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 François, Moritz UG Kraemer, Nuno R Faria, JT McCrone, Jinju Peng, Qianling Xiong, Runyu Yuan, Lilian Zeng, Pingping Zhou, Chumin Liang, Lina Yi, Jun Liu, Jianpeng XiaoJianxiong Hu, Tao Liu, Wenjun Ma, Wei li, Juan Su, Huanying Zheng, Bo Peng, Shisong Fang, Wenzhe Su, Li Kuibiao, Ruilin Sun, Ru Bai, Xi Tang, Minfeng Liang, Joshua Quick, Tie Song, Andrew Rambaut, Nick Loman, Jayna Raghwani, Oliver G. Pybus, Changwen Ke

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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 due to 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 as the number of cases imported from other countries has increased.
Original languageEnglish
Pages (from-to)1-7
Publication statusPublished - 30 Apr 2020

Keywords / Materials (for Non-textual outputs)

  • COVID-19
  • SARS-COV-2
  • genomic epidemiology
  • phylogenetics
  • virus evolution
  • real-time disease surveillance


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