Author: 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
Title: Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China Document date: 2020_4_4
ID: ju9japd8_54
Snippet: All available SARS-CoV-2 sequences (n=323) on GISAID (gisaid.org) on 13 th March 2020 were downloaded. Sequences from GISAID that were error-rich, those which represented multiple sequences from the same patient, and those without a date of sampling were removed. Finally, the dataset was reduced by only retaining the earliest and most recently sampled sequences from epidemiologically linked outbreaks (e.g. the Diamond Princess cruise ship). The r.....
Document: All available SARS-CoV-2 sequences (n=323) on GISAID (gisaid.org) on 13 th March 2020 were downloaded. Sequences from GISAID that were error-rich, those which represented multiple sequences from the same patient, and those without a date of sampling were removed. Finally, the dataset was reduced by only retaining the earliest and most recently sampled sequences from epidemiologically linked outbreaks (e.g. the Diamond Princess cruise ship). The resulting dataset of 250 sequences therefore represents the global diversity of the virus while minimizing the impact of sampling bias. Sequences were aligned using MAFFT v7.4 (Katoh and Standley, 2013) and manually inspected in Geneious v11.0.3 (https://www.geneious.com). The final alignment length was 29,923 nucleotides.
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