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

Adrian A. Pater¹, Michael S. Bosmeny², Adam A. White², Rourke J. Sylvain², Seth B. Eddington², Mansi Parasrampuria², Katy N. Ovington², Paige E. Metz², Abadat O. Yinusa¹, Christopher L. Barkau², Ramadevi Chilamkurthy², Scott W. Ben-zinger¹, Madison. M. Hebert¹, Keith T. Gagnon^1,2

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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

JBM 2021 , 8(4), 1; https://doi.org/10.14440/jbm.2021.360

Published: 27 September 2021

(This article belongs to the Special Issue Methods to Facilitate SARS-CoV-2 and COVID-19 Research)

© 2021 by the author. Licensee POL Scientific, USA. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution 4.0 International License ( https://creativecommons.org/licenses/by/4.0/ )

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.

Keywords

SARS-CoV-2

sequencing

nanopore

MinION

COVID-19

genome

mutations

protocol

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