Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
Open accessAbstract
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.
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SARS-CoV-2 spike-derived CD8+ T cell epitopes after natural infection, including the immunodominant HLA-A*0201-restricted peptide YLQPRTFLL also identified here, have been published, but this is to our knowledge the first report of epitopes recognized by vaccine-induced T cells.
“Although SARS-CoV-2 S-derived CD8 + T cell epitopes after natural infection have previously been published (including the immunodominant HLA-A*0201-restricted peptide YLQPRTFLL that is also identified in this Article) 37,38 , to our knowledge this is the first report of epitopes recognized by vaccine-induced T cells.”
From BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans (2021) · cites this paper as [38]
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Experimental — accuracy not yet measuredThe B.1.351 lineage is defined by the D80A and D215G mutations in the NTD; the K417N, E484K, and N501Y mutations in the RBD; and the D614G mutation in S1.
“the B.1.351 lineage, which is defined by the D80A (amino acid substitution from aspartic acid to alanine at position 80) and D215G mutations in the NTD; the K417N, E484K, and N501Y mutations in the RBD; and the D614G mutation in S1 (52, 56).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [56]
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- [9]O'Toole A: Accession IDs included in publication Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 [Data set]. Zenodo. 2021. 10.5281/zenodo.4642401 PMC8176267 34095513 · DOI
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- Authors
- O'Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., The COVID-19 Genomics UK (COG-UK) consortium, Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, 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., 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., Swiss Viollier Sequencing Consortium, 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., Seemann, T., Arnott, A., Draper, J., Gall, M., Rawlinson, W., Deveson, I., Schlebusch, S., McMahon, J., Leong, L., Lim, C. K., Chironna, M., Loconsole, D., Bal, A., Josset, L., Holmes, E., St. George, K., Lasek-Nesselquist, E., Sikkema, R. S., 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., SEARCH Alliance San Diego, Laboratory, N. V. R., SeqCOVID-Spain, Danish Covid-19 Genome Consortium (DCGC), Communicable Diseases Genomic Network (CDGN), program, D. N. S.-C.-2. S., (KDCA), D. O. E. I. D., de Oliveira, T., Faria, N., Rambaut, A., & Kraemer, M. U. G.
- Affiliations
- Yale University (US)
- Kenya Medical Research Institute (KE)
- St. Michael's Hospital (CA)
- University of Oxford (GB)
- Australian National University (AU)
- University of KwaZulu-Natal (ZA)
- Botswana Institute for Technology Research and Innovation (BW)
- Ministry of Health (BW)
- Lebanese University (LB)
- Lebanese American University (LB)
- New Zealand Institute for Public Health and Forensic Science (NZ)
- Massey University (NZ)
- National Institute of Mental Health and Neurosciences (IN)
- Medizinische Hochschule Hannover (DE)
- ETH Zurich (CH)
- Hospital General Universitario Gregorio Marañón (ES)
- National Institute of Health Dr. Ricardo Jorge (PT)
- Sheba Medical Center (IL)
- The University of Melbourne (AU)
- NSW Health Pathology (AU)
- Prince of Wales Hospital (AU)
- South Australia Pathology (AU)
- Hospices Civils de Lyon (FR)
- The University of Sydney (AU)
- Erasmus MC (NL)
- Public Health Agency of Sweden (SE)
- University College Dublin (IE)
- University of Edinburgh (GB)
- Corresponding author
- Kraemer, Moritz U. G.
- ORCID
- O'Toole, Áine
- Hill, Verity
- Pybus, Oliver G.
- Watts, Alexander
- Bogoch, Issac I.
- Khan, Kamran
- Messina, Jane P.
- Tegally, Houriiyah
- Lessells, Richard R.
- Giandhari, Jennifer
- Pillay, Sureshnee
- Tumedi, Kefentse Arnold
- Matsheka, Maitshwarelo
- Tokajian, Sima
- Hassan, Hamad
- Salloum, Tamara
- Merhi, Georgi
- Koweyes, Jad
- Geoghegan, Jemma L.
- de Ligt, Joep
- Ren, Xiaoyun
- Freed, Nikki E.
- Pattabiraman, Chitra
- Prasad, Pramada
- Desai, Anita S.
- Schulz, Thomas F.
- Steinbrück, Lars
- Stadler, Tanja
- Bianco, Angelica
- Buenestado-Serrano, Sergio
- Borges, Vítor
- Isidro, Joana
- Duarte, Sílvia
- Gomes, João Paulo
- Zuckerman, Neta S.
- Mandelboim, Michal
- Mor, Orna
- Seemann, Torsten
- Arnott, Alicia
- Draper, Jenny
- Gall, Mailie
- Rawlinson, William
- Deveson, Ira
- Schlebusch, Sanmarié
- McMahon, Jamie
- Leong, Lex
- Lim, Chuan Kok
- Chironna, Maria
- Loconsole, Daniela
- Bal, Antonin
- Josset, Laurence
- Holmes, Edward
- Sikkema, Reina S.
- Koopmans, Marion
- Sudha rani, V.
- Pavani, S.
- Smura, Teemu
- Heim, Albert
- Kurkela, Satu
- Umair, Massab
- Salman, Muhammad
- Bartolini, Barbara
- Rueca, Martina
- Drosten, Christian
- Wolff, Thorsten
- Silander, Olin
- Eggink, Dirk
- Reusken, Chantal
- Vennema, Harry
- Carrington, Christine
- Sahadeo, Nikita
- Carr, Michael
- Faria, Nuno
- Rambaut, Andrew
- Kraemer, Moritz U. G.
- Venue
- Wellcome Open Research
- Publisher
- F1000 Research Ltd
- Published
- 2021-05-19
- Volume
- 6
- Pages
- 121
- ISSN
- 2398-502X (ISSN-L)
- PMC
- PMC8176267
- OpenAlex
- W3161034134
- Cited by
- 192
- References
- 17
- Citations by year
- 2025: 5 · 2024: 13 · 2023: 36 · 2022: 61 · 2021: 77
- FWCI
- 14.81
- Type
- journal article
- Language
- en
- Update notices
- new_version (2021-09-17)
- Open access
- gold
- doi.org
- Licence
- Locations
- Wellcome Open Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Northumbria Research Link (Northumbria University) (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (acceptedVersion, cc-by)
- Publication server of the Robert Koch Institute (Robert Kock Institute) (submittedVersion, cc-by)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Työväentutkimus Vuosikirja (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Pure Amsterdam UMC (submittedVersion, cc-by)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Rivm Repository (Netherlands National Institute for Public Health and the Environment) (submittedVersion)
- Rivm (National Institute for Public Health and the Environment) (submittedVersion)
- The Sydney eScholarship Repository (The University of Sydney) (submittedVersion)
- Robert-Koch-Institut (RKI) (cc-by)
- Greater South Information System
- Funders
- European Research Council (725422)
- Medical Research Council
- Wellcome Trust (206298/Z/17/Z, grant.203783/Z/16/Z, 206298)
- Branco Weiss Fellowship – Society in Science
- Instituto de Salud Carlos III (COV0020/00140)
- South African Medical Research Council
- Fast Grants (2236)
- Department of Science and Innovation (DSI) of South Africa
- Canadian Institutes of Health Research, COVID-19 Rapid Research Funding Opportunity (02179-000)
- EU grant (874850 MOOD)
- Biotechnology and Biological Sciences Research Council (BB/M010996/1)
- BlueDot
- MRC SHIP
- Oxford Martin School
- Genome Research Limited
- Deutsche Forschungsgemeinschaft (SFB900, EXC2155 RESIST)
- Wellcome Trust and Royal Society Sir Henry Dale Fellowship (204311/Z/16/Z)
- UK Research & Innovation
- Medical Research Council-São Paulo Research Foundation CADDE partnership award (MR/S0195/1,FAPESP 18/14389-0)
- National Institute of Health Research
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, B.1.1.7 lineage, Omicron variant, international spread, genomic surveillance, passenger volume, travel, variants of concern
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