Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

The COVID-19 Genomics UK (COG-UK) Consortium; Áine O'Toole; Moritz U.G. Kraemer; Verity Hill; Oliver G. Pybus; Alexander Watts; Issac I. Bogoch; Kamran Khan; Jane P. Messina; Houriiyah Tegally; Richard R. Lessells; Jennifer Giandhari; Sureshnee Pillay; Kefentse Arnold Tumedi; Gape Nyepetsi; Malebogo Kebabonye; Maitshwarelo Matsheka; Madisa Mine; Sima Tokajian; Hamad Hassan; Tamara Salloum; Georgi Merhi; Jad Koweyes; Jemma L. Geoghegan; Joep de Ligt; Xiaoyun Ren; Matthew Storey; Nikki E. Freed; Chitra Pattabiraman; Pramada Prasad; Anita S. Desai; Ravi Vasanthapuram; Thomas F. Schulz; Lars Steinbrück; Tanja Stadler; Antonio Parisi; Angelica Bianco; Darío García de Viedma; Sergio Buenestado-Serrano; Vítor Borges; Joana Isidro; Sílvia Duarte; João Paulo Gomes; Neta S. Zuckerman; Michal Mandelboim; Orna Mor; Torsten Seemann; Alicia Arnott; Jenny Draper; Mailie Gall; William Rawlinson; Matthew Bashton; Darren Smith; Andrew Nelson; Greg Young; Clare McCann

doi:10.12688/wellcomeopenres.16661.1

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

The COVID-19 Genomics UK (COG-UK) Consortium, Áine O'Toole^*, Moritz U.G. Kraemer, Verity Hill, Oliver G. Pybus, Alexander Watts, Issac I. Bogoch, Kamran Khan, Jane P. Messina, Houriiyah Tegally, Richard R. Lessells, Jennifer Giandhari, Sureshnee Pillay, Kefentse Arnold Tumedi, Gape Nyepetsi, Malebogo Kebabonye, Maitshwarelo Matsheka, Madisa Mine, Sima Tokajian, Hamad HassanTamara Salloum, Georgi Merhi, Jad Koweyes, Jemma L. Geoghegan, Joep de Ligt, Xiaoyun Ren, Matthew Storey, Nikki E. Freed, Chitra Pattabiraman, Pramada Prasad, Anita S. Desai, Ravi Vasanthapuram, Thomas F. Schulz, Lars Steinbrück, Tanja Stadler, Antonio Parisi, Angelica Bianco, Darío García de Viedma, Sergio Buenestado-Serrano, Vítor Borges, Joana Isidro, Sílvia Duarte, João Paulo Gomes, Neta S. Zuckerman, Michal Mandelboim, Orna Mor, Torsten Seemann, Alicia Arnott, Jenny Draper, Mailie Gall, William Rawlinson, Matthew Bashton, Darren Smith, Andrew Nelson, Greg Young, Clare McCann

^*Corresponding author for this work

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Abstract

Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

Original language	English
Article number	121
Pages (from-to)	1-14
Number of pages	14
Journal	Wellcome Open Research
Volume	6
DOIs	https://doi.org/10.12688/wellcomeopenres.16661.1
Publication status	Published - 19 Sept 2021

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Air travel
B.1.1.7
B.1.351
Coronavirus
Genome sequencing
Genomic epidemiology
Genomic surveillance
Genomics
N501Y
Pandemic
SARS-CoV-2
Sequencing
Surveillance
Virus

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1c579401-4da0-4e13-a586-352009e02f4c_16661_-_aine_otooleFinal published version, 1.3 MBLicence: CC BY

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The COVID-19 Genomics UK (COG-UK) Consortium, O'Toole, Á., Kraemer, M. U. G., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., Tegally, H., Lessells, R. R., Giandhari, J., Pillay, S., Tumedi, K. A., Nyepetsi, G., Kebabonye, M., Matsheka, M., Mine, M., Tokajian, S., ... McCann, C. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research, 6, 1-14. Article 121. https://doi.org/10.12688/wellcomeopenres.16661.1

@article{eee6ba44475e4e8e86ea1127bb821ec7,

title = "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2",

abstract = "Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global\_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.",

keywords = "Air travel, B.1.1.7, B.1.351, Coronavirus, Genome sequencing, Genomic epidemiology, Genomic surveillance, Genomics, N501Y, Pandemic, SARS-CoV-2, Sequencing, Surveillance, Virus",

author = "\{The COVID-19 Genomics UK (COG-UK) Consortium\} and {\'A}ine O'Toole and Kraemer, \{Moritz U.G.\} and Verity Hill and Pybus, \{Oliver G.\} and Alexander Watts and Bogoch, \{Issac I.\} and Kamran Khan and Messina, \{Jane P.\} and Houriiyah Tegally and Lessells, \{Richard R.\} and Jennifer Giandhari and Sureshnee Pillay and Tumedi, \{Kefentse Arnold\} and Gape Nyepetsi and Malebogo Kebabonye and Maitshwarelo Matsheka and Madisa Mine and Sima Tokajian and Hamad Hassan and Tamara Salloum and Georgi Merhi and Jad Koweyes and Geoghegan, \{Jemma L.\} and \{de Ligt\}, Joep and Xiaoyun Ren and Matthew Storey and Freed, \{Nikki E.\} and Chitra Pattabiraman and Pramada Prasad and Desai, \{Anita S.\} and Ravi Vasanthapuram and Schulz, \{Thomas F.\} and Lars Steinbr{\"u}ck and Tanja Stadler and Antonio Parisi and Angelica Bianco and \{Garc{\'i}a de Viedma\}, Dar{\'i}o and Sergio Buenestado-Serrano and V{\'i}tor Borges and Joana Isidro and S{\'i}lvia Duarte and Gomes, \{Jo{\~a}o Paulo\} and Zuckerman, \{Neta S.\} and Michal Mandelboim and Orna Mor and Torsten Seemann and Alicia Arnott and Jenny Draper and Mailie Gall and William Rawlinson and Matthew Bashton and Darren Smith and Andrew Nelson and Greg Young and Clare McCann",

note = "Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: I.I.B. is supported by the Canadian Institutes of Health Research, COVID-19 Rapid Research Funding Opportunity (02179-000). K.K. is the founder of BlueDot, a social enterprise that develops digital technologies for public health. K.K., A.W., A.T.B. and C.H. are employed at BlueDot. I.I.B. has consulted for BlueDot. T.d.O. and the NGS-SA is funded by the South African Medical Research Council (SAMRC), MRC SHIP and the Department of Science and Innovation (DSI) of South Africa. N.R.F. acknowledges support from a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and a Medical Research Council-S{\~a}o Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/M010996/1]. M.U.G.K. acknowledges support from the Branco Weiss Fellowship and EU grant 874850 MOOD. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. O.G.P. , J.P.M. and M.U.G.K. acknowledge support from the Oxford Martin School. AR acknowledges the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network) and the European Research Council (grant agreement no. 725422 – ReservoirDOCS). A.OT is supported by the Wellcome Trust Hosts, Pathogens \& Global Health Programme [grant number: grant.203783/Z/16/Z] and Fast Grants [award number: 2236]. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research \& Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute.TFS acknowledges support from the Deutsche Forschungsgemeinschaft (SFB900, EXC2155 RESIST). SeqCOVID-SPAIN is supported by a grant from the Instituto de Salud Carlos III COV0020/00140.",

year = "2021",

month = sep,

day = "19",

doi = "10.12688/wellcomeopenres.16661.1",

language = "English",

volume = "6",

pages = "1--14",

journal = "Wellcome Open Research",

issn = "2398-502X",

publisher = "F1000 Research Ltd",

}

The COVID-19 Genomics UK (COG-UK) Consortium, O'Toole, Á, Kraemer, MUG, Hill, V, Pybus, OG, Watts, A, Bogoch, II, Khan, K, Messina, JP, Tegally, H, Lessells, RR, Giandhari, J, Pillay, S, Tumedi, KA, Nyepetsi, G, Kebabonye, M, Matsheka, M, Mine, M, Tokajian, S, Hassan, H, Salloum, T, Merhi, G, Koweyes, J, Geoghegan, JL, de Ligt, J, Ren, X, Storey, M, Freed, NE, Pattabiraman, C, Prasad, P, Desai, AS, Vasanthapuram, R, Schulz, TF, Steinbrück, L, Stadler, T, Parisi, A, Bianco, A, García de Viedma, D, Buenestado-Serrano, S, Borges, V, Isidro, J, Duarte, S, Gomes, JP, Zuckerman, NS, Mandelboim, M, Mor, O, Seemann, T, Arnott, A, Draper, J, Gall, M, Rawlinson, W, Bashton, M , Smith, D , Nelson, A, Young, G & McCann, C 2021, 'Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2', Wellcome Open Research, vol. 6, 121, pp. 1-14. https://doi.org/10.12688/wellcomeopenres.16661.1

TY - JOUR

T1 - Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

AU - The COVID-19 Genomics UK (COG-UK) Consortium

AU - O'Toole, Áine

AU - Kraemer, Moritz U.G.

AU - Hill, Verity

AU - Pybus, Oliver G.

AU - Watts, Alexander

AU - Bogoch, Issac I.

AU - Khan, Kamran

AU - Messina, Jane P.

AU - Tegally, Houriiyah

AU - Lessells, Richard R.

AU - Giandhari, Jennifer

AU - Pillay, Sureshnee

AU - Tumedi, Kefentse Arnold

AU - Nyepetsi, Gape

AU - Kebabonye, Malebogo

AU - Matsheka, Maitshwarelo

AU - Mine, Madisa

AU - Tokajian, Sima

AU - Hassan, Hamad

AU - Salloum, Tamara

AU - Merhi, Georgi

AU - Koweyes, Jad

AU - Geoghegan, Jemma L.

AU - de Ligt, Joep

AU - Ren, Xiaoyun

AU - Storey, Matthew

AU - Freed, Nikki E.

AU - Pattabiraman, Chitra

AU - Prasad, Pramada

AU - Desai, Anita S.

AU - Vasanthapuram, Ravi

AU - Schulz, Thomas F.

AU - Steinbrück, Lars

AU - Stadler, Tanja

AU - Parisi, Antonio

AU - Bianco, Angelica

AU - García de Viedma, Darío

AU - Buenestado-Serrano, Sergio

AU - Borges, Vítor

AU - Isidro, Joana

AU - Duarte, Sílvia

AU - Gomes, João Paulo

AU - Zuckerman, Neta S.

AU - Mandelboim, Michal

AU - Mor, Orna

AU - Seemann, Torsten

AU - Arnott, Alicia

AU - Draper, Jenny

AU - Gall, Mailie

AU - Rawlinson, William

AU - Bashton, Matthew

AU - Smith, Darren

AU - Nelson, Andrew

AU - Young, Greg

AU - McCann, Clare

N1 - Matthew Bashton, Darren L. Smith, Gregory R. Young, Clare McCann and Andrew Nelson are member of the COVID-19 Genomics UK (COG-UK) Consortium. Funding information: I.I.B. is supported by the Canadian Institutes of Health Research, COVID-19 Rapid Research Funding Opportunity (02179-000). K.K. is the founder of BlueDot, a social enterprise that develops digital technologies for public health. K.K., A.W., A.T.B. and C.H. are employed at BlueDot. I.I.B. has consulted for BlueDot. T.d.O. and the NGS-SA is funded by the South African Medical Research Council (SAMRC), MRC SHIP and the Department of Science and Innovation (DSI) of South Africa. N.R.F. acknowledges support from a Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z) and a Medical Research Council-São Paulo Research Foundation CADDE partnership award (MR/S0195/1 and FAPESP 18/14389-0). VH was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/M010996/1]. M.U.G.K. acknowledges support from the Branco Weiss Fellowship and EU grant 874850 MOOD. The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. O.G.P. , J.P.M. and M.U.G.K. acknowledge support from the Oxford Martin School. AR acknowledges the support of the Wellcome Trust (Collaborators Award 206298/Z/17/Z – ARTIC network) and the European Research Council (grant agreement no. 725422 – ReservoirDOCS). A.OT is supported by the Wellcome Trust Hosts, Pathogens & Global Health Programme [grant number: grant.203783/Z/16/Z] and Fast Grants [award number: 2236]. COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute.TFS acknowledges support from the Deutsche Forschungsgemeinschaft (SFB900, EXC2155 RESIST). SeqCOVID-SPAIN is supported by a grant from the Instituto de Salud Carlos III COV0020/00140.

PY - 2021/9/19

Y1 - 2021/9/19

N2 - Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

AB - Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.

KW - Air travel

KW - B.1.1.7

KW - B.1.351

KW - Coronavirus

KW - Genome sequencing

KW - Genomic epidemiology

KW - Genomic surveillance

KW - Genomics

KW - N501Y

KW - Pandemic

KW - SARS-CoV-2

KW - Sequencing

KW - Surveillance

KW - Virus

UR - https://www.scopus.com/pages/publications/85107141280

U2 - 10.12688/wellcomeopenres.16661.1

DO - 10.12688/wellcomeopenres.16661.1

M3 - Article

AN - SCOPUS:85107141280

SN - 2398-502X

VL - 6

SP - 1

EP - 14

JO - Wellcome Open Research

JF - Wellcome Open Research

M1 - 121

ER -

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

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Keywords

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