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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, View ORCID ProfileSam J Wilson, Richard Harrigan, View ORCID ProfileTerrance P Snutch, View ORCID ProfileNicholas J Loman, View ORCID ProfileJoshua Quick
doi: https://doi.org/10.1101/2020.09.04.283077
John R Tyson
1Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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Phillip James
2Oxford Nanopore Technologies Ltd., Oxford, UK
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David Stoddart
2Oxford Nanopore Technologies Ltd., Oxford, UK
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Natalie Sparks
3Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Arthur Wickenhagen
4MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Grant Hall
5Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
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Ji Hyun Choi
6Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Hope Lapointe
6Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Kimia Kamelian
7British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
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Andrew D Smith
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Natalie Prystajecky
7British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada
8Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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Ian Goodfellow
5Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
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Sam J Wilson
4MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Richard Harrigan
6Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada
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Terrance P Snutch
1Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
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  • ORCID record for Terrance P Snutch
Nicholas J Loman
3Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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Joshua Quick
3Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
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  • ORCID record for Joshua Quick
  • For correspondence: j.quick@bham.ac.uk
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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.

Competing Interest Statement

J.R.T., J.Q., and N.J.L. have all received travel expenses and accommodation from Oxford Nanopore Technologies to speak at organised events. P.J. and D.S. are employees of Oxford Nanopore Technologies.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 04, 2020.
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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
bioRxiv 2020.09.04.283077; doi: https://doi.org/10.1101/2020.09.04.283077
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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
bioRxiv 2020.09.04.283077; doi: https://doi.org/10.1101/2020.09.04.283077

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