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

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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


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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