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 is divided into three sublineages according to PANGO classification and derives from the B.1 lineage (D614G).
“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]
The Lineage naming rules section describes the hierarchical nomenclature and reports sublineages of B.1, so the paper supports identifying this as the classification scheme. It does not identify B.1.617, state that it has three sublineages, or link it to D614G; those specific claims are not supported by our copy. (LLM, conf=0.88)
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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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960 · see citing works
(1986) · Cited by 2,570 · see citing works
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 · see citing works
King, A. M. Q., Lefkowitz, E. J., Mushegian, A. R., Adams, M. J., Dutilh, B. E., Gorbalenya, A. E., Balázs Harrach, B., Harrison, R. L., Junglen, S., Knowles, N. J., et al. (2018) · Archives of Virology · doi:10.1007/s00705-018-3847-1 · Cited by 1,078 · see citing works
Robertson, D. L., Anderson, J. P., Bradac, J. A., Carr, J., Foley, B. T., Funkhouser, R. K., Gao, F., Hahn, B. H., Kalish, M. L., KUIKEN, C. L., et al. (2000) · Science · doi:10.1126/science.288.5463.55d · Cited by 965 · see citing works
Walker, P. J., Siddell, S. G., Lefkowitz, E. J., Mushegian, A. R., Dempsey, D. M., Dutilh, B. E., Balázs Harrach, B., Harrison, R. L., Hendrickson, R. C., Junglen, S., et al. (2019) · Archives of Virology · doi:10.1007/s00705-019-04306-w · Cited by 341 · see citing works
Continued evolution of highly pathogenic avian influenza A (H5N1): updated nomenclature
WHO/OIE/FAO H5N1 Evolution Working Group (2011) · Influenza and Other Respiratory Viruses · doi:10.1111/j.1750-2659.2011.00298.x · Cited by 257 · see citing works
An emergent clade of SARS-CoV-2 linked to returned travellers from Iran
Eden, J., Rockett, R. J., Carter, I. W. J., Rahman, H., de Ligt, J., Hadfield, J., Storey, M., Ren, X., Tulloch, R. L., Basile, K., et al. (2020) · Virus Evolution · doi:10.1093/ve/veaa027 · Cited by 159 · see citing works
Self-citationGenomic characterization and phylogenetic analysis of SARS‐COV‐2 in Italy
Zehender, G., Lai, A., Bergna, A., Meroni, L., Riva, A., Balotta, C., Tarkowski, M., Gabrieli, A., Bernacchia, D., Rusconi, S., et al. (2020) · Journal of Medical Virology · doi:10.1002/jmv.25794 · Cited by 123 · see citing works
Flagged first, then by citations
2 of the 18 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
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 · see citing works
Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2021) · Science · doi:10.1126/science.abg3055 · Cited by 2,633 · see citing works
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 · see citing works
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 · see citing works
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 1,653 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
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 · see citing works
Self-citationAssignment of epidemiological lineages in an emerging pandemic using the pangolin tool
O’Toole, A. N., 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 1,079 · see citing works
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 · see citing works
mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant
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 · see citing works
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 · see citing works
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 · see citing works
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 867 · see citing works
Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution
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 801 · see citing works
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 · see citing works
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
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 775 · see citing works
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 · see citing works
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 730 · see citing works
Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa
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 · see citing works
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 703 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity
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 · see citing works
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 · see citing works
Geographic and Genomic Distribution of SARS-CoV-2 Mutations
Mercatelli, D., & Giorgi, F. M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01800 · Cited by 589 · see citing works
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 · see citing works
Self-citationEstimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England
Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., et al. (2020) · doi:10.1101/2020.12.24.20248822 · Cited by 2,557 · see citing works
Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Deng, 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) · Cell · doi:10.1016/j.cell.2021.04.025 · Cited by 651 · see citing works
Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
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 519 · see citing works
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 · see citing works
The origins of SARS-CoV-2: A critical review
Holmes, E. C., Goldstein, S. A., Rasmussen, A. L., Robertson, D. L., Crits‐Christoph, A., Wertheim, J. O., Anthony, S. J., Barclay, W., Boni, M. F., Doherty, P. C., et al. (2021) · Cell · doi:10.1016/j.cell.2021.08.017 · Cited by 512 · see citing works
Self-citationWastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
Karthikeyan, S., Levy, J. I., Hoff, P. L. D., Humphrey, G. C., Birmingham, A., Jepsen, K., Farmer, S., Tubb, H. M., Valles, T., Tribelhorn, C., et al. (2022) · Nature · doi:10.1038/s41586-022-05049-6 · Cited by 472 · see citing works
SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern
McCallum, M., Bassi, J., De Marco, A., Chen, A., Walls, A. C., Di Iulio, J., Tortorici, M. A., Navarro, M.-J., Silacci-Fregni, C., Saliba, C., et al. (2021) · Science · doi:10.1126/science.abi7994 · Cited by 412 · see citing works
COVID-19 in Amazonas, Brazil, was driven by the persistence of endemic lineages and P.1 emergence
Naveca, F. G., do Nascimento, V. A., de Souza, V. C., Corado, A. D. L. G., Nascimento, F., Silva, G., Costa, Á., Duarte, D., Pessoa, K., Mejía, M., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01378-7 · Cited by 474 · see citing works
Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
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. (2021) · Nature · doi:10.1038/s41586-021-03677-y · Cited by 425 · see citing works
SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution
Zahradník, J., Marciano, S., Shemesh, M., Zoler, E., Harari, D., Chiaravalli, J., Meyer, B., Rudich, Y., Li, C., Marton, I., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00954-4 · Cited by 440 · see citing works
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic
Worobey, M., Levy, J. I., Serrano, L. M. M., Crits‐Christoph, A., Pekar, J. E., Goldstein, S. A., Rasmussen, A. L., Kraemer, M. U. G., Newman, C., Koopmans, M., et al. (2022) · Science · doi:10.1126/science.abp8715 · Cited by 441 · see citing works
Self-citationEstablishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK
du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutiérrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., et al. (2021) · Science · doi:10.1126/science.abf2946 · Cited by 408 · see citing works
Self-citationThe emergence, genomic diversity and global spread of SARS-CoV-2
Li, J., Lai, S., Gao, G. F., & Shi, W. (2021) · Nature · doi:10.1038/s41586-021-04188-6 · Cited by 408 · see citing works
Lu, L., Mok, B. W.-Y., Chen, L. L., Chan, J. M. C., Tsang, O. T. Y., Lam, B. H. S., Chuang, V. W., Chu, A. W., Chan, W. M., Ip, J. D., et al. (2021) · Clinical Infectious Diseases · doi:10.1093/cid/ciab1041 · Cited by 408 · see citing works
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 397 · see citing works
Self-citationSARS-CoV-2 infection in free-ranging white-tailed deer
Hale, V. L., Dennis, P. M., McBride, D. S., Nolting, J. M., Madden, C. C., Huey, D. D., Ehrlich, M., Grieser, J. M., Winston, J. A., Lombardi, D., et al. (2021) · Nature · doi:10.1038/s41586-021-04353-x · Cited by 404 · see citing works
SARS-CoV-2 within-host diversity and transmission
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 381 · see citing works
Gangavarapu, K., Latif, A. A., Mullen, J. L., Alkuzweny, M., Hufbauer, E. C., 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 393 · see citing works
Sixteen novel lineages of SARS-CoV-2 in South Africa
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 · see citing works
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 · see citing works
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 375 · see citing works
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 418 · see citing works
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 397 · see citing works
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 359 · see citing works
Self-citationBarton, M. I., MacGowan, S., Kutuzov, M. A., Dushek, O., Barton, G., & van der Merwe, P. A. (2021) · eLife · doi:10.7554/elife.70658 · Cited by 301 · see citing works
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 · see citing works
Lessons learned 1 year after SARS-CoV-2 emergence leading to COVID-19 pandemic
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 350 · see citing works
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 341 · see citing works
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 · see citing works
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 338 · see citing works
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 · see citing works
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 328 · see citing works
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 · see citing works
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 · see citing works
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 310 · see citing works
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 · see citing works
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 291 · see citing works
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 273 · see citing works
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 · see citing works
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 · see citing works
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 261 · see citing works
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 · see citing works
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 267 · see citing works
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 · see citing works
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 · see citing works
Sikkema, R. S., Pas, S. D., Nieuwenhuijse, D. F., O’Toole, A. N., 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 263 · see citing works
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 250 · see citing works
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 248 · see citing works
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 · see citing works
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 255 · see citing works
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 237 · see citing works
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 238 · see citing works
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 238 · see citing works
Self-citationAlm, E., Broberg, E., Connor, T. R., Hodcroft, E. B., Komissarov, A. B., Maurer‐Stroh, S., Melidou, A., Neher, R. A., O’Toole, A. N., Pereyaslov, D. I., et al. (2020) · Eurosurveillance · doi:10.2807/1560-7917.es.2020.25.32.2001410 · Cited by 235 · see citing works
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 229 · see citing works
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 226 · see citing works
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 223 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 210 · see citing works
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 218 · see citing works
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 216 · see citing works
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch
O’Toole, A. N., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., Network for Genomic Surveillance in South Africa (NGS-SA), Brazil-UK CADDE Genomic Network, Tegally, H., et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16661.2 · Cited by 213 · see citing works
Self-citationSARS-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 210 · see citing works
- 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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