CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.



Baker, Dave J, Aydin, Alp, Le-Viet, Thanh, Kay, Gemma L ORCID: 0000-0002-1176-8459, Rudder, Steven, de Oliveira Martins, Leonardo, Tedim, Ana P ORCID: 0000-0003-1016-7173, Kolyva, Anastasia, Diaz, Maria ORCID: 0000-0003-3423-9872, Alikhan, Nabil-Fareed
et al (show 19 more authors) (2021) CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes. Genome medicine, 13 (1). 21 - ?.

Access the full-text of this item by clicking on the Open Access link.

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: Humans, RNA, Viral, Genome, Viral, Pandemics, High-Throughput Nucleotide Sequencing, Whole Genome Sequencing, COVID-19, SARS-CoV-2
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 19 May 2022 07:53
Last Modified: 05 Oct 2022 20:00
DOI: 10.1186/s13073-021-00839-5
Open Access URL: https://doi.org/10.1186/s13073-021-00839-5
URI: https://livrepository.liverpool.ac.uk/id/eprint/3155103