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

Baker, Dave J., Aydin, Alp, Le Viet, Thanh, Kay, Gemma L., Rudder, Steven, de Oliveira Martins, Leonardo, Tedim, Ana P., Kolyva, Anastasia, Diaz, Maria, Alikhan, Nabil-Fareed, Meadows, Lizzie, Bell, Andrew, Gutierrez, Ana Victoria, Trotter, Alexander J., Thomson, Nicholas M., Gilroy, Rachel, Griffith, Luke, Adriaenssens, Evelien M., Stanley, Rachael, Charles, Ian, Franslem-Elumogo, Ngozi, Wain, John, Prakash, Reenesh, Meader, Emma, Mather, Alison, Webber, Mark, Dervisevic, Samir, Page, Andrew J. and O'Grady, Justin (2021) CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes. Genome Medicine, 13. ISSN 1756-994X

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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.

Item Type: Article
Uncontrolled Keywords: artic,genetic,genome,multiplexing,ngs,nanopore,sars-cov-2,sequencing,molecular medicine,molecular biology,genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1313
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 09 Feb 2021 01:03
Last Modified: 13 May 2021 16:14
URI: https://ueaeprints.uea.ac.uk/id/eprint/79193
DOI: 10.1186/s13073-021-00839-5

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