Genomic epidemiology of a densely sampled COVID19 outbreak in China
Erik Volz, Han Fu, Haowei Wang, Xiauoyue Xi, Wei Chen, Dehui Liu, Yingying Chen, Mengmeng Tian, Wei Tan, Junjie Zai, Wanying Zan, Xinguang Li, Qing Nie
doi: https://doi.org/10.1101/2020.03.09.20033365
Abstract
Analysis of genetic sequence data from the pandemic SARS Coronavirus 2 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 the reproduction number for the outbreak to be 1.99(95% CI:1.48-3.14).
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