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, Shanfang Ma, Mingxi Hua, Fengting Yu, Lin Wang, Wei Wang, Kang An, Jianjun Chen, Haizhou Liu, Guiju Gao, Sa Wang, Yanyi Huang, Angela R. Wu, Jianbin Wang (), Di Liu (), Hui Zeng () and Chen Chen ()
Additional contact information
Pengcheng Du: Capital Medical University
Nan Ding: Capital Medical University
Jiarui Li: Capital Medical University
Fujie Zhang: Capital Medical University
Qi Wang: Capital Medical University
Zhihai Chen: Capital Medical University
Chuan Song: Capital Medical University
Kai Han: Capital Medical University
Wen Xie: Capital Medical University
Jingyuan Liu: Capital Medical University
Linghang Wang: Capital Medical University
Lirong Wei: Capital Medical University
Shanfang Ma: Capital Medical University
Mingxi Hua: Capital Medical University
Fengting Yu: Capital Medical University
Lin Wang: MGI, BGI-Shenzhen
Wei Wang: MGI, BGI-Shenzhen
Kang An: BGI-Genomics, BGI-Shenzhen
Jianjun Chen: CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences
Haizhou Liu: National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences
Guiju Gao: Capital Medical University
Sa Wang: Capital Medical University
Yanyi Huang: Peking University
Angela R. Wu: Hong Kong University of Science and Technology
Jianbin Wang: Tsinghua University
Di Liu: CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences
Hui Zeng: Capital Medical University
Chen Chen: Capital Medical University

Nature Communications, 2020, vol. 11, issue 1, 1-9

Abstract: 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.

Date: 2020
References: Add references at CitEc
Citations: View citations in EconPapers (2)

Downloads: (external link)
https://www.nature.com/articles/s41467-020-19345-0 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19345-0

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-19345-0

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().