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; Chuming 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 Pybus; Changwen Ke

We used both the maximum likelihood (ML) and Bayesian coalescent methods to explore the phylogenetic structure of SARS-CoV-2. The ML phylogeny was estimated with PhyML (Guindon et al., 2010) using the HKY+Ⲅ4 substitution model (Hasegawa et al., 1985) with gamma-distributed rate variation (Yang, 1994) . Linear regression of root-to-tip genetic distance against sampling date indicated that the SARS-CoV-2 sequences evolve in clock-like manner (r = 0.539) ( Figure S4 ). The Bayesian coalescent tree analysis was undertaken in the BEAST (Ayres et al., 2012; Suchard et al., 2018) framework, also using the HKY+Ⲅ4 substitution model with gamma-distributed rate variation with an exponential population growth tree prior and a strict molecular clock. Taxon sets were defined and used to estimate the posterior probability of monophyly and the posterior distribution of the tMRCA of observed phylogenetic clusters A-E (Supplementary Table 1 ). Four independent chains were run for 100 million states and parameters and trees were sampled every 10,000 states. Upon completion, chains were combined using LogCombiner after removing 10% of states as burn-in and convergence was assessed with Tracer (Rambaut et al., 2018) . The maximum clade credibility (MCC) tree was inferred from the Bayesian posterior tree distribution using TreeAnnotator, and visualised with figtreejs-react (https://github.com/jtmccr1/figtreejs-react@9874a5b). Code for Figure 3B is available at https://github.com/jtmccr1/tree-for-oli and a live version of the tree can be found at https://jtmccr1.github.io/tree-for-oli/. Monophyly and tMRCA (times to the most recent common ancestor) statistics were calculated for each taxon set from the posterior tree distribution.