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Genomic surveillance of COVID-19 cases in Beijing

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 B...

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Autores principales: Du, Pengcheng, Ding, Nan, Li, Jiarui, Zhang, Fujie, Wang, Qi, Chen, Zhihai, Song, Chuan, Han, Kai, Xie, Wen, Liu, Jingyuan, Wang, Linghang, Wei, Lirong, Ma, Shanfang, Hua, Mingxi, Yu, Fengting, Wang, Lin, Wang, Wei, An, Kang, Chen, Jianjun, Liu, Haizhou, Gao, Guiju, Wang, Sa, Huang, Yanyi, Wu, Angela R., Wang, Jianbin, Liu, Di, Zeng, Hui, Chen, Chen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603498/
https://www.ncbi.nlm.nih.gov/pubmed/33127911
http://dx.doi.org/10.1038/s41467-020-19345-0
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author Du, Pengcheng
Ding, Nan
Li, Jiarui
Zhang, Fujie
Wang, Qi
Chen, Zhihai
Song, Chuan
Han, Kai
Xie, Wen
Liu, Jingyuan
Wang, Linghang
Wei, Lirong
Ma, Shanfang
Hua, Mingxi
Yu, Fengting
Wang, Lin
Wang, Wei
An, Kang
Chen, Jianjun
Liu, Haizhou
Gao, Guiju
Wang, Sa
Huang, Yanyi
Wu, Angela R.
Wang, Jianbin
Liu, Di
Zeng, Hui
Chen, Chen
author_facet Du, Pengcheng
Ding, Nan
Li, Jiarui
Zhang, Fujie
Wang, Qi
Chen, Zhihai
Song, Chuan
Han, Kai
Xie, Wen
Liu, Jingyuan
Wang, Linghang
Wei, Lirong
Ma, Shanfang
Hua, Mingxi
Yu, Fengting
Wang, Lin
Wang, Wei
An, Kang
Chen, Jianjun
Liu, Haizhou
Gao, Guiju
Wang, Sa
Huang, Yanyi
Wu, Angela R.
Wang, Jianbin
Liu, Di
Zeng, Hui
Chen, Chen
author_sort Du, Pengcheng
collection PubMed
description 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.
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spelling pubmed-76034982020-11-10 Genomic surveillance of COVID-19 cases in Beijing Du, Pengcheng Ding, Nan Li, Jiarui Zhang, Fujie Wang, Qi Chen, Zhihai Song, Chuan Han, Kai Xie, Wen Liu, Jingyuan Wang, Linghang Wei, Lirong Ma, Shanfang Hua, Mingxi Yu, Fengting Wang, Lin Wang, Wei An, Kang Chen, Jianjun Liu, Haizhou Gao, Guiju Wang, Sa Huang, Yanyi Wu, Angela R. Wang, Jianbin Liu, Di Zeng, Hui Chen, Chen Nat Commun Article 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. Nature Publishing Group UK 2020-10-30 /pmc/articles/PMC7603498/ /pubmed/33127911 http://dx.doi.org/10.1038/s41467-020-19345-0 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Du, Pengcheng
Ding, Nan
Li, Jiarui
Zhang, Fujie
Wang, Qi
Chen, Zhihai
Song, Chuan
Han, Kai
Xie, Wen
Liu, Jingyuan
Wang, Linghang
Wei, Lirong
Ma, Shanfang
Hua, Mingxi
Yu, Fengting
Wang, Lin
Wang, Wei
An, Kang
Chen, Jianjun
Liu, Haizhou
Gao, Guiju
Wang, Sa
Huang, Yanyi
Wu, Angela R.
Wang, Jianbin
Liu, Di
Zeng, Hui
Chen, Chen
Genomic surveillance of COVID-19 cases in Beijing
title Genomic surveillance of COVID-19 cases in Beijing
title_full Genomic surveillance of COVID-19 cases in Beijing
title_fullStr Genomic surveillance of COVID-19 cases in Beijing
title_full_unstemmed Genomic surveillance of COVID-19 cases in Beijing
title_short Genomic surveillance of COVID-19 cases in Beijing
title_sort genomic surveillance of covid-19 cases in beijing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7603498/
https://www.ncbi.nlm.nih.gov/pubmed/33127911
http://dx.doi.org/10.1038/s41467-020-19345-0
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