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

Author:

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 JORCID,Harrigan Richard,Snutch Terrance PORCID,Loman Nicholas JORCID,Quick JoshuaORCID

Abstract

AbstractGenome 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.

Publisher

Cold Spring Harbor Laboratory

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