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奥密克戎BA.2引起的12起云南省边境地区本土疫情首例病例新冠病毒基因特征分析

SARS-CoV-2 genetic characterization of the first cases from 12 local epidemics in border areas of Yunnan province caused by Omicron variant
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摘要 目的了解云南省边境地区新型冠状病毒肺炎本土疫情特征, 分析感染的新型冠状病毒(severe acute respiratory syndrome coronavirus 2, SARS-CoV-2)基因组变异情况并进行溯源。方法收集2022年2月中旬至4月期间云南省边境地区12起本土疫情首例病例基本信息及标本, 应用全基因组测序技术进行病毒基因序列测定, 通过在线分析平台和软件, 判断病毒型别, 分析病毒突变情况, 结合流调内容, 推测疫情病毒感染来源。结果 12起云南省边境地区本土疫情首例病例职业较多样, 且活动区域均未离开过当地。Pangolin分型结果显示12起疫情SARS-CoV-2基因组均属Omicron (BA.2)变异株, 其中各2起疫情SARS-CoV-2基因组进一步分属BA.2.10和BA.2.3.2进化分支。全基因组核苷酸突变分析表明, 有十起疫情首例病例病毒基因序列存在1个及以上数目的特有核苷酸突变位点, 结合流行病学调查内容, 提示12起疫情可能均存在不同的病毒感染来源。进一步分析氨基酸突变发现, 病例间基因序列除具备进化分支代表性突变位点外, 还具有特有的氨基酸突变位点(如S:E1188D), 其影响同样值得关注。序列系统发育树分析结果与Pangolin分型及突变分析结果相吻合。结论 12起云南本土疫情可能存在各自不同的病毒感染来源, 这提示云南省边境地区疫情极具复杂性和挑战性。加强重点人群范围及核酸筛查频次, 跟踪监测病毒变异规律, 对疫情精准防控具有重要指导意义。 Objective To understand the characteristics of the local Coronavirus Disease 2019(COVID-19)epidemic in the border areas of Yunnan province,and to analyze and trace the genome variation of the severe acute respiratory syndrome coronavirus 2(SARS-COV-2).Methods The basic information and samples of the first cases of 12 local epidemics in the border areas of Yunnan province from mid-February to April 2022 were collected.The virus genomes,genotypes and mutations were determined by the whole genome sequencing technology,the Pangolin COVID-19 Lineage Assigner and MEGA software.The sources of virus infection were estimated based on the contents of epidemiological investigations.Results The first cases from 12 local epidemics in the border areas of Yunnan province had diverse occupations,and none of them had ever left the local area.The virus genomes of 12 first cases were Omicron(BA.2)variants and every two of them further belonged to the evolutionary clades BA.2.10 and BA.2.3.2,respectively.The genome-wide nucleotide-level mutation analysis showed that there were 1 or more specific nucleotide mutation sites in 10 first cases of the local epidemics.Combined with the epidemiological investigations,it was suggested that there might be different sources of virus infection in all 12 local epidemics.Further analysis of amino acid mutations revealed that in addition to the representative mutation sites of evolutionary clades,there were also specific amino acid mutation sites(such as S:E1188 D)in the genome sequences between the cases,which also deserved attention.The result of phylogenetic tree analysis were consistent with Pangolin Assigner and mutation analysis.Conclusions The 12 local epidemics in Yunnan may have different sources of virus infection,which indicates that the COVID-19 epidemic in the border areas of Yunnan province is extremely complicated.Strengthening the frequency of nucleic acid screening and the scope of key populations and monitoring the variation of SARS-CoV-2 are of great significance for the precise prevention and control of the epidemic.
作者 张美玲 伏晓庆 张勇 罗春蕊 刘照生 赵晓南 周洁楠 Zhang Meiling;Fu Xiaoqing;Zhang Yong;Luo Chunrui;Liu Zhaosheng;Zhao Xiaonan;Zhou Jienan(Yunnan Center for Disease Control and Prevention,Kunming 650022,China)
出处 《中华实验和临床病毒学杂志》 CAS CSCD 2023年第1期13-19,共7页 Chinese Journal of Experimental and Clinical Virology
关键词 新型冠状病毒 病毒基因组 Omicron变异株 突变位点 病毒感染来源 severe acute respiratory syndrome coronavirus 2 Virus genome Omicron variant Mutation site Source of virus infection
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