Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]

COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network; National Virus Reference Laboratory; SeqCOVID-Spain; Danish Covid-19 Genome Consortium (DCGC); Communicable Diseases Genomic Network (CDGN); Dutch National SARS-CoV-2 surveillance program; Division of Emerging Infectious Diseases (KDCA); Swiss Viollier Sequencing Consortium

doi:10.12688/wellcomeopenres.16661.2

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]

COVID-19 Genomics UK (COG-UK) consortium
, Network for Genomic Surveillance in South Africa (NGS-SA)
, Brazil-UK CADDE Genomic Network
, National Virus Reference Laboratory
, SeqCOVID-Spain
, Danish Covid-19 Genome Consortium (DCGC)
, Communicable Diseases Genomic Network (CDGN)
, Dutch National SARS-CoV-2 surveillance program
, Division of Emerging Infectious Diseases (KDCA)
, Swiss Viollier Sequencing Consortium

Virology

The Business School, Edinburgh Napier University, Edinburgh, UK
Rijksinstituut voor Volksgezondheid en Milieu (RIVM)
University of Oxford

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

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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
Pages (from-to)	121
Journal	Wellcome Open Research
Volume	6
DOIs	https://doi.org/10.12688/wellcomeopenres.16661.2
Publication status	Published - 17 Sept 2021

Bibliographical note

This article is included in the Coronavirus (COVID-19) collection.

Copyright: © 2021 O'Toole Á et al.

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10.12688/wellcomeopenres.16661.2Licence: CC BY

Tracking the international spreadFinal published version, 2.08 MBLicence: CC BY

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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
Network for Genomic Surveillance in South Africa (NGS-SA), The COVID-19 Genomics UK (COG-UK) consortium, Brazil-UK CADDE Genomic Network, Swiss Viollier Sequencing Consortium, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), 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. & 40 others, Giandhari, J., Pillay, S., Tumedi, K. A., Nyepetsi, G., Kebabonye, M., Matsheka, M., Mine, M., Tokajian, S., Hassan, H., Salloum, T., Merhi, G., Koweyes, J., Geoghegan, J. L., de Ligt, J., Ren, X., Storey, M., Freed, N. E., Pattabiraman, C., Prasad, P., Desai, A. S., Vasanthapuram, R., Schulz, T. F., Steinbrück, L., Stadler, T., Parisi, A., Bianco, A., García de Viedma, D., Buenestado-Serrano, S., Borges, V., Isidro, J., Duarte, S., Gomes, J. P., Zuckerman, N. S., Mandelboim, M., Mor, O., Sikkema, R. S., Oude Munnink, B., Koopmans, M., Eggink, D. & Reusken, C., 19 May 2021, In: Wellcome Open Research. 6, 121.
Research output: Contribution to journal › Article › Academic › peer-review

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COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA), & Swiss Viollier Sequencing Consortium (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]. Wellcome Open Research, 6, 121. https://doi.org/10.12688/wellcomeopenres.16661.2

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title = "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]",

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.",

author = "\{COVID-19 Genomics UK (COG-UK) consortium\} and \{Network for Genomic Surveillance in South Africa (NGS-SA)\} and \{Brazil-UK CADDE Genomic Network\} and \{National Virus Reference Laboratory\} and SeqCOVID-Spain and \{Danish Covid-19 Genome Consortium (DCGC)\} and \{Communicable Diseases Genomic Network (CDGN)\} and \{Dutch National SARS-CoV-2 surveillance program\} and \{Division of Emerging Infectious Diseases (KDCA)\} and \{Swiss Viollier Sequencing Consortium\} and {\'A}ine O'Toole and Sikkema, \{Reina S.\} and \{Oude Munnink\}, Bas and Marion Koopmans and Dirk Eggink and Chantal Reusken and Kraemer, \{Moritz U.G.\}",

note = "This article is included in the Coronavirus (COVID-19) collection. Copyright: {\textcopyright} 2021 O'Toole {\'A} et al.",

year = "2021",

month = sep,

day = "17",

doi = "10.12688/wellcomeopenres.16661.2",

language = "English",

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COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), Dutch National SARS-CoV-2 surveillance program, Division of Emerging Infectious Diseases (KDCA) & Swiss Viollier Sequencing Consortium 2021, 'Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]', Wellcome Open Research, vol. 6, pp. 121. https://doi.org/10.12688/wellcomeopenres.16661.2

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]. / COVID-19 Genomics UK (COG-UK) consortium; Network for Genomic Surveillance in South Africa (NGS-SA); Brazil-UK CADDE Genomic Network et al.
In: Wellcome Open Research, Vol. 6, 17.09.2021, p. 121.

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

TY - JOUR

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

T2 - [version 2]

AU - COVID-19 Genomics UK (COG-UK) consortium

AU - Network for Genomic Surveillance in South Africa (NGS-SA)

AU - Brazil-UK CADDE Genomic Network

AU - National Virus Reference Laboratory

AU - SeqCOVID-Spain

AU - Danish Covid-19 Genome Consortium (DCGC)

AU - Communicable Diseases Genomic Network (CDGN)

AU - Dutch National SARS-CoV-2 surveillance program

AU - Division of Emerging Infectious Diseases (KDCA)

AU - Swiss Viollier Sequencing Consortium

AU - O'Toole, Áine

AU - Sikkema, Reina S.

AU - Oude Munnink, Bas

AU - Koopmans, Marion

AU - Eggink, Dirk

AU - Reusken, Chantal

AU - Kraemer, Moritz U.G.

PY - 2021/9/17

Y1 - 2021/9/17

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.

U2 - 10.12688/wellcomeopenres.16661.2

DO - 10.12688/wellcomeopenres.16661.2

M3 - Article

C2 - 34095513

SN - 2398-502X

VL - 6

SP - 121

JO - Wellcome Open Research

JF - Wellcome Open Research

ER -

COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, National Virus Reference Laboratory, SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC) et al. Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]. Wellcome Open Research. 2021 Sept 17;6:121. doi: 10.12688/wellcomeopenres.16661.2

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch: [version 2]

Abstract

Bibliographical note

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Research output

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

Cite this