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 Charles; Ngozi Franslem-Elumogo; John Wain; Reenesh Prakash; Emma Meader; Alison Mather; Mark Webber; Samir Dervisevic; Andrew J. Page; Justin O'Grady

doi:10.1186/s13073-021-00839-5

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 CharlesNgozi Franslem-Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison Mather, Mark Webber, Samir Dervisevic, Andrew J. Page, Justin O'Grady

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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.

Original language	English
Article number	21
Journal	Genome Medicine
Volume	13
DOIs	https://doi.org/10.1186/s13073-021-00839-5
Publication status	Published - 9 Feb 2021

Keywords

ARTIC
Genetic
Genome
Multiplexing
NGS
Nanopore
SARS-CoV-2
Sequencing

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10.1186/s13073-021-00839-5Licence: CC BY

2020.06.24.162156v2.fullAccepted author manuscript, 617 KBLicence: CC BY
Published_VersionFinal published version, 1.51 MBLicence: CC BY

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Baker, D. J., Aydin, A., Le Viet, T., Kay, G. L., Rudder, S., de Oliveira Martins, L., Tedim, A. P., Kolyva, A., Diaz, M., Alikhan, N-F., Meadows, L., Bell, A., Gutierrez, A. V., Trotter, A. J., Thomson, N. M., Gilroy, R., Griffith, L., Adriaenssens, E. M., Stanley, R., ... O'Grady, J. (2021). CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes. Genome Medicine, 13, [21]. https://doi.org/10.1186/s13073-021-00839-5

Baker, Dave J. ; Aydin, Alp ; Le Viet, Thanh ; Kay, Gemma L. ; Rudder, Steven ; de Oliveira Martins, Leonardo ; Tedim, Ana P. ; Kolyva, Anastasia ; Diaz, Maria ; Alikhan, Nabil-Fareed ; Meadows, Lizzie ; Bell, Andrew ; Gutierrez, Ana Victoria ; Trotter, Alexander J. ; Thomson, Nicholas M. ; Gilroy, Rachel ; Griffith, Luke ; Adriaenssens, Evelien M. ; Stanley, Rachael ; Charles, Ian ; Franslem-Elumogo, Ngozi ; Wain, John ; Prakash, Reenesh ; Meader, Emma ; Mather, Alison ; Webber, Mark ; Dervisevic, Samir ; Page, Andrew J. ; O'Grady, Justin. / CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes. In: Genome Medicine. 2021 ; Vol. 13.

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title = "CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes",

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",

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

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Baker, DJ, Aydin, A, Le Viet, T, Kay, GL, Rudder, S, de Oliveira Martins, L, Tedim, AP, Kolyva, A, Diaz, M, Alikhan, N-F, Meadows, L, Bell, A, Gutierrez, AV, Trotter, AJ, Thomson, NM, Gilroy, R, Griffith, L, Adriaenssens, EM, Stanley, R , Charles, I, Franslem-Elumogo, N, Wain, J, Prakash, R, Meader, E, Mather, A , Webber, M, Dervisevic, S, Page, AJ & O'Grady, J 2021, 'CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes', Genome Medicine, vol. 13, 21. https://doi.org/10.1186/s13073-021-00839-5

CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes. / Baker, Dave J. ; Aydin, Alp; Le Viet, Thanh; Kay, Gemma L. ; Rudder, Steven; de Oliveira Martins, Leonardo; Tedim, Ana P. ; Kolyva, Anastasia; Diaz, Maria; Alikhan, Nabil-Fareed; Meadows, Lizzie; Bell, Andrew; Gutierrez, Ana Victoria ; Trotter, Alexander J.; Thomson, Nicholas M.; Gilroy, Rachel; Griffith, Luke; Adriaenssens, Evelien M. ; Stanley, Rachael ; Charles, Ian; Franslem-Elumogo, Ngozi; Wain, John; Prakash, Reenesh; Meader, Emma; Mather, Alison ; Webber, Mark; Dervisevic, Samir; Page, Andrew J.; O'Grady, Justin.

In: Genome Medicine, Vol. 13, 21, 09.02.2021.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes

AU - Baker, Dave J.

AU - Aydin, Alp

AU - Le Viet, Thanh

AU - Kay, Gemma L.

AU - Rudder, Steven

AU - de Oliveira Martins, Leonardo

AU - Tedim, Ana P.

AU - Kolyva, Anastasia

AU - Diaz, Maria

AU - Alikhan, Nabil-Fareed

AU - Meadows, Lizzie

AU - Bell, Andrew

AU - Gutierrez, Ana Victoria

AU - Trotter, Alexander J.

AU - Thomson, Nicholas M.

AU - Gilroy, Rachel

AU - Griffith, Luke

AU - Adriaenssens, Evelien M.

AU - Stanley, Rachael

AU - Charles, Ian

AU - Franslem-Elumogo, Ngozi

AU - Wain, John

AU - Prakash, Reenesh

AU - Meader, Emma

AU - Mather, Alison

AU - Webber, Mark

AU - Dervisevic, Samir

AU - Page, Andrew J.

AU - O'Grady, Justin

PY - 2021/2/9

Y1 - 2021/2/9

N2 - 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.

AB - 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.

KW - ARTIC

KW - Genetic

KW - Genome

KW - Multiplexing

KW - NGS

KW - Nanopore

KW - SARS-CoV-2

KW - Sequencing

UR - http://www.scopus.com/inward/record.url?scp=85100781737&partnerID=8YFLogxK

U2 - 10.1186/s13073-021-00839-5

DO - 10.1186/s13073-021-00839-5

M3 - Article

VL - 13

JO - Genome Medicine

JF - Genome Medicine

SN - 1756-994X

M1 - 21

ER -

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

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Keywords

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