A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Rachel Colquhoun; Áine O’Toole; Verity Hill; J T McCrone; Xiaoyu Yu; Samuel M Nicholls; Radoslaw Poplawski; Thomas Whalley; Natalie Groves; Nicholas Ellaby; Nick Loman; Tom Connor; Andrew Rambaut

doi:10.1093/ve/veae083

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Rachel Colquhoun^*, Áine O’Toole, Verity Hill, J T McCrone, Xiaoyu Yu, Samuel M Nicholls, Radoslaw Poplawski, Thomas Whalley, Natalie Groves, Nicholas Ellaby, Nick Loman, Tom Connor, Andrew Rambaut

^*Corresponding author for this work

School of Biological Sciences

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

Abstract / Description of output

In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.

Original language	English
Article number	veae083
Number of pages	6
Journal	Virus Evolution
Volume	10
Issue number	1
Early online date	17 Oct 2024
DOIs	https://doi.org/10.1093/ve/veae083
Publication status	E-pub ahead of print - 17 Oct 2024

Access to Document

10.1093/ve/veae083

veae083Final published version, 1.97 MBLicence: Creative Commons: Attribution (CC-BY)

Cite this

Colquhoun, R., O’Toole, Á., Hill, V., McCrone, J. T., Yu, X., Nicholls, S. M., Poplawski, R., Whalley, T., Groves, N., Ellaby, N., Loman, N., Connor, T., & Rambaut, A. (2024). A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK. Virus Evolution, 10(1), Article veae083. Advance online publication. https://doi.org/10.1093/ve/veae083

@article{012f7db2a4dd427ca5430bef11175130,

title = "A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK",

abstract = "In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.",

author = "Rachel Colquhoun and {\'A}ine O{\textquoteright}Toole and Verity Hill and McCrone, {J T} and Xiaoyu Yu and Nicholls, {Samuel M} and Radoslaw Poplawski and Thomas Whalley and Natalie Groves and Nicholas Ellaby and Nick Loman and Tom Connor and Andrew Rambaut",

note = "The authors would like to thank all those who generated sequences for their rapid data sharing as part of COG-UK. We also thank the research labs and public health bodies who made their genome data accessible on GISAID. We would like to thank Ben C. Jackson for the huge amount of work he put into development and maintenance of the pipeline in its first year. We thank Angie Hinrichs for her eagle eye and Derek Wright, Anthony Underwood, and Matt Bull for helpful suggestions along the way.",

year = "2024",

month = oct,

day = "17",

doi = "10.1093/ve/veae083",

language = "English",

volume = "10",

journal = "Virus Evolution",

issn = "2057-1577",

publisher = "Oxford University Press",

number = "1",

}

TY - JOUR

T1 - A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

AU - Colquhoun, Rachel

AU - O’Toole, Áine

AU - Hill, Verity

AU - McCrone, J T

AU - Yu, Xiaoyu

AU - Nicholls, Samuel M

AU - Poplawski, Radoslaw

AU - Whalley, Thomas

AU - Groves, Natalie

AU - Ellaby, Nicholas

AU - Loman, Nick

AU - Connor, Tom

AU - Rambaut, Andrew

N1 - The authors would like to thank all those who generated sequences for their rapid data sharing as part of COG-UK. We also thank the research labs and public health bodies who made their genome data accessible on GISAID. We would like to thank Ben C. Jackson for the huge amount of work he put into development and maintenance of the pipeline in its first year. We thank Angie Hinrichs for her eagle eye and Derek Wright, Anthony Underwood, and Matt Bull for helpful suggestions along the way.

PY - 2024/10/17

Y1 - 2024/10/17

N2 - In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.

AB - In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.

UR - https://github.com/COG-UK/datapipe

UR - https://github.com/virus-evolution/phylopipe

U2 - 10.1093/ve/veae083

DO - 10.1093/ve/veae083

M3 - Article

SN - 2057-1577

VL - 10

JO - Virus Evolution

JF - Virus Evolution

IS - 1

M1 - veae083

ER -

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Abstract / Description of output

Access to Document

Other files and links

Fingerprint

Putting genomic surveillance at the heart of viral epidemic response.

Wellcome Trust Four-Year PhD Studentship

Cite this

A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK

Abstract / Description of output

Access to Document

Other files and links

Fingerprint

Projects

Putting genomic surveillance at the heart of viral epidemic response.

Wellcome Trust Four-Year PhD Studentship

Cite this