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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.
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基本信息:
DOI：10.13242/j.cnki.bingduxuebao.004447
中图分类号:R511
引用信息:
[1]魏丹,杜阳光,杜昱,等.徐州市本土新冠病毒流行趋势及基因组特征分析[J].病毒学报,2024,40(01):88-96.DOI:10.13242/j.cnki.bingduxuebao.004447.
2023-07-18
2023
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2024-01-15
2024
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2024-01-13
2024-01-13
2024-01-13