Wellcome Open Research (Sep 2021)
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch [version 2; peer review: 3 approved]
- Áine O'Toole,
- Verity Hill,
- Oliver G. Pybus,
- Alexander Watts,
- Issac I. Bogoch,
- Kamran Khan,
- Jane P. Messina,
- The COVID-19 Genomics UK (COG-UK) consortium,
- Network for Genomic Surveillance in South Africa (NGS-SA),
- Brazil-UK CADDE Genomic Network,
- 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,
- Swiss Viollier Sequencing Consortium,
- 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,
- SEARCH Alliance San Diego,
- 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),
- Tulio de Oliveira,
- Nuno Faria,
- Andrew Rambaut,
- Moritz U. G. Kraemer
Affiliations
- Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Alexander Watts
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada
- Issac I. Bogoch
- Department of Medicine, University of Toronto, Toronto, Canada
- Kamran Khan
- Department of Medicine, University of Toronto, Toronto, Canada
- Jane P. Messina
- Department of Geography, University of Oxford, Oxford, UK
- The COVID-19 Genomics UK (COG-UK) consortium
- Network for Genomic Surveillance in South Africa (NGS-SA)
- Brazil-UK CADDE Genomic Network
- Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Richard R. Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Kefentse Arnold Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Gape Nyepetsi
- National Health Laboratory, Gaborone, Botswana
- Malebogo Kebabonye
- Ministry of Health and Wellness, Gaborone, Botswana
- Maitshwarelo Matsheka
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Madisa Mine
- National Health Laboratory, Gaborone, Botswana
- Sima Tokajian
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Hamad Hassan
- Faculty of Public Health, Lebanese University, Beirut, Lebanon
- Tamara Salloum
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Georgi Merhi
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Jad Koweyes
- Department of Natural Sciences, Lebanese American University, Beirut, Lebanon
- Jemma L. Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Joep de Ligt
- Institute of Environmental Science and Research, Wellington, New Zealand
- Xiaoyun Ren
- Institute of Environmental Science and Research, Wellington, New Zealand
- Matthew Storey
- Institute of Environmental Science and Research, Wellington, New Zealand
- Nikki E. Freed
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Chitra Pattabiraman
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Pramada Prasad
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Anita S. Desai
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Ravi Vasanthapuram
- Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India
- Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Lars Steinbrück
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland
- Swiss Viollier Sequencing Consortium
- Antonio Parisi
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Angelica Bianco
- Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy
- Darío García de Viedma
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Sergio Buenestado-Serrano
- Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Sílvia Duarte
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal
- Neta S. Zuckerman
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Michal Mandelboim
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Orna Mor
- Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel
- Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
- Alicia Arnott
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- Jenny Draper
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- Mailie Gall
- New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia
- William Rawlinson
- New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia
- Ira Deveson
- Kinghorn Centre for Clinical Genomics, Sydney, Australia
- Sanmarié Schlebusch
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- Jamie McMahon
- Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia
- Lex Leong
- South Australia Pathology, Adelaide, Australia
- Chuan Kok Lim
- South Australia Pathology, Adelaide, Australia
- Maria Chironna
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy
- Antonin Bal
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- Laurence Josset
- Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France
- Edward Holmes
- University of Sydney, Sydney, Australia
- Kirsten St. George
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Reina S. Sikkema
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- Bas Oude Munnink
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- Marion Koopmans
- ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands
- Mia Brytting
- The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden
- V. Sudha rani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- S. Pavani
- Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India
- Teemu Smura
- Department of Virology, University of Helsinki, Helsinki, Finland
- Albert Heim
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Massab Umair
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- Muhammad Salman
- Department of Virology, National Institute of Health, Islamabad, Pakistan
- Barbara Bartolini
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy
- Christian Drosten
- Institute for Virology, Charité Universitätsmedizin, Berlin, Germany
- Thorsten Wolff
- Robert Koch-Institut, , Head, Unit 17, Influenza and other Respiratory Viruses, Seestr. 10, Berlin, Germany
- Olin Silander
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
- Dirk Eggink
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Chantal Reusken
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Harry Vennema
- WHO COVID-19 reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- Aekyung Park
- Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea
- Christine Carrington
- University of the West Indies, St. Augustine, Trinidad and Tobago
- Nikita Sahadeo
- University of the West Indies, St. Augustine, Trinidad and Tobago
- Michael Carr
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- Gabo Gonzalez
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
- SEARCH Alliance San Diego
- 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)
- Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Nuno Faria
- Department of Zoology, University of Oxford, Oxford, UK
- Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
- Moritz U. G. Kraemer
- Department of Zoology, University of Oxford, Oxford, UK
- DOI
- https://doi.org/10.12688/wellcomeopenres.16661.2
- Journal volume & issue
-
Vol. 6
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.
