瑞丽市2021年7—11月COVID-19境外输入病例分子流行病学分析

郑学东; 赵晓南; 吴研鹏; 陈志元; 王岩; 余宏杰; 伏晓庆; 赵世文

doi:10.16462/j.cnki.zhjbkz.2023.02.006

瑞丽市2021年7—11月COVID-19境外输入病例分子流行病学分析

doi: 10.16462/j.cnki.zhjbkz.2023.02.006

1.
650500 昆明，昆明医科大学公共卫生学院
2.
650022 昆明，云南省疾病预防控制中心急性传染病防制所
3.
200032 上海，复旦大学公共卫生学院流行病学教研室，公共卫生安全教育部重点实验室

基金项目:

云南省科技厅重点研发计划 202103AC100006

详细信息

通讯作者:
赵世文，E-mail：ynzsw1368@sina.com

中图分类号: R181.3
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- 被引次数: 0
出版历程
- 收稿日期: 2022-11-03
- 修回日期: 2023-01-13
- 网络出版日期: 2023-02-20
- 刊出日期: 2023-02-10

Molecular epidemiological analysis of COVID-19 imported cases in Ruili from July to November, 2021

1.
School of public health, Kunming Medical University, Kunming 650500, China
2.
Acute Infectious Disease Prevention and Control Institute, Yunnan Center for Disease Control and Prevention, Kunming 650022, China
3.
School of Public Health/Key Laboratory of Public Health Safety, Ministry of Education, Fudan University, Shanghai 200032, China

Funds:

Key Research and Development Program of Yunnan Province Science and Technology Department 202103AC100006

More Information

Corresponding author: ZHAO Shi-wen, E-mail: ynzsw1368@sina.com

摘要

摘要: 目的分析瑞丽市境外陆路输入COVID-19病例的流行特征和基因组特征，为云南省边境疫情防控工作提供参考依据。方法收集2021年7月至11月瑞丽市境外陆路输入SARS-CoV-2感染者相关信息，对流行病学特征进行统计分析；筛选40例阳性样本使用Illumina公司二代测序平台进行高通量测序，分析基因分型情况及变异特征。结果研究期间瑞丽市累计报告SARS-CoV-2感染者796例，年龄范围1~85岁, 年龄M(IQR)为28.5(10)岁；男女性别比4.61∶1；职业以商业服务49.75%(396/796)为主；轻型、普通型占比95.60%。获得的34例测序结果按照Nextstrain分型法可分为3个型，24例属于21A(Delta)分支，9例属于21I(Delta)分支，1例属于20I(Alpha, V1)分支。结论本研究中的病例病毒基因分型主要分为三大支系且互相之间有一定差异，其中大部分为Delta株。应继续落实好边境管控措施，持续对境外输入病例进行病毒变异监测，以评估变异株对云南省疫情防控现状的威胁。
- 新型冠状病毒肺炎 /
- 境外输入 /
- 流行病学特征 /
- 全基因组测序
Abstract: Objective To analyze the epidemiological and genomic characteristics of COVID-19 cases imported by land in Ruili, and to provide reference for border epidemic prevention and control in Yunnan Province. Methods We collected information about SARS-CoV-2 infected individuals from overseas land in Ruili, Yunnan from July to November, 2021. The epidemiological characteristics were statistically analyzed. The second-generation sequencing platform of Illumina was used to conduct high-throughput sequencing on the selected 40 positive samples and to analyze their genotyping and variation characteristics. Results During the study period, Ruili City reported 796 COVID-19 cases from abroad.The median age of COVID-19 cases was 28.5 years (Interquantile range 10; range 1-85). The gender ratio between men and women was 4.61∶1; Most of these infected individuals engaged in business services, accounting for 49.75% (396/796); 95.60% of COVID-19 cases were mild and moderate cases. The sequencing results of 34 cases can be divided into three clades according to Nextstrain typing method, including 24 cases belong to 21A(Delta) clade, 9 cases belong to 21I(Delta) clade and 1 case belongs to 20I(Alpha V1) clade. Conclusions The virus genotypes of the cases in this study were mainly divided into three branches and there were some differences among them, most of which were Delta mutants.We should continue to implement border control measures and continue to monitor the virus mutation of imported cases, so as to evaluate the threat of the mutant strain to the current situation of epidemic prevention and control in Yunnan Province.
- COVID-19 /
- Imported case /
- Epidemiological characteristic /
- Whole genome sequencing

HTML全文

图 1 瑞丽市2021年7月1日—11月15日COVID-19境外陆路输入病例确诊时间分布

Figure 1. Diagnostic time distribution for COVID-19 from July 1th to November 15th, 2021 in Ruili

下载: 全尺寸图片幻灯片

图 2 瑞丽市796例境外陆路输入病例输入来源地区分布

Figure 2. Regional distribution of 796 cases imported by overseas land in Ruili City

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图 3 瑞丽市796例COVID-19病例临床分型

Figure 3. Clinical type of 796 COVID-19 cases in Ruili City

下载: 全尺寸图片幻灯片

图 4 瑞丽市34例测序样本病例的时间分布

Figure 4. Time distribution of 34 sequencing sample cases in Ruili City

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图 5 34条SARS-CoV-2序列与25个参比毒株基于最大似然法系统发育树

注：带“▲”标识的为本研究测定的序列。

Figure 5. 34 SARS-CoV-2 sequences and 25 reference strains were phylogenetic tree based on maximum likelihood method

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表 1 2021年7月1日—11月15日瑞丽市境外陆路输入COVID-19病例人群分布[n(%)]

Table 1. The population distribution of COVID-19 infections in Ruili from July 1th to November 15th, 2021 [n(%)]

基本情况	确诊病例(n=768)	无症状感染者(n=28)	合计(N=796)	χ²/Z值	P值
性别				0.062	0.804
男	630(82.03)	24(85.71)	654(82.16)
女	138(17.97)	4(14.29)	142(17.84)
年龄(x±s, 岁)	29.29±9.02	27.36±5.46		-1.167	0.243
0~＜10	7(0.91)	0(0.00)	7(0.88)
10~＜20	75(9.77)	1(3.57)	76(9.55)
20~＜30	344(44.79)	19(67.86)	363(45.60)
30~＜40	260(33.85)	7(25.00)	267(33.54)
40~＜50	59(7.68)	1(3.57)	60(7.54)
50~＜60	19(2.47)	0(0.00)	19(2.39)
60~＜70	3(0.39)	0(0.00)	3(0.38)
70~＜80	0(0.00)	0(0.00)	0(0.00)
≥80	1(0.13)	0(0.00)	1(0.13)
职业				64.468	< 0.001
餐饮食品业	151(19.66)	0(0.00)	151(18.97)
商业服务	390(50.78)	6(21.43)	396(49.75)
工人/农民	101(13.15)	3(10.71)	104(13.07)
家务及待业	37(4.82)	9(32.14)	46(5.78)
教师/学生	8(1.04)	0(0.00)	8(1.01)
散居儿童	10(1.30)	0(0.00)	10(1.26)
其他	719.24)	1035.71)	8110.18)

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表 2 34条全基因组序列核苷酸突变位点统计表

Table 2. Statistical table of nucleotide mutation sites of 34 whole genome sequences

分支	突变位点
簇21A	G210T, C241T, C1191T, C1267T, C3037T, C5184T, C6539T, C9891T, T11418C, T12946C, C14408T, G15451A, C16466T, A20262G, C20320T, C21618G, G21987A, T22917G, C22995A, A23403G, C23604G, G24410A, A28461G, G28881T, G29402T, G29427A, G29742T
簇21I	G210T, C241T, C3037T, C5184T, A5584G, C9891T, T11418C, C11514T, C13019T, C14408T, G15451A, C16466T, C21618G, G21987A, C22227T, T22917G, C22995A, A23403G, C23604G, G24410A, A28461G, G28881T, G29402T, G29742T
簇20I	C241T, C913T, C1825T, C3037T, C3267T, C5388A, C5986T, T6954C, T7462C, C11750T, C14408T, C14676T, T15096C, C15279T, T16176C, C17862T, C21588T, G22273T, C23029T, A23063T, C23063A, A23403G, C23604A, C23709T, C24109T, A28095T, A28111G, G28280C, A28281T, T28282A, G28436T, G28881A, G28882A, G28883C, C28977T, C29149T, C29585T, G29868C

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参考文献(20)

[1]	Paules CI, Marston HD, Fauci AS. Corona virus infections more than just the common cold[J]. JAMA, 2020, 323(8): 707-708. DOI: 10.1001/jama.2020.0757.
[2]	World Health Organization. WHO coronavirus (COVID-19) dashboard \| WHO coronavirus (COVID-19) dashboard with vaccination data[EB/OL]. (2021-06-21)[2022-8-19]. https://covid19.who.int/info.
[3]	刘晓瑜, 魏永伟. SARS-CoV-2 S蛋白: 研究进展与挑战[J]. 病毒学报, 2020, 36(6): 1157-1164. DOI: 10.13242/j.cnki.bingduxuebao.003787 Liu XY, Wei YW. S protein of SARS-CoV-2: research progress and challenges[J]. Chin J Virol, 2020, 36(6): 1157-1164. DOI: 10.13242/j.cnki.bingduxuebao.003787.
[4]	Prajapat M, Handa V, Sarma P, et al. Update on geographical variation and distribution of SARS-nCoV-2: a systematic review[J]. Indian J Pharmacol, 2021, 53(4): 310-316. DOI: 10.4103/ijp.ijp_483_21.
[5]	国务院应对新型冠状病毒肺炎疫情联防联控机制综合组. 关于印发新型冠状病毒肺炎防控方案(第八版)的通知[J]. 中华人民共和国国家卫生健康委员会公报, 2021, (5): 4-60. https://www.cnki.com.cn/Article/CJFDTOTAL-WSGB202105002.htm Comprehensive Team of the State Council's Joint Prevention and Control Mechanism for COVID-19 Epidemic Response. Notice on the issuance of the prevention and control plan for novel coronavirus pneumonia (8th edition)[J]. Gazette of the National Health Commission of People's Republic of China, 2021, (5): 4-60. https://www.cnki.com.cn/Article/CJFDTOTAL-WSGB202105002.htm
[6]	王丽珍. 瑞丽市边境口岸经济发展现状研究[J]. 投资与创业, 2021, 32(20): 73-75. doi: 10.3969/j.issn.1672－3414.2021.20.023 Wang LZ. Research on the present situation of economic development of Ruili City[J]. Investment and Entrepreneurship, 2021, 32(20): 73-75. doi: 10.3969/j.issn.1672－3414.2021.20.023
[7]	田路路, 姚歆, 王梦媛, 等. 四川省664例新型冠状病毒肺炎病例的流行病学特征分析[J]. 现代预防医学, 2021, 48(10): 1765-1768, 1783. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202110010.htm Tian LL, Yao X, Wang MY, et al. Epidemiological characteristics of 664 COVID-19 cases in Sichuan Province[J]. Mod Prev Med, 2021, 48(10): 1765-1768, 1783. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202110010.htm
[8]	中国疾病预防控制中心新型冠状病毒肺炎应急响应机制流行病学组, 张彦平. 新型冠状病毒肺炎流行病学特征分析[J]. 中华流行病学杂志, 2020, 41(2): 145-151. DOI: 10.3760/cma.j.issn.0254-6450.2020.02.003. Epidemiology Working Group for NCIP Epidemic Response, Zhang YP. The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China[J]. Chin J Epidemiol, 2020, 41(2): 145-151. DOI: 10.3760/cma.j.issn.0254-6450.2020.02.003.
[9]	晏月平, 李忠骥. 新冠肺炎感染人群的人口学分析——以我国10省市区为例[J]. 人口与发展, 2020, 26(3): 73-85, 64. https://www.cnki.com.cn/Article/CJFDTOTAL-SCRK202003007.htm Yan YP, Li ZJ. Demographic analysis of the population affected by COVID-19—a case study of 10 provinces and municipalities in China[J]. Population and Development, 2020, 26(3): 73-85, 64. https://www.cnki.com.cn/Article/CJFDTOTAL-SCRK202003007.htm
[10]	李文艳, 杜志成, 王莹, 等. 新型冠状病毒Delta变异株引起的广州市荔湾区本土疫情流行特征分析[J]. 中华流行病学杂志, 2021, 42(10): 1763-1768. DOI: 10.3760/cma.j.cn112338-20210613-00472. Li WY, Du ZC, Wang Y, et al. Epidemiological characteristics of local outbreak of COVID-19 caused by SARS-CoV-2 Delta variant in Liwan District, Guangzhou[J]. Chin J Epidemiol, 2021, 42(10): 1763-1768. DOI: 10.3760/cma.j.cn112338-20210613-00472.
[11]	保跃平. 脆弱、流动与风险: 中缅边境新冠肺炎疫情跨境传播问题研究[J]. 青海民族大学学报(社会科学版), 2021, 47(4): 66-80. doi: 10.3969/j.issn.1674-9227.2021.04.009 Bao YP. Vulnerability, mobility and risk: a study of the cross-border spread of COVID-19 on the China-Myanmar border[J]. Journal of Qinghai Minzu University(Social Sciences), 2021, 47(4): 66-80. doi: 10.3969/j.issn.1674-9227.2021.04.009
[12]	Wang CT, Liu ZP, Chen ZX, et al. The establishment of reference sequence for SARS-CoV-2 and variation analysis[J]. J Med Virol, 2020, 92(6): 667-674. DOI: 10.1002/jmv.25762.
[13]	Callaway E. Delta coronavirus variant: scientists brace for impact[J]. Nature, 2021, 595(7865): 17-18. DOI: 10.1038/d41586-021-01696-3.
[14]	Torjesen I. COVID-19: delta variant is now UK's most dominant strain and spreading through schools[J]. BMJ, 2021, 373: n1445. DOI: 10.1136/bmj.n1445.
[15]	王廉皓, 张翔宇, 王雪纯, 等. 中国新型冠状病毒德尔塔突变株传播强度分析[J]. 现代预防医学, 2022, 49(7): 1165-1169. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202207003.htm Wang LH, Zhang XY, Wang XC, et al. Transmission intensity analysis of SARS-Cov-2 Delta mutant in China[J]. Modern Preventive Medicine, 2022, 49(7): 1165-1169. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202207003.htm
[16]	孙丹, 杨金燕, 夏婷婷, 等. 新型冠状病毒Omicron变异株的流行病学特征及防控研究进展[J]. 中华医院感染学杂志, 2022, 32(8): 1266-1270. DOI: 10.11816/cn.ni.2022-213762. Sun D, Yang JY, Xia TT, et al. Progress of research on epidemiological characteristics of novel coronavirus Omicron variant and prevention measures[J]. Chin J Nosocomiol, 2022, 32(8): 1266-1270. DOI: 10.11816/cn.ni.2022-213762.
[17]	阎思宇, 靳英辉, 王永博, 等. 常态化疫情防控阶段中国内地COVID-19境外输入确诊病例时空分布特征分析[J]. 现代预防医学, 2021, 48(13): 2305-2308. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202113001.htm Yan SY, Jin YH, Wang YB, et al. Analysis of spatiotemporal distribution characteristics of COVID-19 imported confirmed cases in mainland China during the stage of normalized epidemic prevention and control[J]. Modern Preventive Medicine, 2021, 48(13): 2305-2308. https://www.cnki.com.cn/Article/CJFDTOTAL-XDYF202113001.htm
[18]	郭西亚, 郭雯雯, 李鹏, 等. 中国内地境外输入新型冠状病毒肺炎确诊病例流行病学特征分析[J]. 中国公共卫生, 2020, 36(12): 1763-1766. DOI: 10.11847/zgggws1131945. Guo XY, Guo WW, Li P, et al. Epidemiological characteristics of imported COVID-19 cases from abroad in Mainland China[J]. Chin J Public Health, 2020, 36(12): 1763-1766. DOI: 10.11847/zgggws1131945.
[19]	刘小龙. 加强边境通道便道管控严防境外疫情输入云南[J]. 创造, 2020, (4): 56-59. https://www.cnki.com.cn/Article/CJFDTOTAL-CUZA202004012.htm Liu XL. Strengthen the control of epidemic import routes in Yunnan[J]. Creation, 2020, (4): 56-59. https://www.cnki.com.cn/Article/CJFDTOTAL-CUZA202004012.htm
[20]	赵翔, 冯晔囡, 陈志肖, 等. 输入病毒导致的十起本土疫情首例病例新冠病毒基因特征分析[J]. 病毒学报, 2021, 37(2): 259-266. DOI: 10.13242/j.cnki.bingduxuebao.003863. Zhao X, Feng YN, Chen ZX, et al. SARS-CoV-2 genetic characterization of imported from first case in ten local outbreaks of China[J]. Chin J Virol, 2021, 37(2): 259-266. DOI: 10.13242/j.cnki.bingduxuebao.003863.