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

Title
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
Author
Baker, Dave J; Aydin, Alp; Le-Viet, Thanh; Kay, Gemma L; Rudder, Steven; de Oliveira Martins, Leonardo; Tedim, Ana P; Kolyva, Anastasia; Diaz, Maria; Nabil-Fareed Alikhan; 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; Reenesh Prakash; Meader, Emma; Mather, Alison E; Webber, Mark A; Dervisevic, Samir; Page, Andrew J  VIAFID ORCID Logo  ; Justin O’Grady
Pages
1-11
Section
Method
Publication year
2021
Publication date
2021
Publisher
BioMed Central
e-ISSN
1756994X
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1186/s13073-021-00839-5
ProQuest document ID
2491246762
Copyright
© 2021. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.