Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Jing Lu; Louis du Plessis; Zhe Liu; Verity Hill; Min Kang; Huifang Lin; Jiufeng Sun; Sarah Francois; Moritz U. G. Kraemer; Nuno R. Faria; John T. McCrone; Jinju Peng; Qianling Xiong; Runyu Yuan; Lilian Zeng; Pingping Zhou; Chumin Liang; Lina Yi; Jun Liu; Jianpeng Xiao; Jianxiong Hu; Tao Liu; Wenjun Ma; Wei Li; Juan Su; Huanying Zheng; Bo Peng; Shisong Fang; Wenzhe Su; Kuibiao Li; Ruilin Sun; Ru Bai; Xi Tang; Minfeng Liang; Josh Quick; Tie Song; Andrew Rambaut; Nick Loman; Jayna Raghwani; Oliver G. Pybus; Changwen Ke

doi:10.1016/j.cell.2020.04.023

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Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

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Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China

Jing Lu, Louis du Plessis, Zhe Liu, Verity Hill, Min Kang, Huifang Lin, Jiufeng Sun, Sarah Francois, Moritz U. G. Kraemer, Nuno R. Faria, …

Cell, Vol.181(5), p.997

28/05/2020

DOI: https://doi.org/10.1016/j.cell.2020.04.023

PMID: 32703910

Résumé

Biochemistry & Molecular Biology

Cell Biology

Life Sciences & Biomedicine

Science & Technology

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA-positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China, we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain because of low virus genetic variation early in the pandemic. Our results illustrate how the timing, size, and duration of putative local transmission chains were constrained by national travel restrictions and by the province's large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required, because the number of cases imported from other countries has increased.

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Titre: Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China
Créateurs - sans rôle: Jing Lu - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Louis du Plessis - Univ Oxford, Dept Zool, Oxford OX1 3SZ, England
Zhe Liu - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Verity Hill - Univ Edinburgh, Inst Evolutionary Biol, Edinburgh EH8 9YL, Midlothian, Scotland
Min Kang - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Huifang Lin - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Jiufeng Sun - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Sarah Francois - Univ Oxford, Dept Zool, Oxford OX1 3SZ, England
Moritz U. G. Kraemer - Univ Oxford, Dept Zool, Oxford OX1 3SZ, England
Nuno R. Faria - Univ Oxford, Dept Zool, Oxford OX1 3SZ, England
John T. McCrone - University of Edinburgh
Jinju Peng - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Qianling Xiong - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Runyu Yuan - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Lilian Zeng - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Pingping Zhou - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Chumin Liang - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Lina Yi - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Jun Liu - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Jianpeng Xiao - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Jianxiong Hu - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Tao Liu - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Wenjun Ma - Guangdong Prov Inst Publ Hlth, Guangzhou 511430, Peoples R China
Wei Li - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Juan Su - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Huanying Zheng - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Bo Peng - Shenzhen Ctr Dis Control & Prevent, Shenzhen 518055, Peoples R China
Shisong Fang - Shenzhen Ctr Dis Control & Prevent, Shenzhen 518055, Peoples R China
Wenzhe Su - Guangzhou Ctr Dis Control & Prevent, Guangzhou 510440, Peoples R China
Kuibiao Li - Guangzhou Ctr Dis Control & Prevent, Guangzhou 510440, Peoples R China
Ruilin Sun - Guangdong Prov Second Peoples Hosp, Guangzhou 510320, Peoples R China
Ru Bai - Guangdong Prov Second Peoples Hosp, Guangzhou 510320, Peoples R China
Xi Tang - Foshan First Peoples Hosp, Foshan 528000, Peoples R China
Minfeng Liang - Foshan First Peoples Hosp, Foshan 528000, Peoples R China
Josh Quick - Univ Birmingham, Inst Microbiol & Infect, Birmingham B15 2TT, W Midlands, England
Tie Song - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Andrew Rambaut - University of Edinburgh
Nick Loman - Univ Birmingham, Inst Microbiol & Infect, Birmingham B15 2TT, W Midlands, England
Jayna Raghwani - University of Oxford
Oliver G. Pybus - University of Oxford
Changwen Ke - Guangdong Prov Ctr Dis Control & Prevent, Guangzhou 511430, Peoples R China
Détails de publication: Cell, Vol.181(5), p.997
Éditeur: Elsevier
Nombre de pages: 16
Note de subvention: 206298/Z/17/Z / Wellcome Trust Wellcome Trust Medical Research Council; UK Research & Innovation (UKRI); Medical Research Council UK (MRC) MR/S0195/1 / FAPESP; Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 725422-ReservoirDOCS / European Research Council; European Research Council (ERC) MR/S035362/1 / FLF; UK Research & Innovation (UKRI) BB/S011269/1 / UKRI; UK Research & Innovation (UKRI) 2020111107001 / Guangdong Provincial Novel Coronavirus Scientific and Technological Project 2018B020207006 / Science and Technology Planning Project of Guangdong 17/13981-0; 19/12000-1; 20/04558-0; 18/17176-8; 18/14933-2; 19/21301-5; 19/24251-9; 18/09383-3; 18/14389-0; 16/18445-7; 16/00194-8; 20/04836-0 / Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)
Identifiants: 99136565509311
Unité académique: Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Langue: English
Type de ressource: Journal article