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

Áine O'Toole; 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; Ira Deveson; Sanmarié Schlebusch; Jamie McMahon; Lex Leong; Chuan Kok Lim; Maria Chironna; Daniela Loconsole; Antonin Bal; Laurence Josset; Edward Holmes; Kirsten St. George; Erica Lasek-nesselquist; Reina S. Sikkema; Bas Oude Munnink; Marion Koopmans; Mia Brytting; V. Sudha Rani; S. Pavani; Teemu Smura; Albert Heim; Satu Kurkela; Massab Umair; Muhammad Salman; Barbara Bartolini; Martina Rueca; Christian Drosten; Thorsten Wolff; Olin Silander; Dirk Eggink; Chantal Reusken; Harry Vennema; Aekyung Park; Christine Carrington; Nikita Sahadeo; Michael Carr; Gabo Gonzalez; Tulio De Oliveira; Nuno Faria; Andrew Rambaut; Moritz U. G. Kraemer

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

Áine O'Toole, 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 MerhiJad 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, Ira Deveson, Sanmarié Schlebusch, Jamie McMahon, Lex Leong, Chuan Kok Lim, Maria Chironna, Daniela Loconsole, Antonin Bal, Laurence Josset, Edward Holmes, Kirsten St. George, Erica Lasek-nesselquist, Reina S. Sikkema, Bas Oude Munnink, Marion Koopmans, Mia Brytting, V. Sudha Rani, S. Pavani, Teemu Smura, Albert Heim, Satu Kurkela, Massab Umair, Muhammad Salman, Barbara Bartolini, Martina Rueca, Christian Drosten, Thorsten Wolff, Olin Silander, Dirk Eggink, Chantal Reusken, Harry Vennema, Aekyung Park, Christine Carrington, Nikita Sahadeo, Michael Carr, Gabo Gonzalez, Tulio De Oliveira, Nuno Faria, Andrew Rambaut, Moritz U. G. Kraemer

School of Biological Sciences

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

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 501YV2). 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
Number of pages	121
Journal	Wellcome Open Research
Volume	6
DOIs	https://doi.org/10.12688/wellcomeopenres.16661.1
Publication status	Published - 15 Sep 2021

Keywords

genomic surveillance
air travel
SARS-CoV-2
genomics
genome sequencing
virus
surveillance
pandemic
B.1.1.7
B.1.351
N501Y
coronavirus
sequencing
genomic epidemiology

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10.12688/wellcomeopenres.16661.1Licence: Creative Commons: Attribution (CC-BY)

Tracking the international spread of SARS-CoV-2Final published version, 1.3 MBLicence: Creative Commons: Attribution (CC-BY)

1 Finished
2 Active

Putting genomic surveillance at the heart of viral epidemic response.
Rambaut, A.
UK-based charities
1/08/17 → 31/07/24
Project: Research
The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control
Rambaut, A.
EU government bodies
1/08/17 → 31/07/23
Project: Research
Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)
Matthews, K. & Woolhouse, M.
UK-based charities
1/10/16 → 1/10/21
Project: Research

Cite this

O'Toole, Á., 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., Hassan, H., Salloum, T., ... Kraemer, M. U. G. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research, 6. https://doi.org/10.12688/wellcomeopenres.16661.1

@article{bfcabdf4fc0c47f1a658633d2737e61d,

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 501YV2). 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.",

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author = "{\'A}ine O'Toole 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 Ira Deveson and Sanmari{\'e} Schlebusch and Jamie McMahon and Lex Leong and Lim, {Chuan Kok} and Maria Chironna and Daniela Loconsole and Antonin Bal and Laurence Josset and Edward Holmes and {St. George}, Kirsten and Erica Lasek-nesselquist and Sikkema, {Reina S.} and {Oude Munnink}, Bas and Marion Koopmans and Mia Brytting and {Sudha Rani}, V. and S. Pavani and Teemu Smura and Albert Heim and Satu Kurkela and Massab Umair and Muhammad Salman and Barbara Bartolini and Martina Rueca and Christian Drosten and Thorsten Wolff and Olin Silander and Dirk Eggink and Chantal Reusken and Harry Vennema and Aekyung Park and Christine Carrington and Nikita Sahadeo and Michael Carr and Gabo Gonzalez and {De Oliveira}, Tulio and Nuno Faria and Andrew Rambaut and Kraemer, {Moritz U. G.}",

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language = "English",

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O'Toole, Á, 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, Deveson, I, Schlebusch, S, McMahon, J, Leong, L, Lim, CK, Chironna, M, Loconsole, D, Bal, A, Josset, L, Holmes, E, St. George, K, Lasek-nesselquist, E, Sikkema, RS, Oude Munnink, B, Koopmans, M, Brytting, M, Sudha Rani, V, Pavani, S, Smura, T, Heim, A, Kurkela, S, Umair, M, Salman, M, Bartolini, B, Rueca, M, Drosten, C, Wolff, T, Silander, O, Eggink, D, Reusken, C, Vennema, H, Park, A, Carrington, C, Sahadeo, N, Carr, M, Gonzalez, G, De Oliveira, T, Faria, N, Rambaut, A & Kraemer, MUG 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. 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 - O'Toole, Áine

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 - Deveson, Ira

AU - Schlebusch, Sanmarié

AU - McMahon, Jamie

AU - Leong, Lex

AU - Lim, Chuan Kok

AU - Chironna, Maria

AU - Loconsole, Daniela

AU - Bal, Antonin

AU - Josset, Laurence

AU - Holmes, Edward

AU - St. George, Kirsten

AU - Lasek-nesselquist, Erica

AU - Sikkema, Reina S.

AU - Oude Munnink, Bas

AU - Koopmans, Marion

AU - Brytting, Mia

AU - Sudha Rani, V.

AU - Pavani, S.

AU - Smura, Teemu

AU - Heim, Albert

AU - Kurkela, Satu

AU - Umair, Massab

AU - Salman, Muhammad

AU - Bartolini, Barbara

AU - Rueca, Martina

AU - Drosten, Christian

AU - Wolff, Thorsten

AU - Silander, Olin

AU - Eggink, Dirk

AU - Reusken, Chantal

AU - Vennema, Harry

AU - Park, Aekyung

AU - Carrington, Christine

AU - Sahadeo, Nikita

AU - Carr, Michael

AU - Gonzalez, Gabo

AU - De Oliveira, Tulio

AU - Faria, Nuno

AU - Rambaut, Andrew

AU - Kraemer, Moritz U. G.

PY - 2021/9/15

Y1 - 2021/9/15

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 501YV2). 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 501YV2). 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 - genomic surveillance

KW - air travel

KW - SARS-CoV-2

KW - genomics

KW - genome sequencing

KW - virus

KW - surveillance

KW - pandemic

KW - B.1.1.7

KW - B.1.351

KW - N501Y

KW - coronavirus

KW - sequencing

KW - genomic epidemiology

U2 - 10.12688/wellcomeopenres.16661.1

DO - 10.12688/wellcomeopenres.16661.1

M3 - Article

VL - 6

JO - Wellcome Open Research

JF - Wellcome Open Research

SN - 2398-502X

ER -

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

Abstract

Keywords

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Projects

Putting genomic surveillance at the heart of viral epidemic response.

The evolutionary dynamics of pathogen emergence and establishment: from Reservoir Detection to Outbreak Control

Wellcome Trust Four-Year PhD Studentship (Ms Aine O'Toole)

Cite this