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Pater AA, Bosmeny MS, White AA, et al. High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples. J Biol Methods. 2021;8:e155doi: 10.14440/jbm.2021.360.
Pater, A. A., Bosmeny, M. S., White, A. A., Sylvain, R. J., Eddington, S. B., Parasrampuria, M., Ovington, K. N., Metz, P. E., Yinusa, A. O., Barkau, C. L., Chilamkurthy, R., Benzinger, S. W., Hebert, M. M., & Gagnon, K. T. (2021). High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples. Journal of biological methods, 8e155. https://doi.org/10.14440/jbm.2021.360
Pater, Adrian A, et al. "High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples." Journal of biological methods vol. 8 (2021): e155. doi: https://doi.org/10.14440/jbm.2021.360
Pater AA, Bosmeny MS, White AA, Sylvain RJ, Eddington SB, Parasrampuria M, Ovington KN, Metz PE, Yinusa AO, Barkau CL, Chilamkurthy R, Benzinger SW, Hebert MM, Gagnon KT. High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples. J Biol Methods. 2021 Sep 27;8:e155. doi: 10.14440/jbm.2021.360. eCollection 2021. PMID: 34631911; PMCID: PMC8493558.
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J Biol Methods. 2021 Sep 27;8:e155. doi: 10.14440/jbm.2021.360. eCollection 2021.

High throughput nanopore sequencing of SARS-CoV-2 viral genomes from patient samples.

Journal of biological methods

Adrian A Pater, Michael S Bosmeny, Adam A White, Rourke J Sylvain, Seth B Eddington, Mansi Parasrampuria, Katy N Ovington, Paige E Metz, Abadat O Yinusa, Christopher L Barkau, Ramadevi Chilamkurthy, Scott W Benzinger, Madison M Hebert, Keith T Gagnon

Affiliations

  1. Chemistry and Biochemistry, Southern Illinois University, Carbondale, IL 62901, USA.
  2. Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.

PMID: 34631911 PMCID: PMC8493558 DOI: 10.14440/jbm.2021.360

Abstract

In late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking introduction, spread and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using established visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable "how-to" reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and long-read nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.

© 2013-2021 The Journal of Biological Methods, All rights reserved.

Keywords: COVID-19; MinION; SARS-CoV-2; genome; nanopore; sequencing

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