Epidemiological and genetic characteristics of imported COVID-19 cases in Guangxi
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摘要:
目的 分析广西壮族自治区(广西)境外输入性COVID-19感染者的流行病学特点及病毒基因特征，为境外输入疫情防控提供依据。 方法 收集2020年3月1日―2022年3月31日广西境外输入性COVID-19感染者的相关信息，使用CLC Genomics Workbench软件进行序列拼接，MEGA软件构建系统进化树。 结果 广西累计报告输入性感染者1 662例，纳入分析1 643例，平均年龄为37.4岁，男女比例为6.4∶1，68.4%接种过疫苗。输入性感染者来源国以越南为主(92.5%)，入境口岸以凭祥友谊关为主(87.4%)。2020年输入性感染者主要为B.1.351和B.1.1分支，2021年主要为Delta分支，2022年主要为Omicron分支。 结论 广西持续存在从东南亚疫情高风险国家通过口岸输入疫情的风险，输入感染者的病毒主要为当年的关切变异株(variants of concern，VOC)，口岸疫情防控形势严峻，需要持续关注输入性病例。 Abstract:Objective To analyze epidemiological and genetic characteristics of imported COVID-19 cases in Guangxi, and to provide scientific evidence for risk assessment and control strategies for imported COVID-19 in Guangxi. Methods The data of imported cases reported in Guangxi from March 1, 2020 to March 31, 2022 were collected. Whole genome sequencing was performed on samples that met sequencing criteria. CLC Genomics Workbench software was used for sequence assembly and analysis. A phylogenetic tree was constructed using MEGA software based on the neighbor-joining method. Results A total of 1 662 imported cases of COVID-19 were reported in Guangxi, of which 1 643 cases were included in the analysis. The average age was 37.4 years old. The male to female ratio of the cases was 6.4∶1. And the cases that had been vaccinated accounted for 68.4%. The imported cases could obviously be attributed to the increased importation of COVID-19 mainly from Vietnam, accounting for 92.5%, and 87.4% of cases came from Pingxiang Friendship Gate. The genotyping of imported cases mainly were the branch of B.1.351 and B.1.1, Delta, Omicron in 2020, 2021, and 2022, respectively. Conclusions Guangxi is at high risk of experiencing an epidemic of imported COVID-19 cases from Southeast Asia. The imported cases of SARS-CoV-2 were mainly variants of concern (VOC) from the same year. The focus on preventing imported cases should be on sustainable strategies for port cities. -
Key words:
- COVID-19 /
- Imported case /
- Whole genome sequencing
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图 1 输入性COVID-19感染者的来源国家、入境口岸及户籍的分布
Figure 1. Distribution of source countries, ports of entry and household registration of imported COVID-19 cases
图 2 基于全基因组核苷酸序列构建SARS-CoV-2系统发育树
1. 2020年广西输入病例的基因组序列(●)；2. 2021年广西输入病例的基因组序列(■)；3. 2022年广西输入病例的基因组序列(▲)；4. 武汉参考株序列(◆)；5. 与广西输入病例序列高度同源的基因组序列(○)；6. 使用MEGA7.0软件基于邻接法构建系统进化树，Bootstrap值设置为1 000，以评估可靠性。
Figure 2. Phylogenetic tree of SARS-CoV-2 based on the whole genome sequences
1. Genome sequence of imported cases from Guangxi in 2020 (●); 2. Genome sequence of imported cases from Guangxi in 2021 (■); 3. Genome sequence of imported cases from Guangxi in 2022 (▲); 4. NC-04572.2 SARS-CoV-2 Wuhan-Hu-1 (◆); 5. Highly homologous genome sequence with Guangxi (○); 6. MEGA7.0 software was applied to construct the phylogenetic tree based on the adjacency method. The value Bootstrap was set to 1 000, to assess reliability.
表 1 输入性COVID-19感染者的流行病学特征
Table 1. Epidemiological characteristics of imported COVID-19 cases
变量Variable 输入性感染者①
Imported cases ① n= 1 643确诊病例①
Confirmed cases ① (n=839)无症状感染者①
Asymptomatic infection ①(n=804)t值
t valueP值
P value性别Sex 0.096 0.756 男Male 1 422(86.5) 724(86.3) 698(86.8) 女Female 221(13.5) 115(13.7) 106(13.2) 年龄/岁, x±s Age/years, x±s 37.4±9.6 38.6±9.7 36.1±9.3 5.302 < 0.001 年龄组/岁Age group/years 31.323 < 0.001 ≤18 8(0.5) 4(0.5) 4(0.5) 19~＜35 713(43.4) 311(37.1) 402(50.0) 35~＜60 904(55.0) 510(60.8) 394(49.0) ≥60 18(1.1) 14(1.7) 4(0.5) 职业Occupation 37.402 < 0.001 工人Worker 504(30.7) 282(33.6) 222(27.6) 商业服务Commercial service 401(24.4) 211(25.1) 190(23.6) 干部职员Staff 330(20.1) 132(15.7) 198(24.6) 家务及待业Housework and unemployment 179(10.9) 89(10.6) 90(11.2) 海员及长途驾驶员Seafarer and long-distance driver 102(6.2) 56(6.7) 46(5.7) 农民Farmer 42(2.5) 33(3.9) 9(1.1) 其他Other 85(5.2) 36(4.3) 49(6.1) 国籍Nationality 0.381 0.537 中国籍Chinese nationality 1 605(97.7) 821(97.9) 784(97.5) 外籍Foreign nationality 38(2.3) 18(2.1) 20(2.5) 疫苗接种情况Vaccination 13.822 0.001 未接种过疫苗No 123(7.5) 59(7.0) 64(8.0) 接种过疫苗Yes 1 124(68.4) 608(72.5) 516(64.2) 不详Unknown 396(24.1) 172(20.5) 224(27.9) 注：①以[人数(占比/%)]表示。
Note: ① [Number of people (proportion /%)].
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