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

The copyright holder for this preprint . https://doi.org/10.1101/2020.04.01.20047076 doi: medRxiv preprint that most detected cases were linked to travel rather than local community transmission. Despite this, there were a number of instances where sequences from Guangdong appeared to cluster together, sometimes with sequences sampled from other regions. To explore these lineages in more detail, we performed a Bayesian molecular clock analysis that places the phylogenetic history of the genomes on an estimated timescale. A summary visualisation of the maximum clade credibility tree from that analysis is shown in Figure 3B and is largely congruent with the ML tree. The current low genetic diversity of SARS-CoV-2 genomes worldwide means that most internal nodes have very low posterior probabilities; we caution that no conclusions should be drawn from these branching events as they will be informed by the phylogenetic prior distribution rather than variable nucleotide sites ( Figure 3A ). Nevertheless, five clusters (denoted A-E) containing Guangdong sequences had posterior probability support of >80% (i.e. their sequences grouped monophyletically in over 80% of trees in the posterior sample; Figure 3B ). These clusters are also observed in ML phylogeny ( Figure 3A ). From the molecular clock analysis, we were able to estimate the times of the most recent common ancestor (tMRCA) of clusteres A-E. We find that SARS-CoV-2 lineages were imported multiple . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. Figure 3,4) , none of which are placed at the root of the cluster, and it is tempting to conclude that the whole cluster derived from community transmission within Guangdong. However, 6 of the 8 genomes in this cluster reported travel from Hubei and therefore the cluster in fact represents multiple SARS-CoV-2 introductions into Guangdong, with dates of symptom onset around or shortly after the shutdown of travel from Wuhan (Figure 4) .