Selected article for: "genome assembly and metagenomic sequencing"
Author: Xianding Deng; Wei Gu; Scot Federman; Louis Du Plessis; Oliver Pybus; Nuno Faria; Candace Wang; Guixia Yu; Chao-Yang Pan; Hugo Guevara; Alicia Sotomayor-Gonzalez; Kelsey Zorn; Allan Gopez; Venice Servellita; Elaine Hsu; Steve Miller; Trevor Bedford; Alexander Greninger; Pavitra Roychoudhury; Michael Famulare; Helen Y Chu; Jay Shendure; Lea Starita; Catie Anderson; Karthik Gangavarapu; Mark Zeller; Emily Spencer; Kristian Andersen; Duncan MacCannell; Suxiang Tong; Gregory Armstrong; Clinton Paden; Yan Li; Ying Zhang; Scott Morrow; Matthew Willis; Bela Matyas; Sundari Mase; Olivia Kasirye; Maggie Park; Curtis Chan; Alexander Yu; Shua Chai; Elsa Villarino; Brandon Bonin; Debra Wadford; Charles Y Chiu
Title: A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage
  • Document date: 2020_3_30
    • ID: cbc98t7x_7
    Snippet: We performed MSSPE on each sample to enrich for the SARS-CoV-2 RNA genome (15), followed by metagenomic next-generation sequencing (mNGS) of pooled and indexed samples on Illumina NextSeq or MiSeq instruments (16, 17) (Figure 1A ). Virus loads for the 29 patients ranged from 1.3x10 4 -2.5x10 8 copies/mL. An average of 31 million reads (interquartile ratio, IQR, 23-57 million) were generated per sample, and virus genomes were assembled by mapping .....
    Document: We performed MSSPE on each sample to enrich for the SARS-CoV-2 RNA genome (15), followed by metagenomic next-generation sequencing (mNGS) of pooled and indexed samples on Illumina NextSeq or MiSeq instruments (16, 17) (Figure 1A ). Virus loads for the 29 patients ranged from 1.3x10 4 -2.5x10 8 copies/mL. An average of 31 million reads (interquartile ratio, IQR, 23-57 million) were generated per sample, and virus genomes were assembled by mapping to reference genome NC_045512 (Wuhan-Hu-1). The assembly yielded 28 SARS-CoV-2 genomes with genome coverage >60%, and were thus included in this study. We also retained one partial genome (UC29) with 16.2% coverage, as a full genome from this individual had been already sequenced from a high-titer earlier sample by the US CDC (MT027062). The median coverage achieved across all samples was 96.5% (IQR 84.0%-99.7%).

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