Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China

Yang Li; Hao-Rui Si; Yan Zhu; Nan Xie; Bei Li; Xiang-Ping Zhang; Jun-Feng Han; Hong-Hong Bao; Yong Yang; Kai Zhao; Zi-Yuan Hou; Si-Jia Cheng; Shuan-Hu Zhang; Zheng-Li Shi; Peng Zhou

doi:10.1016/j.virs.2022.01.030

April 2022

Yang Li, Hao-Rui Si, Yan Zhu, Nan Xie, Bei Li, Xiang-Ping Zhang, Jun-Feng Han, Hong-Hong Bao, Yong Yang, Kai Zhao, Zi-Yuan Hou, Si-Jia Cheng, Shuan-Hu Zhang, Zheng-Li Shi and Peng Zhou. Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China[J]. Virologica Sinica, 2022, 37(2): 187-197. doi: 10.1016/j.virs.2022.01.030

Citation: Yang Li, Hao-Rui Si, Yan Zhu, Nan Xie, Bei Li, Xiang-Ping Zhang, Jun-Feng Han, Hong-Hong Bao, Yong Yang, Kai Zhao, Zi-Yuan Hou, Si-Jia Cheng, Shuan-Hu Zhang, Zheng-Li Shi, Peng Zhou. Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China .VIROLOGICA SINICA, 2022, 37(2) : 187-197. http://dx.doi.org/10.1016/j.virs.2022.01.030

中国早期疫情时新冠病毒在具有传统社区结构中型城市的传播特征

李洋 ^a,b,c ,
司昊睿 ^a,c ,
朱燕 ^a ,
谢楠 ^b ,
李贝 ^a ,
张相萍 ^b ,
韩俊峰 ^b ,
包红红 ^b ,
杨勇 ^a,c ,
赵凯 ^a,c ,
侯自员 ^b ,
程思嘉 ^b ,
张栓虎 ^b,, ,
石正丽 ^a,, ,
周鹏 ^a,,

1. 中科院武汉病毒研究所
2. 安阳市疾病预防控制中心
3. 国家科学院大学

通讯作者： 张栓虎, ayzshlx@163.com; 石正丽, zlshi@wh.iov.cn; 周鹏, peng.zhou@wh.iov.cn
收稿日期： 2021-10-23
录用日期： 2022-01-21

摘要

武汉首次新冠疫情暴发仅几个月后，全国性的疫情就已经终结。在此期间大部分的病例发生在湖北省，少部分病例发生在其它的中国省市。虽然少数几个大城市的早期新冠疫情流行特征已见报道。但是广大中小城市的早期疫情研究仍十分少见。考虑到这些中小城市多维系着较为传统的家庭和社区结构，因此新冠病毒在这些中小城市的传播特征可能与大城市存在较大不同。在这项研究中，我们以安阳市作为中小城市的代表，对来自该地区的60条新冠病毒基因组特征进行了分析，将它们与国内外地区同时期流行的400余条新冠病毒的基因组进行了比较，进而揭示了该地区的新冠病毒流行和传播特征。基于病毒基因组的分子流行病学研究显示：安阳疫情中的新冠病毒为多源头输入，并且较大的家庭规模促使疫情延伸较广。研究者发现在同一社区暴发事件中，由于社交行为不同，新冠病毒在不同的家庭中表现出不同的传播模式。研究者捕捉到病毒突变在社区传播中从单个病例中出现、到通过跨个体传播固定，直至演变为群体优势突变的完整过程。研究指出，对病毒在宿主内的变异进行分析是一种用来研究聚集性疫情的有效方法。综上所述，这项研究提供了有关中国中小城市新冠病毒传播的新资料以及中国早期新冠疫情中病毒的进化信息。
- 流行病学
- , 社区传播
- , SNP
- , 宿主内突变

Characteristics of SARS-CoV-2 transmission in a medium-sized city with traditional communities during the early COVID-19 epidemic in China

Yang Li ^a,b,c ,
Hao-Rui Si ^a,c ,
Yan Zhu ^a ,
Nan Xie ^b ,
Bei Li ^a ,
Xiang-Ping Zhang ^b ,
Jun-Feng Han ^b ,
Hong-Hong Bao ^b ,
Yong Yang ^a,c ,
Kai Zhao ^a,c ,
Zi-Yuan Hou ^b ,
Si-Jia Cheng ^b ,
Shuan-Hu Zhang ^b,, ,
Zheng-Li Shi ^a,, ,
Peng Zhou ^a,,

a CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
b Anyang Municipal Center for Disease Control and Prevention, Anyang, 455000, China
c University of Chinese Academy of Sciences, Beijing, 101409, China

Corresponding author: Shuan-Hu Zhang, ayzshlx@163.com Zheng-Li Shi, zlshi@wh.iov.cn Peng Zhou, peng.zhou@wh.iov.cn
Received Date: 23 October 2021
Accepted Date: 21 January 2022

Abstract

The nationwide COVID-19 epidemic ended in 2020, a few months after its outbreak in Wuhan, China at the end of 2019. Most COVID-19 cases occurred in Hubei Province, with a few local outbreaks in other provinces of China. A few studies have reported the early SARS-CoV-2 epidemics in several large cities or provinces of China. However, information regarding the early epidemics in small and medium-sized cities, where there are still traditionally large families and community culture is more strongly maintained and thus, transmission profiles may differ, is limited. In this study, we characterized 60 newly sequenced SARS-CoV-2 genomes from Anyang as a representative of small and medium-sized Chinese cities, compared them with more than 400 reference genomes from the early outbreak, and studied the SARS-CoV-2 transmission profiles. Genomic epidemiology revealed multiple SARS-CoV-2 introductions in Anyang and a large-scale expansion of the epidemic because of the large family size. Moreover, our study revealed two transmission patterns in a single outbreak, which were attributed to different social activities. We observed the complete dynamic process of single-nucleotide polymorphism development during community transmission and found that intrahost variant analysis was an effective approach to studying cluster infections. In summary, our study provided new SARS-CoV-2 transmission profiles representative of small and medium-sized Chinese cities as well as information on the evolution of SARS-CoV-2 strains during the early COVID-19 epidemic in China.
- SARS-CoV-2
- , Epidemiology
- , Community transmission
- , Single-nucleotide polymorphism

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