.The age group showed a younger trend.The sequencing results were uploaded to the Pangolin and Nextclade to obtain lineage and mutation information.The sequencing cases were all Omicron variants:with 30 strains of BA.5.2 sub-lineage,58 strains of BF.7 sub-lineage,and 29 strains of XBB sub-lineage.BF.7 sub-lineages were the dominant strains in Xuzhou,China from January to March,while XBB sub-lineages were dominant from April to May.A total of 125 amino acid substitutions were detected in 17 different types of SARS-CoV-2,most of them were located in the spike protein(52).Compared with other lineages,XBB sub-lineages have 3 amino acid substitutions in different directions,12 unique amino acid substitutions and 7 missing amino acid substitutions.The phylogenetic tree showed that BA.5.2 sub-lineages,BF.7 sub-lineages and XBB sub-lineages are divided into three clusters,which is basically consistent with the typing results of Pangolin.Using high-throughput sequencing technology to trace the source and analyze the molecular characteristics of SARS-CoV-2 is of great significance for the study and judgment of the epidemic situation,the establishment of epidemic prevention policies and monitoring of the mutant strains in Xuzhou,China.
关键词
新型冠状病毒/奥密克戎/全基因组测序/氨基酸突变/系统进化树Key words
SARS-CoV-2/Omicron/Whole Genome Sequencing/Amino Acid Substitutions/Phylogenetic Tree引用本文复制引用
出版年
2024
NETL
NSTL
万方数据