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

Journal: Wellcome open research

Volume: 6

Issue: 

Year of Publication: 

Affiliated Institutions:  Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK. Department of Zoology, University of Oxford, Oxford, UK. Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, Canada. Department of Medicine, University of Toronto, Toronto, Canada. Department of Geography, University of Oxford, Oxford, UK. KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa. Botswana Institute for Technology Research and Innovation, Gaborone, Botswana. National Health Laboratory, Gaborone, Botswana. Ministry of Health and Wellness, Gaborone, Botswana. Department of Natural Sciences, Lebanese American University, Beirut, Lebanon. Faculty of Public Health, Lebanese University, Beirut, Lebanon. Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. Institute of Environmental Science and Research, Wellington, New Zealand. School of Natural and Computational Sciences, Massey University, Auckland, New Zealand. Department of Neurovirology, National Institute of Mental Health and Neurosciences, Bengaluru, India. Institute of Virology, Hannover Medical School, Hannover, Germany. Department of Biosystems Science and Engineering, ETH Zürich, Zurich, Switzerland. Istituto Zooprofilattico sperimentale della Puglia e della Basilicata, Puglia, Italy. Hospital General Universitario Gregorio Marañón; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain. Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal. Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge (INSA), Lisbon, Portugal. Central Virology Laboratory, Israel Ministry of Health, Sheba Medical Center, Ramat Gan, Israel. Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia. New South Wales Health Pathology - Institute of Clinical Pathology and Medical Research, Sydney, Australia. New South Wales Health Pathology Randwick, Prince of Wales Hospital, Sydney, Australia. Kinghorn Centre for Clinical Genomics, Sydney, Australia. Queensland Reference Centre for Microbial and Public Health Genomics, Forensic and Scientific Services, Health Support Queensland, Queensland Health South Australia Pathology, Adelaide, Australia. South Australia Pathology, Adelaide, Australia. Department of Biomedical Sciences and Human Oncology, University of Bari, Bari, Italy. Centre National de Référence des virus des infections respiratoires, Hospices Civils de Lyon, Lyon, France. University of Sydney, Sydney, Australia. Wadsworth Center, New York State Department of Health, Albany, New York, USA. ErasmusMC, Department of Viroscience, WHO collaborating centre for arbovirus and viral hemorrhagic fever Reference and Research, Rotterdam, The Netherlands. The Public Health Agency of Sweden, Department of Microbiology, Solna, Sweden. Upgraded Department of Microbiology, Osmania Medical College, Hyderabad, Telangana, India. Department of Virology, University of Helsinki, Helsinki, Finland. HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. Department of Virology, National Institute of Health, Islamabad, Pakistan. National Institute for Infectious Diseases "L. Spallanzani", Rome, Italy. Institute for Virology, Charité Universitätsmedizin, Berlin, Germany. Robert Koch-Institut, , Head, Unit , Influenza and other Respiratory Viruses, Seestr. , Berlin, Germany. WHO COVID- reference laboratory, Centre for Infectious Disease Control-National Institute for Public Health and the Environment, Bilthoven, The Netherlands. Division of Emerging Infectious Diseases, Bureau of Infectious Disease Diagnosis Control, Korea Disease Control and Prevention Agency, Cheongju-si, Chungcheongbuk-do, South Korea. University of the West Indies, St. Augustine, Trinidad and Tobago. National Virus Reference Laboratory, University College Dublin, Dublin, Ireland.

Abstract summary 

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.

Authors & Co-authors:  O'Toole Hill Pybus Watts Bogoch Khan Messina Tegally Lessells Giandhari Pillay Tumedi Nyepetsi Kebabonye Matsheka Mine Tokajian Hassan Salloum Merhi Koweyes Geoghegan de Ligt Ren Storey Freed Pattabiraman Prasad Desai Vasanthapuram Schulz Steinbrück Stadler Parisi Bianco García de Viedma Buenestado-Serrano Borges Isidro Duarte Gomes Zuckerman Mandelboim Mor Seemann Arnott Draper Gall Rawlinson Deveson Schlebusch McMahon Leong Lim Chironna Loconsole Bal Josset Holmes St George Lasek-Nesselquist Sikkema Oude Munnink Koopmans Brytting Sudha Rani Pavani Smura Heim Kurkela Umair Salman Bartolini Rueca Drosten Wolff Silander Eggink Reusken Vennema Park Carrington Sahadeo Carr Gonzalez de Oliveira Faria Rambaut Kraemer

Study Outcome 

Source Link: Visit source

Statistics
Citations :  COVID-19 Genomics UK (COG-UK) consortiumcontact@cogconsortium.uk: An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microbe. 2020;1(3):e99–100. 10.1016/S2666-5247(20)30054-9
Authors :  100
Identifiers
Doi : 121
SSN : 2398-502X
Study Population
Male,Female
Mesh Terms
Other Terms
B.1.1.7;B.1.351;N501Y;SARS-CoV-2;air travel;coronavirus;genome sequencing;genomic epidemiology;genomic surveillance;genomics;pandemic;sequencing;surveillance;virus
Study Design
Study Approach
Country of Study
South Africa
Publication Country
England