Selected article for: "genome read depth and read depth"
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_47
    Snippet: To mimic clinical samples with different viral loads, we diluted this viral RNA with SARS-CoV-2 negative RNA extracted from nasopharyngeal swab specimens. Viral loads were estimated using RT-PCR with serial diluted plasmid as a standard. At each dilution level we performed multiplex PCR and nanopore sequencing and assembly as per the approach above, except that reads were assembled against the consensus genome obtained from the original sample us.....
    Document: To mimic clinical samples with different viral loads, we diluted this viral RNA with SARS-CoV-2 negative RNA extracted from nasopharyngeal swab specimens. Viral loads were estimated using RT-PCR with serial diluted plasmid as a standard. At each dilution level we performed multiplex PCR and nanopore sequencing and assembly as per the approach above, except that reads were assembled against the consensus genome obtained from the original sample using metagenomic sequencing. As expected, relative virus load, % genome coverage and average read depth decreased at higher dilutions. Genome coverage exceeded 75% for all except the final dilution (Table S3) .

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