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. 2021 Feb 9;13(1):21.
doi: 10.1186/s13073-021-00839-5.

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

Dave J Baker #  1 , Alp Aydin #  1 , Thanh Le-Viet  1 , Gemma L Kay  1 , Steven Rudder  1 , Leonardo de Oliveira Martins  1 , Ana P Tedim  1   2 , Anastasia Kolyva  1   3 , Maria Diaz  1 , Nabil-Fareed Alikhan  1 , Lizzie Meadows  1 , Andrew Bell  1 , Ana Victoria Gutierrez  1 , Alexander J Trotter  1   4 , Nicholas M Thomson  1 , Rachel Gilroy  1 , Luke Griffith  4 , Evelien M Adriaenssens  1 , Rachael Stanley  3 , Ian G Charles  1   4 , Ngozi Elumogo  1   3 , John Wain  1   4 , Reenesh Prakash  3 , Emma Meader  3 , Alison E Mather  1   4 , Mark A Webber  1   4 , Samir Dervisevic  3 , Andrew J Page #  5 , Justin O'Grady #  6   7
Affiliations

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

Dave J Baker et al. Genome Med. .

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.

Keywords: ARTIC; Genetic; Genome; Multiplexing; NGS; Nanopore; SARS-CoV-2; Sequencing.

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Conflict of interest statement

LG received a partial support for his PhD from Roche. The use of Roche technology for diagnostics in NNUH is coincidental. The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Workflow of CoronaHiT-ONT library preparation
Fig. 2
Fig. 2
Ct value of the SARS-CoV-2 positive RNA samples sequenced using all three sequencing methods vs total number of Ns in the consensus sequence for the a routine sample set b and the rapid response sample set
Fig. 3
Fig. 3
Maximum likelihood tree of the consensus genomes from each sequencing methods, showing agreement between methods for the a routine samples and b rapid response samples
See this image and copyright information in PMC

References

    1. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20(5):533–534. doi: 10.1016/S1473-3099(20)30120-1. - DOI - PMC - PubMed
    1. Shu Y, McCauley J. GISAID: global initiative on sharing all influenza data – from vision to reality. Eurosurveillance. 2017;22(13):30494. doi: 10.2807/1560-7917.ES.2017.22.13.30494. - DOI - PMC - PubMed
    1. COVID-19 Genomics UK Consortium. COVID-19 Genomics UK Consortium [Internet]. [cited 2021 Jan 22]. Available from: https://www.cogconsortium.uk/.
    1. Wu F, Zhao S, Yu B, Chen Y-M, Wang W, Song Z-G, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265–269. doi: 10.1038/s41586-020-2008-3. - DOI - PMC - PubMed
    1. ARTIC Network. ARTIC Network - real-time molecular epidemiology for outbreak response [Internet]. [cited 2021 Jan 22]. Available from: https://artic.network/.

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