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

John R Tyson; Phillip James; David Stoddart; Natalie Sparks; Arthur Wickenhagen; Grant Hall; Ji Hyun Choi; Hope Lapointe; Kimia Kamelian; Andrew D Smith; Natalie Prystajecky; Ian Goodfellow; Sam J Wilson; Richard Harrigan; Terrance P Snutch; Nicholas J Loman; Joshua Quick

doi:10.1101/2020.09.04.283077

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

bioRxiv [Preprint]. 2020 Sep 4:2020.09.04.283077. doi: 10.1101/2020.09.04.283077.

Authors

John R Tyson¹, Phillip James², David Stoddart², Natalie Sparks³, Arthur Wickenhagen⁴, Grant Hall⁵, Ji Hyun Choi⁶, Hope Lapointe⁶, Kimia Kamelian⁷, Andrew D Smith^{1

2

3

4

5

6

7

8}, Natalie Prystajecky^{7

8}, Ian Goodfellow⁵, Sam J Wilson⁴, Richard Harrigan⁶, Terrance P Snutch¹, Nicholas J Loman³, Joshua Quick³

Affiliations

¹ Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.
² Oxford Nanopore Technologies Ltd., Oxford, UK.
³ Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
⁴ MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
⁵ Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
⁶ Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
⁷ British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
⁸ Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.

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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Preprint

Abstract

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