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CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

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Authors

  • Dave J. Baker
  • Thanh Le Viet
  • Gemma L. Kay
  • Steven Rudder
  • Leonardo de Oliveira Martins
  • Ana P. Tedim
  • Anastasia Kolyva
  • Maria Diaz
  • Nabil-Fareed Alikhan
  • Lizzie Meadows
  • Andrew Bell
  • Ana Victoria Gutierrez
  • Alexander J. Trotter
  • Nicholas M. Thomson
  • Rachel Gilroy
  • Evelien M. Adriaenssens
  • Rachael Stanley
  • Ngozi Franslem-Elumogo
  • Reenesh Prakash
  • Andrew J. Page

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Abstract

We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.

Details

Original languageEnglish
Article number21
JournalGenome Medicine
Volume13
DOIs
Publication statusPublished - 9 Feb 2021
Peer-reviewedYes

Keywords

    Research areas

  • ARTIC, Genetic, Genome, Multiplexing, NGS, Nanopore, SARS-CoV-2, Sequencing

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