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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
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Abstract
The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.
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“The B.1.617 lineage, which is divided into three sublineages according to the PANGO classification 12 , derives from the B.1 lineage (D614G).”
From Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization (2021) · cites this paper as [12]
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Cites
A novel coronavirus from patients with pneumonia in China, 2019
Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa2001017 · Cited by 28,244
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
Katoh, K. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf436 · Cited by 17,027
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Minh, B. Q., Schmidt, H. A., Chernomor, O., Schrempf, D., Woodhams, M. D., von Haeseler, A., & Lanfear, R. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa015 · Cited by 16,873
Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., et al. (2020) · The Lancet · doi:10.1016/s0140-6736(20)30251-8 · Cited by 11,907
Self-citationA new coronavirus associated with human respiratory disease in China
Wu, F., Zhao, S., Yu, B., Chen, Y.-M., Wang, W., Song, Z.-G., Hu, Y., Tao, Z.-W., Tian, J.-H., Pei, Y.-Y., et al. (2020) · Nature · doi:10.1038/s41586-020-2008-3 · Cited by 11,688
Self-citationUltrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844
GISAID: Global initiative on sharing all influenza data – from vision to reality
Shu, Y., & McCauley, J. (2017) · Eurosurveillance · doi:10.2807/1560-7917.es.2017.22.13.30494 · Cited by 3,039
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
(1986) · Cited by 2,570
Smith, D. B., Bukh, J., KUIKEN, C. L., Muerhoff, A. S., Rice, C. M., Stapleton, J. T., & Peter Simmonds, K. (2013) · Hepatology · doi:10.1002/hep.26744 · Cited by 1,352
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SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528
Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
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Detection of a SARS-CoV-2 variant of concern in South Africa
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2021) · Nature · doi:10.1038/s41586-021-03402-9 · Cited by 2,510
Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization
Planas, D., Veyer, D., Baidaliuk, A., Staropoli, I., Guivel-Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., et al. (2021) · Nature · doi:10.1038/s41586-021-03777-9 · Cited by 1,992
Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1038/s41586-022-04411-y · Cited by 1,678
Self-citationGenomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., et al. (2021) · Science · doi:10.1126/science.abh2644 · Cited by 1,461
Self-citationEscape from neutralizing antibodies by SARS-CoV-2 spike protein variants
Weisblum, Y., Schmidt, F., Zhang, F., DaSilva, J., Poston, D., Lorenzi, J. C., Muecksch, F., Rutkowska, M., Hoffmann, H.-H., Michailidis, E., et al. (2020) · eLife · doi:10.7554/elife.61312 · Cited by 1,308
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion
Mlcochova, P., Kemp, S. A., Dhar, M. S., Papa, G., Meng, B., Ferreira, I. A. T. M., Datir, R., Collier, D. A., Albecka, A., Singh, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03944-y · Cited by 1,337
Markov, P. V., Ghafari, M., Beer, M., Lythgoe, K., Simmonds, P., Stilianakis, N. I., & Katzourakis, A. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00878-2 · Cited by 1,179
Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., et al. (2020) · doi:10.1101/2020.12.21.20248640 · Cited by 2,535
SARS-CoV-2 evolution during treatment of chronic infection
Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., Hosmillo, M., Rees-Spear, C., Mlcochova, P., Lumb, I. U., et al. (2021) · Nature · doi:10.1038/s41586-021-03291-y · Cited by 1,097
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Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.020 · Cited by 1,006
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O’Toole, Á., Scher, E., Underwood, A. P., Jackson, B., Hill, V., McCrone, J. T., Colquhoun, R., Ruis, C., Abudahab, K., Taylor, B. E. W., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab064 · Cited by 1,082
Self-citationPartners, C.-N. M. A., Xue, Y., Bào, Y., Zhang, Z., Zhao, W., Xiao, J., He, S., Zhang, G., Li, Y., Zhao, G., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab951 · Cited by 1,037
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Garcia-Beltran, W. F., St. Denis, K. J., Hoelzemer, A., Lam, E. C., Nitido, A. D., Sheehan, M. L., Berrios, C., Ofoman, O., Chang, C. C., Hauser, B. M., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.033 · Cited by 1,045
The biological and clinical significance of emerging SARS-CoV-2 variants
Tao, K., Tzou, P. L., Nouhin, J., Gupta, R. K., de Oliveira, T., Kosakovsky Pond, S. L., Fera, D., & Shafer, R. W. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00408-x · Cited by 1,009
SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses
Dejnirattisai, W., Huo, J., Zhou, D., Zahradník, J., Supasa, P., Liu, C., Duyvesteyn, H. M. E., Ginn, H. M., Mentzer, A. J., Tuekprakhon, A., et al. (2022) · Cell · doi:10.1016/j.cell.2021.12.046 · Cited by 930
Self-citationRapid spread of the SARS-CoV-2 Delta variant in some French regions, June 2021
Alizon, S., Haïm‐Boukobza, S., Foulongne, V., Verdurme, L., Trombert‐Paolantoni, S., Lecorché, E., Roquebert, B., & Sofonea, M. T. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.28.2100573 · Cited by 870
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Cao, Y., Jian, F., Wang, J., Yu, Y., Song, W., Yisimayi, A., Wang, J., An, R., Chen, X., Zhang, N., et al. (2022) · Nature · doi:10.1038/s41586-022-05644-7 · Cited by 850
To, K. K.-W., Hung, I. F.-N., Ip, J. D., Chu, A. W.-H., Chan, W.-M., Tam, A. R., Fong, C. H.-Y., Yuan, S., Tsoi, H.-W., Ng, A. C.-K., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1275 · Cited by 746
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van Dorp, L., Acman, M., Richard, D., Shaw, L. P., Ford, C. E., Ormond, L., Owen, C. J., Pang, J., Tan, C. C. S., Boshier, F. A. T., et al. (2020) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2020.104351 · Cited by 780
Leung, K., Shum, M. H., Leung, G. M., Lam, T. T., & Wu, J. T. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.26.1.2002106 · Cited by 694
Cherian, S., Potdar, V. A., Jadhav, S., Yadav, P. D., Gupta, N., Das, M., Rakshit, P., Singh, S. K., Abraham, P., Panda, S., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9071542 · Cited by 726
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Tegally, H., Moir, M., Everatt, J., Giovanetti, M., Scheepers, C., Wilkinson, E., Subramoney, K., Makatini, Z., Moyo, S., Amoako, D. G., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01911-2 · Cited by 707
Self-citationAvanzato, V. A., Matson, M. J., Seifert, S. N., Pryce, R., Williamson, B. N., Anzick, S. L., Barbian, K., Judson, S. D., Fischer, E. R., Martens, C., et al. (2020) · Cell · doi:10.1016/j.cell.2020.10.049 · Cited by 720
Vaccine Breakthrough Infections with SARS-CoV-2 Variants
Hacisuleyman, E., Hale, C., Saito, Y., Blachere, N. E., Bergh, M., Conlon, E. G., Schaefer-Babajew, D. J., DaSilva, J., Muecksch, F., Gaebler, C., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2105000 · Cited by 716
SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020
Oreshkova, N., Molenaar, R. J., Vreman, S., Harders, F., Munnink, B. B. O., der Honing, R. W. H., Gerhards, N. M., Tolsma, P., Bouwstra, R., Sikkema, R. S., et al. (2020) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.25.23.2001005 · Cited by 700
Association Between mRNA Vaccination and COVID-19 Hospitalization and Disease Severity
Tenforde, M. W., Self, W. H., Adams, K., Gaglani, M., Ginde, A. A., McNeal, T., Ghamande, S., Douin, D. J., Talbot, H. K., Casey, J. D., et al. (2021) · JAMA · doi:10.1001/jama.2021.19499 · Cited by 633
Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., et al. (2021) · Cell · doi:10.1016/j.cell.2021.01.037 · Cited by 606
Self-citationEvolution and epidemic spread of SARS-CoV-2 in Brazil
Candido, D. S., Claro, I. M., de Jesus, J. G., Souza, W. M., Moreira, F. R. R., Dellicour, S., Mellan, T. A., du Plessis, L., Pereira, R. H. M., Sales, F. C. S., et al. (2020) · Science · doi:10.1126/science.abd2161 · Cited by 573
Self-citationLauring, A. S., Tenforde, M. W., Chappell, J. D., Gaglani, M., Ginde, A. A., McNeal, T., Ghamande, S., Douin, D. J., Talbot, H. K., Casey, J. D., et al. (2022) · BMJ · doi:10.1136/bmj-2021-069761 · Cited by 656
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Motozono, C., Toyoda, M., Zahradnik, J., Saito, A., Nasser, H., Tan, T. S., Ngare, I., Kimura, I., Uriu, K., Kosugi, Y., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.006 · Cited by 586
Addetia, A., Crawford, K. H. D., Dingens, A., Zhu, H., Roychoudhury, P., Huang, M.-L., Jerome, K. R., Bloom, J. D., & Greninger, A. L. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.02107-20 · Cited by 525
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Li, B., Deng, A., Li, K., Hu, Y., Li, Z., Shi, Y., Xiong, Q., Liu, Z., Guo, Q., Zou, L., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28089-y · Cited by 566
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Temmam, S., Vongphayloth, K., Baquero, E., Munier, S., Bonomi, M., Regnault, B., Douangboubpha, B., Karami, Y., Chrétien, D., Sanamxay, D., et al. (2022) · Nature · doi:10.1038/s41586-022-04532-4 · Cited by 553
Rivett, L., Sridhar, S., Sparkes, D., Routledge, M., Jones, N. K., Forrest, S., Young, J., Pereira-Dias, J., Hamilton, W. L., Ferris, M., et al. (2020) · eLife · doi:10.7554/elife.58728 · Cited by 519
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Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7
Meng, B., Kemp, S. A., Papa, G., Datir, R. P., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109292 · Cited by 407
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Lythgoe, K., Hall, M. D., Luca Ferretti, A., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M. I., Otecko, N. O., Wise, E. L., Moore, N. A., et al. (2021) · Science · doi:10.1126/science.abg0821 · Cited by 389
Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E., Tsueng, G., Haag, E., Zeller, M., Aceves, C. M., Zaiets, K., et al. (2023) · Nature Methods · doi:10.1038/s41592-023-01769-3 · Cited by 409
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Tegally, H., Wilkinson, E., Lessells, R. J., Giandhari, J., Pillay, S., Msomi, N., Mlisana, K., Bhiman, J. N., von Gottberg, A., Walaza, S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01255-3 · Cited by 349
Meredith, L. W., Hamilton, W. L., Warne, B., Houldcroft, C. J., Hosmillo, M. D. T., Jahun, A. S., Curran, M. D., Parmar, S., Caller, L., Caddy, S., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30562-4 · Cited by 387
Tackling COVID-19 with neutralizing monoclonal antibodies
Corti, D., Purcell, L. A., Snell, G., & Veesler, D. (2021) · Cell · doi:10.1016/j.cell.2021.05.005 · Cited by 386
Ong, S. W. X., Chiew, C. J., Ang, L. W., Mak, T. M., Cui, L., Toh, M. P. H., Lim, Y. D., Lee, P. H., Lee, T. H., Chia, P. Y., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab721 · Cited by 430
Suryadevara, N., Shrihari, S., Gilchuk, P., VanBlargan, L. A., Binshtein, E., Zost, S. J., Nargi, R. S., Sutton, R. E., Winkler, E. S., Chen, E. C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.029 · Cited by 345
The emergence of SARS-CoV-2 in Europe and North America
Worobey, M., Pekar, J. E., Larsen, B. B., Nelson, M. I., Hill, V., Joy, J. B., Rambaut, A., Suchard, M. A., Wertheim, J. O., & Lemey, P. (2020) · Science · doi:10.1126/science.abc8169 · Cited by 356
Self-citationBarton, M. I., MacGowan, S. A., Kutuzov, M. A., Dushek, O., Barton, G. J., & van der Merwe, P. A. (2021) · eLife · doi:10.7554/elife.70658 · Cited by 346
Kustin, T., Harel, N., Finkel, U., Perchik, S., Harari, S., Tahor, M., Caspi, I., Levy, R., Leshchinsky, M., Ken Dror, S., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01413-7 · Cited by 373
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To, K. K., Sridhar, S., Chiu, K. H., Hung, D. L. L., Li, X., Hung, I. F., Tam, A. R., Chung, T. W., Chan, J. F., Zhang, J., et al. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1898291 · Cited by 359
Novel SARS-CoV-2 variants: the pandemics within the pandemic
Boehm, E., Kronig, I., Neher, R. A., Eckerle, I., Vetter, P., & Kaiser, L. (2021) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.05.022 · Cited by 346
Urgent need for a non-discriminatory and non-stigmatizing nomenclature for monkeypox virus
Happi, C. T., Adetifa, I., Kingebeni, P. M., Njouom, R., Nakouné, E. R., Happi, A., Ndodo, N. D., Ayansola, O., Mboowa, G., Bedford, T., et al. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001769 · Cited by 341
Self-citationAnalysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness
Obermeyer, F. H., Jankowiak, M., Barkas, N., Schaffner, S. F., Pyle, J. D., Yurkovetskiy, L., Bosso, M., Park, D. J., Babadi, M., MacInnis, B. L., et al. (2022) · Science · doi:10.1126/science.abm1208 · Cited by 332
Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons
Kissler, S. M., Fauver, J. R., Mack, C., Tai, C. G., Breban, M. I., Watkins, A. E., Samant, R. M., Anderson, D. J., Metti, J., Khullar, G., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmc2102507 · Cited by 335
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Washington, N. L., Gangavarapu, K., Zeller, M., Bolze, A., Cirulli, E. T., Barrett, K. M. S., Larsen, B. B., Anderson, C., White, S., Cassens, T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.052 · Cited by 324
Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020Preprint
Hodcroft, E. B., Zuber, M., Nadeau, S., Vaughan, T. G., Crawford, K. H. D., Althaus, C. L., Reichmuth, M. L., Bowen, J. E., Walls, A. C., Corti, D., et al. (2020) · medRxiv · doi:10.1101/2020.10.25.20219063 · Cited by 326
An integrated national scale SARS-CoV-2 genomic surveillance network
(2020) · The Lancet Microbe · doi:10.1016/s2666-5247(20)30054-9 · Cited by 261
No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
van Dorp, L., Richard, D., Tan, C. C. S., Shaw, L. P., Acman, M., & Balloux, F. (2020) · Nature Communications · doi:10.1038/s41467-020-19818-2 · Cited by 311
Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Dhar, M. S., Marwal, R., Radhakrishnan, V., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., et al. (2021) · doi:10.1101/2021.06.02.21258076 · Cited by 296
Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India
Dhar, M. S., Marwal, R., Radhakrishnan, V. S., Ponnusamy, K., Jolly, B., Bhoyar, R. C., Sardana, V., Naushin, S., Rophina, M., Mellan, T. A., et al. (2021) · Science · doi:10.1126/science.abj9932 · Cited by 300
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.003 · Cited by 282
Su, Y. C. F., Anderson, D. E., Young, B. E., Linster, M., Zhu, F., Jayakumar, J., Zhuang, Y., Kalimuddin, S., Low, J. G. H., Tan, C. W., et al. (2020) · mBio · doi:10.1128/mbio.01610-20 · Cited by 313
SARS-CoV-2 Variants of Interest and Concern naming scheme conducive for global discourse
Konings, F. A. J., Perkins, M. D., Kuhn, J. H., Pallen, M. J., Alm, E., Archer, B. N., Barakat, A., Bedford, T., Bhiman, J. N., Caly, L., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00932-w · Cited by 276
Self-citationCryptic transmission of SARS-CoV-2 in Washington state
Bedford, T., Greninger, A. L., Roychoudhury, P., Starita, L. M., Famulare, M., Huang, M.-L. W., Nalla, A. K., Pepper, G., Reinhardt, A., Xie, H. J., et al. (2020) · Science · doi:10.1126/science.abc0523 · Cited by 270
Cherian, S., Potdar, V., Jadhav, S., Yadav, P., Gupta, N., Das, M., Rakshit, P., Singh, S., Abraham, P., Panda, S., et al. (2021) · doi:10.1101/2021.04.22.440932 · Cited by 730
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
Bull, R. A., Adikari, T. N., Ferguson, J. M., Hammond, J. W., Stevanovski, I., Beukers, A. G., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20075-6 · Cited by 275
Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission
Pickering, B., Lung, O., Maguire, F., Kruczkiewicz, P., Kotwa, J. D., Buchanan, T., Gagnier, M., Guthrie, J. L., Jardine, C. M., Marchand‐Austin, A., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01268-9 · Cited by 266
Planas, D., Veyer, D. L., Baidaliuk, A., Staropoli, I., Guivel‐Benhassine, F., Rajah, M. M., Planchais, C., Porrot, F., Robillard, N., Puech, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.26.445838 · Cited by 272
Sikkema, R. S., Pas, S. D., Nieuwenhuijse, D. F., O’Toole, Á., Verweij, J. J., van der Linden, A., Chestakova, I., Schapendonk, C. M. E., Pronk, M., Lexmond, P., et al. (2020) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(20)30527-2 · Cited by 265
Self-citationRapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa
Viana, R. P. E. S., Moyo, S. M., Amoako, D. G., Tegally, H., Scheepers, C., Althaus, C. L., Anyaneji, U. J., Bester, P. A., Boni, M. F., Chand, M., et al. (2022) · Nature · doi:10.1101/2021.12.19.21268028 · Cited by 253
Self-citationThe molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
Pekar, J. E., Magee, A. F., Parker, E., Moshiri, N., Izhikevich, K., Havens, J. L., Gangavarapu, K., Serrano, L. M. M., Crits‐Christoph, A., Matteson, N. L., et al. (2022) · Science · doi:10.1126/science.abp8337 · Cited by 277
Self-citationDeng, X., Garcia-Knight, M. A., Khalid, M. M., Servellita, V., Wang, C., Morris, M. K., Sotomayor-González, A., Glasner, D. R., Reyes, K. R., Gliwa, A. S., et al. (2021) · doi:10.1101/2021.03.07.21252647 · Cited by 651
Innate immune evasion strategies of SARS-CoV-2
Minkoff, J. M., & tenOever, B. R. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-022-00839-1 · Cited by 267
SARS-CoV-2 Vaccines Based on the Spike Glycoprotein and Implications of New Viral Variants
Martínez-Flores, D., Zepeda–Cervantes, J., Cruz-Reséndiz, A., Aguirre‐Sampieri, S., Sampieri, A., & Vaca, L. A. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.701501 · Cited by 244
Elslande, J. V., Vermeersch, P., Vandervoort, K., Wawina-Bokalanga, T., Vanmechelen, B., Wollants, E., Laenen, L., André, E., Ranst, M. A. V., Lagrou, K., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa1330 · Cited by 271
Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic
Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R., Darby, A. C., Haldenby, S. T., Hill, V., Lucaci, A. O., McCrone, J. T., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.014 · Cited by 229
Self-citationAlm, E., Broberg, E., Connor, T. R., Hodcroft, E. B., Komissarov, A. B., Maurer‐Stroh, S., Melidou, A., Neher, R. A., O’Toole, Á., Pereyaslov, D. I., et al. (2020) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.25.32.2001410 · Cited by 224
The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology
Munnink, B. B. O., Worp, N., Nieuwenhuijse, D. F., Sikkema, R. S., Haagmans, B. L., Fouchier, R. A. M., & Koopmans, M. (2021) · Nature Medicine · doi:10.1038/s41591-021-01472-w · Cited by 238
Emergence and expansion of SARS-CoV-2 B.1.526 after identification in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M. S., Zucker, J. E., Sheng, Z., Gomez‐Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · Nature · doi:10.1038/s41586-021-03908-2 · Cited by 227
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
Vogels, C. B. F., Breban, M. I., Ott, I. M., Alpert, T., Petrone, M. E., Watkins, A. E., Kalinich, C. C., Earnest, R., Rothman, J. E., de Jesus, J. G., et al. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001236 · Cited by 225
Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Kemp, S. A., Meng, B., Ferriera, I. A., Datir, R., Harvey, W. T., Papa, G., Lytras, S., Collier, D. A., Mohamed, A., Gallo, G., et al. (2020) · doi:10.1101/2020.12.14.422555 · Cited by 252
Prado, T., Fumian, T. M., Mannarino, C. F., Resende, P. C., Motta, F. C., Eppinghaus, A. L. F., do Vale, V. H. C., Braz, R. M. S., de Andrade, J. D. S. R., Maranhão, A. G., et al. (2021) · Water Research · doi:10.1016/j.watres.2021.116810 · Cited by 223
A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa
Wilkinson, E., Giovanetti, M., Tegally, H., San, J. E., Lessells, R. J., Cuadros, D. F., Martin, D. P., Rasmussen, D. A., Zekri, A. N., Sangaré, A. K., et al. (2021) · Science · doi:10.1126/science.abj4336 · Cited by 213
The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance
Kimura, I., Kosugi, Y., Wu, J., Zahradník, J., Yamasoba, D., Butlertanaka, E. P., Tanaka, Y., Uriu, K., Liu, Y., Morizako, N., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.110218 · Cited by 215
Mutations and Evolution of the SARS-CoV-2 Spike Protein
Magazine, N., Zhang, T., Wu, Y., McGee, M. C., Veggiani, G., & Huang, W. (2022) · Viruses · doi:10.3390/v14030640 · Cited by 225
Izquierdo-Lara, R. W., Elsinga, G., Heijnen, L., Munnink, B. B. O., Schapendonk, C. M. E., Nieuwenhuijse, D. F., Kon, M., Lu, L., Aarestrup, F. M., Lycett, S., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2705.204410 · Cited by 217
SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells
Minervina, A. A., Pogorelyy, M. V., Kirk, A. M., Crawford, J. C., Allen, E. K., Chou, C., Mettelman, R. C., Allison, K., Lin, C.-Y., Brice, D. C., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01184-4 · Cited by 221
Ke, R., Martinez, P. P., Smith, R. L., Gibson, L. L., Mirza, A., Conte, M., Gallagher, N., Luo, C. H., Jarrett, J., Zhou, R., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01105-z · Cited by 209
Metadata
- Authors
- Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G.
- Affiliations
- University of Edinburgh (GB)
- The University of Sydney (AU)
- University of Cambridge (GB)
- University of Oxford (GB)
- Corresponding author
- Rambaut, Andrew
- Holmes, Edward C.
- Pybus, Oliver G.
- ORCID
- Venue
- Nature Microbiology
- Published
- 2020-07-15
- Volume
- 5
- Issue
- 11
- Pages
- 1403-1407
- ISSN
- 2058-5276 (ISSN-L)
- PMC
- PMC7610519
- OpenAlex
- W3043124965
- Cited by
- 2,543
- References
- 18
- Citations by year
- 2026: 86 · 2025: 141 · 2024: 235 · 2023: 365 · 2022: 700 · 2021: 851 · 2020: 163
- FWCI
- 68.76
- Type
- journal article
- Language
- en
- Update notices
- addendum (2021-01-29)
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Microbiology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- The Sydney eScholarship Repository (The University of Sydney) (submittedVersion)
- Funders
- Wellcome Trust (206298/Z/17/Z-ARTIC, FP7/2007–2013, Z/17/Z, 206298/Z/17/Z, 206298, 725422-ReservoirDOCS)
- European Commission (725422, 725422-RESERVOIRDOCS, 2007–2013, FP7 2007-2013, HORIZON2020, FP7/2007, COVID-19)
- Australian Research Council (FL170100022)
- FP7 Ideas: European Research Council (614725)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Keywords
- SARS-CoV-2, COVID-19 pandemic, virus nomenclature, phylogenetic lineages, genomic epidemiology
- MeSH terms
- Betacoronavirus, COVID-19, SARS-CoV-2, Genotype, Humans, Phylogeny, Pneumonia, Viral, Genome, Viral, Molecular Epidemiology, Coronavirus Infections, Pandemics
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