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Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22,...

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Detalles Bibliográficos
Autores principales: Tyson, John R, James, Phillip, Stoddart, David, Sparks, Natalie, Wickenhagen, Arthur, Hall, Grant, Choi, Ji Hyun, Lapointe, Hope, Kamelian, Kimia, Smith, Andrew D, Prystajecky, Natalie, Goodfellow, Ian, Wilson, Sam J, Harrigan, Richard, Snutch, Terrance P, Loman, Nicholas J, Quick, Joshua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480024/
https://www.ncbi.nlm.nih.gov/pubmed/32908977
http://dx.doi.org/10.1101/2020.09.04.283077
Descripción
Sumario:Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.