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 G.; Elumogo, Ngozi; Wain, John; Prakash, Reenesh; Meader, Emma; Mather, Alison E.; Webber, Mark A.; Dervisevic, Samir; Page, Andrew J.; O’Grady, Justin

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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-021-00839-5.