Genomic surveillance of COVID-19 cases in Beijing
Pengcheng Du, Nan Ding, Jiarui Li, Fujie Zhang, Qi Wang, Zhihai Chen, Chuan Song, Kai Han, Wen Xie, Jingyuan Liu, Linghang Wang, Lirong Wei, Shan-Fang Ma, Mingxi Hua, Fengting Yu, Lin Wang, Wei Wang, Kang An, Jianjun Chen, Haizhou Liu, Guiju Gao, Sa Wang, Yanyi Huang, Angela Ruohao Wu, Jianbin Wang, Di Liu, Hui Zeng, Chen Chen
Abstract
The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.