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


  • Adrian A. Pater Southern Illinois University
  • Michael S. Bosmeny Southern Illinois University
  • Adam A. White Southern Illinois University
  • Rourke J. Sylvain Southern Illinois University
  • Seth B. Eddington Southern Illinois University
  • Mansi Parasrampuria Southern Illinois University
  • Katy N. Ovington Southern Illinois University
  • Paige E. Metz Southern Illinois University
  • Abadat O. Yinusa Southern Illinois University
  • Christopher L. Barkau Southern Illinois University
  • Ramadevi Chilamkurthy Southern Illinois University
  • Scott W. Benzinger Southern Illinois University
  • Madison M. Hebert Southern Illinois University
  • Keith T. Gagnon School of Medicine Chemistry and Biochemistry Southern Illinois University


SARS-CoV-2, sequencing, nanopore, MinION, COVID-19, genome, mutations, protocol


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.


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How to Cite

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 [Internet]. 2021Sep.27 [cited 2021Oct.21];8(COVID 19 Special Issue):e155. Available from: https://jbmethods.org/jbm/article/view/360