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

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

Authors :
Alexander J. Trotter
Emma Meader
Maria Diaz
Alp Aydin
Ana Victoria Gutierrez
Lizzie Meadows
Reenesh Prakash
Steven Rudder
Ana P. Tedim
Alison E. Mather
Anastasia Kolyva
Justin O'Grady
Andrew J. Page
Dave Baker
Thanh Le-Viet
Mark A. Webber
Ian G. Charles
Nicholas M. Thomson
Evelien M. Adriaenssens
Leonardo de Oliveira Martins
Rachel Gilroy
Rachael Stanley
Nabil-Fareed Alikhan
John Wain
Samir Dervisevic
Gemma L. Kay
Ngozi Elumogo
Andrew Bell
Luke Griffith
Page, Andrew J [0000-0001-6919-6062]
Apollo - University of Cambridge Repository
Source :
Genome Medicine, Vol 13, Iss 1, Pp 1-11 (2021), Genome Medicine
Publication Year :
2021
Publisher :
BMC, 2021.

Abstract

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with ≥ 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.

Details

Language :
English
Volume :
13
Issue :
1
Database :
OpenAIRE
Journal :
Genome Medicine
Accession number :
edsair.doi.dedup.....07f6afc54018377b15e15c239b54ce27