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

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

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
Available online: 25 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

Electronic Supplementary Material

10.1016j.virs.2022.01.030-ESM.docx
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