Genomic epidemiology of a densely sampled COVID-19 outbreak in China.

Lily Geidelberg, Olivia Boyd, David Jorgensen, Igor Siveroni, Fabrícia F Nascimento, Robert Johnson, Manon Ragonnet-Cronin, Han Fu, Haowei Wang, Xiaoyue Xi, Wei Chen, Dehui Liu, Yingying Chen, Mengmeng Tian, Wei Tan, Junjie Zai, Wanying Sun, Jiandong Li, Junhua Li, Erik M VolzXingguang Li, Qing Nie

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here, we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People's Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number ($\textit{R}$ $_{0}$) of 3.4 (95% highest posterior density interval: 2.1-5.2) in Weifang, and a mean effective reproduction number ($\textit{R$_{t)}$}$ that falls below 1 on 4 February. We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.
Original languageEnglish (US)
JournalVirus Evolution
Issue number1
StatePublished - Mar 22 2021
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2021-09-09
Acknowledgements: We gratefully acknowledge China National GeneBank at Shenzhen, China for the sequencing strategy and capacity support. We also gratefully acknowledge the laboratories that have contributed publicly available genomes via GISAID: The Public Health Agency of Sweden, Sweden; Public Health Ontario Laboratories, Canada; Pathogen Discovery, Respiratory Viruses Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, United States; Programme in Emerging Infectious Diseases, Duke-NUS Medical School, United State; Alaska State Virology Laboratory, United States; Respiratory Virus Unit, Microbiology Services Colindale, Public Health England, United Kingdom; Laboratory for Functional Genome Analysis, Dept. Genomics, Gene Center of the LMU Munich, Germany; Michigan Department of Health and Human Services, Bureau of Laboratories, United State; National Public Health Laboratory, National Centre for Infectious Diseases, Singapore; BGI-shenzhen & The First Affiliated Hospital of Guangzhou Medical University, China; NSW Health Pathology - Institute of Clinical Pathology and Medical Research; Westmead Hospital; University of Sydney, Australia; BCCDC Public Health Laboratory, Canada; COVID-19 Genomics UK (COG-UK) Consortium, United Kingdom; Guangdong Provincial Institution of Public Health, China; Department of Microbiology, Guangdong Provincial Center for Diseases Control and Prevention, China; Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hong Kong; School of Public Health, The University of Hong Kong, Hong Kong; Pathogen Genomics Center, National Institute of Infectious Diseases, Japan; National Research Center for Translational Medicine (Shanghai), Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Public Health Clinical Center, China; Seattle Flu Study, United States; UW Virology Lab, United States; National Institute for Viral Disease Control & Prevention, CCDC, China; Beijing Institute of Microbiology and Epidemiology, China; National Institute for Viral Disease Control and Prevention, China CDC, China; Inspection Center of Hangzhou Center for Disease Control and Prevention, China; Pathogen Genomics Lab King Abdullah University of Science and Technology (KAUST), Saudi Arabia; Chinese PLA Institute for Disease Control and Prevention, China; National Institute of Health. Department of medical Sciences, Ministry of Public Health, Thailand; Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Greece; Wellcome Sanger Institute for the COVID-19 Genomics UK Consortium, United Kingdom; State Key Laboratory of Biotherapy of Sichuan University, China; SeqCOVID-SPAIN consortium/IBV(CSIC), Spain; Oxford University Clinical Research Unit, Hanoi, Vietnam; Institute of Environmental Science and Research (ESR), New Zealand; Erasmus Medical Center, Netherlands.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.


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