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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.
Afiliação
  • John R Tyson; Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.
  • Phillip James; Oxford Nanopore Technologies Ltd., Oxford, UK.
  • David Stoddart; Oxford Nanopore Technologies Ltd., Oxford, UK.
  • Natalie Sparks; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Arthur Wickenhagen; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
  • Grant Hall; Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
  • Ji Hyun Choi; Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
  • Hope Lapointe; Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
  • Kimia Kamelian; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
  • Andrew D Smith; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Natalie Prystajecky; British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada.
  • Ian Goodfellow; Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK.
  • Sam J Wilson; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK.
  • Richard Harrigan; Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada.
  • Terrance P Snutch; Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada.
  • Nicholas J Loman; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
  • Joshua Quick; Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK.
Preprint em Inglês | bioRxiv | ID: ppbiorxiv-283077
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 {pound}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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Texto completo: Disponível Coleções: Preprints Base de dados: bioRxiv Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint
Texto completo
Adicionar na Minha BVS
Imprimir
XML
Buscar no Google
Texto completo: Disponível Coleções: Preprints Base de dados: bioRxiv Idioma: Inglês Ano de publicação: 2020 Tipo de documento: Preprint