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摘要:
目的 调查2022年9月云南省镇康县新型冠状病毒感染本土疫情的感染来源和病毒变异情况。 方法 收集疫情期间采集的9例本土病例和3例境外病例的标本进行新型冠状病毒（SARS-CoV-2）全基因组测序。 通过基因组学分析，结合流行病学调查内容，明确病毒基因组变异情况及感染来源。 结果 来自9例本土病例的病毒株属Omicron变异株BA.5.2和BA.5.2.20进化分支，形成独立的两条传播链，均与境外病例病毒株基因组序列高度同源。 结合流行病学调查，提示可能与直接或间接接触境外病毒感染病例有关。 BA.5.2和BA.5.20基因型毒株基因组序列共享53个氨基酸错义突变和11个氨基酸缺失突变，各自具备其代表性氨基酸突变位点。 在S蛋白上均发现HV69～70del、L452R、T478K、R493Q回复突变、F486V等可能影响病毒传播力和免疫逃逸能力的关键性变异位点。 同时研究发现，S:K147T、S:M1237V、ORF1a:M85del等其他特征性突变位点，其功能作用值得进一步研究。 结论 本次疫情有2个境外病毒感染源，提示云南省边境地区疫情的复杂性和长期性。 因此，边境地区仍要提高监测预警敏感性，不断有方向性地追踪病毒变异动态，以期提高SARS-CoV-2感染防控工作的科学性和精准性。 -
关键词:
- 新型冠状病毒 /
- 溯源 /
- 基因组 /
- Omicron变异株 /
- 突变位点
Abstract:Objective To understand the infection source of an outbreak of coronavirus disease 2019 (COVID-19) occurred in Zhenkang county, Yunnan province in September 2022 and analyze the variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Methods The samples were collected from 9 local cases and 3 imported cases for whole-genome sequencing of SARS-CoV-2. The virus genome variation and the infection source were identified by the genomics analysis and epidemiological investigation. Results The SARS-CoV-2 strains detected in 9 local cases belonged to Omicron BA.5.2 and BA.5.2.20, indicating two independent transmission chains. The genome sequences of the strains were highly homologous to the strains from 3 imported cases. The epidemiological investigation also indicted that the infections might be related to the direct or indirect contacts with the imported cases. The BA.5.2 and BA.5.20 strains shared 53 amino acid missense mutations and 11 amino acid deletion mutations, but each had its representative amino acid mutation site, respectively. HV69-70del, L452R, T478K, R493Q reversion, F486V and other vital mutation sites were found in the S protein of these SARS-CoV-2 strains, which might affect the transmission and immune escape of Omicron variant of SARS-CoV-2. The functional effects of the other characteristic mutations, such as S: K147T, S: M1237V, ORF1a: M85del were discovered in this study, for which further studies are needed. Conclusion The epidemic might be associated with two imported infection sources, indicating the complexity and protracted nature of the epidemic in Yunnan border area. Therefore, the sensitivity of surveillance and forewarning still needs to be enhanced in border areas, and the dynamic surveillance for virus mutation should be continued to further improve the accuracy of the prevention and control of the epidemic. -
图 1 镇康县疫情本土病例传播关系图
Figure 1. Transmission chains in local COVID-19 epidemic in Zhenkang
图 2 9例本土和3例境外病例毒株的基因组序列解析
注：UTR. 非翻译区；ORF. 开放阅读框；S. 刺突蛋白；E. 包膜蛋白；M. 膜蛋白；Intergenic. 基因间隔区；N. 核衣壳蛋白；. 表示核苷酸未突变或氨基酸的同义突变；－. 核苷酸或氨基酸的缺失突变
Figure 2. Analysis on SARS-CoV-2 genome sequences from 9 local cases and 3 imported cases
图 3 9例本土和3例境外病例毒株的基因组序列最大似然树分析
注：红色为本研究中的本土病例和境外病例病毒序列；黄色为GISAID数据库下载的缅甸毒株序列；蓝色为缅甸输入病例病毒序列；灰色为我国云南省临沧市其他本土疫情病例病毒序列；绿色为我国云南省其他州市本土疫情病例病毒序列；黑色为参考序列
Figure 3. Maximum likelihood tree analysis on SARS-CoV-2 genomes from 9 local cases and 3 imported cases
表 1 镇康县疫情本土病例基本信息
Table 1. Basic information of local cases in COVID-19 epidemic in Zhenkang
病例编号 性别 年龄（岁） 职业 确诊日期（月－日） 发现方式 感染来源 1 女性 13 学生 09−21 主动就诊 可能来自境外 2 女性 46 校医 09−22 集中隔离点筛查 病例1的校内密接者 3 男性 30 广告公司工人 09−22 社区筛查 可能为其他境外感染来源 4 男性 16 学生 09−23 集中隔离点筛查 病例1的校内密接者 5 女性 18 学生 09−23 集中隔离点筛查 病例1的校内密接者 6 男性 13 学生 09−23 集中隔离点筛查 病例1的校内密接者 7 女性 41 农村客运司机 09−23 集中隔离点筛查 病例1的家庭密接者 8 女性 42 校医 09−23 集中隔离点筛查 病例1的校内密接者 9 男性 14 学生 09−23 集中隔离点筛查 病例1的校内密接者 10 男性 4 幼托儿童 09−25 集中隔离点筛查 病例1的家庭密接者 11 男性 64 农民 09−26 集中隔离点筛查 病例1的家庭密接者 
下载: 导出CSV
表 2 12例新型冠状病毒感染病例的病毒基因组概况
Table 2. SARS-CoV-2 genomes from 12 COVID-19 cases
病毒来源病例 毒株基因组编号 基因组覆盖度 （%） Pangolin分型 核苷酸突变位点数 缺失突变位点数 病例1 SARS-CoV-2-LCZK202201 99.44 BA.5.2 80 33 病例2 SARS-CoV-2-LCZK202202 99.52 BA.5.2 80 33 病例4 SARS-CoV-2-LCZK202204 99.65 BA.5.2 80 33 病例5 SARS-CoV-2-LCZK202205 99.12 BA.5.2 80 33 病例6 SARS-CoV-2-LCZK202206 99.27 BA.5.2 80 33 病例7 SARS-CoV-2-LCZK202207 99.24 BA.5.2 80 33 病例8 SARS-CoV-2-LCZK202208 99.26 BA.5.2 80 33 病例9 SARS-CoV-2-LCZK202209 99.13 BA.5.2 80 33 境外病例1 SARS-CoV-2-LCZKJW202201 99.35 BA.5.2 80 33 境外病例2 SARS-CoV-2-LCZKJW202202 99.26 BA.5.2 80 33 病例3 SARS-CoV-2-LCZK202203 99.23 BA.5.2.20 80 36 境外病例3 SARS-CoV-2-LCZKJW202203 99.47 BA.5.2.20 80 33 注：缺失突变未纳入核苷酸突变位点数计算
下载: 导出CSV
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