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 Sequencing was performed on 79 clinical samples (throat swabs, n=32, anal swabs n=24, nasopharyngeal swabs n=10, sputum n=13) collected from 65 patients with varying disease symptoms, ranging from asymptomatic to very severe (see methods). RT-PCR Ct (cycle threshold) values of these samples ranged from 19 to 40.86. Figure 2A displays the Ct values for the 53 samples with >50% genome coverage for which we report whole and partial genome sequences (see Figure S2 for details of all 79 samples). When Ct values are <30, sequence reads covered approximately 90% or more of the reference genome (GenBank accession number: MN908947.3) irrespective of the amplification and sequencing approach used (see Methods). However, genome coverage declined for samples with Ct >30 ( Figure S2 ). Using a Kruskal-Wallis rank sum test we found an association between sample Ct values and sample type ( Figure 2B ; p<0.001), and sample Ct values and disease severity ( Figure 2C ; p=0.03; see also Liu et al. 2020 ).