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

Dave J. Baker, Alp Aydin, 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, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian CharlesNgozi Franslem-Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison Mather, Mark Webber, Samir Dervisevic, Andrew J. Page, Justin O'Grady

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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.

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

Keywords

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

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