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

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

in Bioinformatics / Biomedical and Life Sciences / Biomedicine / Cancer Research / Cellular biology / Consortia / Coronaviruses / COVID-19 / COVID-19 - genetics / COVID-19 - virology / Deoxyribonucleic acid / Disease transmission / DNA / DNA sequencing / Epidemiology / Genetic / Genome / Genome, Viral - genetics / Genomes / Genomics / Health aspects / High-Throughput Nucleotide Sequencing / Human Genetics / Humans / Influenza / Medical laboratories / Medicine/Public Health / Metabolomics / Method / Nanopore / Next-generation sequencing / NGS / Nucleotide sequencing / Pandemics / Public health / RNA, Viral - genetics / SARS-CoV-2 / SARS-CoV-2 - genetics / SARS-CoV-2 - pathogenicity / Sequencing / Severe acute respiratory syndrome coronavirus 2 / Systems Biology / Transposase / Whole Genome Sequencing

2021

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

2021

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2021

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Journal Article

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

de Oliveira Martins, Leonardo,

Adriaenssens, Evelien M.,

Wain, John,

Gutierrez, Ana Victoria,

Baker, Dave J.,

Page, Andrew J.,

Aydin, Alp,

Elumogo, Ngozi,

Rudder, Steven,

Meader, Emma,

Dervisevic, Samir,

Tedim, Ana P.,

Charles, Ian G.,

O’Grady, Justin,

Prakash, Reenesh,

Thomson, Nicholas M.,

Le-Viet, Thanh,

Bell, Andrew,

Webber, Mark A.,

Gilroy, Rachel,

Kolyva, Anastasia,

Mather, Alison E.,

Griffith, Luke,

Stanley, Rachael,

Diaz, Maria,

Alikhan, Nabil-Fareed,

Trotter, Alexander J.,

Kay, Gemma L.,

Meadows, Lizzie

2021

Overview

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.

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Publisher

BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC

Subject

Bioinformatics

/ Biomedical and Life Sciences