• 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 G Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E Mather, Mark A Webber, Samir Dervisevic, Andrew J Page, and Justin O'Grady.
• Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
• Genome Med. 2021 Feb 9; 13 (1): 21.

AbstractWe 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.

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