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 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 XiaoJianxiong 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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

102 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)997-1003.e9
JournalCell
Volume181
Issue number5
DOIs
Publication statusPublished - 28 May 2020
Externally publishedYes

Bibliographical note

Funding Information:
We gratefully acknowledge the efforts of local CDCs, hospitals, and the third-party detection institutions in epidemiological investigations, sample collection, and detection. We would like to thank all the authors who have kindly deposited and shared genome data on GISAID. A table with genome sequence acknowledgments can be found in Table S1.4 . This work was supported by grants from Guangdong Provincial Novel Coronavirus Scientific and Technological Project ( 2020111107001 ), Science and Technology Planning Project of Guangdong ( 2018B020207006 ), and the Key Research and Development Program of Guangdong Province ( 2019B111103001 ). O.G.P., M.U.G.K., and L.d.P. were supported by the Oxford Martin School . V.H. is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) ( BB/M010996/1 ). N.R.F. acknowledges funding from a Wellcome Trust and Royal Society Sir Henry Dale Fellowship ( 204311/Z/16/Z ) and from a Medical Research Council and FAPESP award ( MR/S0195/1 ). J.Q. is funded by a UK Research and Innovation Future Leaders Fellowship . A.R. is supported by the European Research Council ( 725422-ReservoirDOCS ). This work was supported by the Wellcome Trust ARTIC network (Collaborators Award 206298/Z/17/Z ).

Funding Information:
We gratefully acknowledge the efforts of local CDCs, hospitals, and the third-party detection institutions in epidemiological investigations, sample collection, and detection. We would like to thank all the authors who have kindly deposited and shared genome data on GISAID. A table with genome sequence acknowledgments can be found in Table S1.4. This work was supported by grants from Guangdong Provincial Novel Coronavirus Scientific and Technological Project (2020111107001), Science and Technology Planning Project of Guangdong (2018B020207006), and the Key Research and Development Program of Guangdong Province (2019B111103001). O.G.P. M.U.G.K. and L.d.P. were supported by the Oxford Martin School. V.H. is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/M010996/1). N.R.F. acknowledges funding from a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and from a Medical Research Council and FAPESP award (MR/S0195/1). J.Q. is funded by a UK Research and Innovation Future Leaders Fellowship. A.R. is supported by the European Research Council (725422-ReservoirDOCS). This work was supported by the Wellcome Trust ARTIC network (Collaborators Award206298/Z/17/Z). J. Lu. O.G.P. and C.K. designed the study. J. Lu, Z.L. H.L. J. Sun, J.P. Q.X. R.Y. L.Z. P.Z. C.L. W.L. J. Su, H.Z. B.P. S.F. W.S. K.L. R.S. R.B. X.T. M.L. and T.S. undertook fieldwork and experiments. L.d.P. J. Lu, Z.L. V.H. S.F. J.T.M. L.Y. J.Q. A.R. N.L. J.R. and O.G.P. performed genetic analyses. L.d.P. M.K. M.U.G.K. J. Liu, J.X. J.H. T.L. and W.M. performed epidemiological analyses. J.R. J. Lu, L.d.P. V.H. N.R.F. and O.G.P. wrote the manuscript. L.d.P. J. Lu, V.H. M.U.G.K. A.R. J.R. and O.G.P. edited the manuscript. All authors were involved in coordination, collection, processing, sequencing, and/or bioinformatics of clinical samples. All authors read and approved the contents of the manuscript. The authors declare no competing interests.

Publisher Copyright:
© 2020 Elsevier Inc.

Keywords

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

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