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

For the multiplex PCR approach, we followed the general method of multiplex PCR as described in (https://artic.network/ncov-2019) (Quick et al., 2017) . Briefly, the multiplex PCR was performed with two pooled primer mixture and the cDNA reverse transcribed with random primers was used as a template. After 35 rounds of amplification, the PCR products were collected and quantified, followed with end-repairing and barcoding ligation. Around 50 fmol of final library DNA was loaded onto the MinION. The nanopore sequencing platform takes less than 24 hours to obtain 10Gb of sequencing data, achieving between 0.3-0.6 million reads per sample. The ARTIC bioinformatics pipeline for COVID (https://artic.network/ncov-2019) was used to generate consensus sequences and call single nucleotide variants relative to the reference sequence.