Genome Medicine (Feb 2021)
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
- 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,
- Justin O’Grady
Affiliations
- Dave J. Baker
- Quadram Institute Bioscience, Norwich Research Park
- Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park
- Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park
- Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park
- Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park
- Leonardo de Oliveira Martins
- Quadram Institute Bioscience, Norwich Research Park
- Ana P. Tedim
- Quadram Institute Bioscience, Norwich Research Park
- Anastasia Kolyva
- Quadram Institute Bioscience, Norwich Research Park
- Maria Diaz
- Quadram Institute Bioscience, Norwich Research Park
- Nabil-Fareed Alikhan
- Quadram Institute Bioscience, Norwich Research Park
- Lizzie Meadows
- Quadram Institute Bioscience, Norwich Research Park
- Andrew Bell
- Quadram Institute Bioscience, Norwich Research Park
- Ana Victoria Gutierrez
- Quadram Institute Bioscience, Norwich Research Park
- Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park
- Nicholas M. Thomson
- Quadram Institute Bioscience, Norwich Research Park
- Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park
- Luke Griffith
- University of East Anglia, Norwich Research Park
- Evelien M. Adriaenssens
- Quadram Institute Bioscience, Norwich Research Park
- Rachael Stanley
- Norfolk and Norwich University Hospital
- Ian G. Charles
- Quadram Institute Bioscience, Norwich Research Park
- Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park
- John Wain
- Quadram Institute Bioscience, Norwich Research Park
- Reenesh Prakash
- Norfolk and Norwich University Hospital
- Emma Meader
- Norfolk and Norwich University Hospital
- Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park
- Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park
- Samir Dervisevic
- Norfolk and Norwich University Hospital
- Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park
- Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park
- DOI
- https://doi.org/10.1186/s13073-021-00839-5
- Journal volume & issue
-
Vol. 13,
no. 1
pp. 1 – 11
Abstract
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
