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

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...

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Detalles Bibliográficos
Autores principales: Pater, Adrian A., Bosmeny, Michael S., White, Adam A., Sylvain, Rourke J., Eddington, Seth B., Parasrampuria, Mansi, Ovington, Katy N., Metz, Paige E., Yinusa, Abadat O., Barkau, Christopher L., Chilamkurthy, Ramadevi, Benzinger, Scott W., Hebert, Madison. M., Gagnon, Keith T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Journal of Biological Methods 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8493558/
https://www.ncbi.nlm.nih.gov/pubmed/34631911
http://dx.doi.org/10.14440/jbm.2021.360
Descripción
Sumario: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.