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

John R. Tyson(University of British Columbia), Phillip James(Oxford Nanopore Technologies (United Kingdom)), David Stoddart(Oxford Nanopore Technologies (United Kingdom)), Natalie Sparks(University of Birmingham), Arthur Wickenhagen(MRC University of Glasgow Centre for Virus Research), Grant Hall(University of Cambridge), Ji Hyun Choi(University of British Columbia), Hope R. Lapointe(University of British Columbia), Kimia Kamelian(BC Centre for Disease Control), Andrew D. Smith(University of British Columbia), Natalie Prystajecky(University of British Columbia), Ian Goodfellow(University of Cambridge), Sam J. Wilson(MRC University of Glasgow Centre for Virus Research), Richard Harrigan(University of British Columbia), Terrance P. Snutch(University of British Columbia), Nicholas J. Loman(University of Birmingham), Joshua Quick(University of Birmingham)
bioRxiv (Cold Spring Harbor Laboratory)
September 4, 2020
10.1101/2020.09.04.283077
Cited by 430Open Access
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Abstract

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.

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