The DOI matches its Crossref record; 50 of the 50 references it cites were found in a registry or an index.
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
Open accessPreprint — published as 10.1038/s41586-021-03402-9 · Paper page
Abstract
Summary: Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Additionally, K417N, Y453F, S477R, N501Y, and D614G represent circulating variants some of which have been associated with rapidly increasing case numbers14,15,19,33–35.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [19]
In the citing paper
“Recently, viral variants of concern have emerged in the UK (B.1.1.7), South Africa (B.1.351), and Brazil (P.1) that harbor specific mutations in their S proteins that may be associated with increased transmissibility (50–55).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [52]
In the citing paper
“An A701V mutation in S2 is also observed at high frequencies, whereas deletions in residues 242 to 244 as well as R246I and L18F mutations in the NTD are present at lower frequencies (52).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [52]
In the citing paper
“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 [52]
In the citing paper
“By contrast, the NTD region itself, which appears to tolerate antigenic variation in SARS-CoV-2 and other coronaviruses (50, 52, 55, 85), does not appear to be the target of cross-nAbs elicited by infection or vaccination.”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [52]
In the citing paper
“However, it should be noted that further mutations in spike protein observed in other novel lineages7, 8 appear to be driven by escape of the virus from the neutralising activity of public antibodies,40, 41 indicating that prevention of transmission might be temporary as the virus adapts to natural or vaccine-induced immunity.”
In the citing paper
“The B.1.351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K, with the latter two having particular functional impact.”
From Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant (2021) · cites this paper as [15]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · cited 1×
“It performs alignment of genotypes in MAFFT 19 , phylogenetic tree inference in IQ-Tree 20 , tree dating and ancestral state construction and annotation (https://github.com/nextstrain/ncov).”
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046 · cited 1×
“It performs alignment of genotypes in MAFFT 19 , phylogenetic tree inference in IQ-Tree 20 , tree dating and ancestral state construction and annotation (https://github.com/nextstrain/ncov).”
Posterior summarization in Bayesian phylogenetics using tracer 1.7
Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018) · Systematic Biology · doi:10.1093/sysbio/syy032 · Cited by 11,159 · cited 1×
“Convergence of MCMC chains was checked using Tracer v.1.7.1 22 .”
InfluentialStructure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., et al. (2020) · Nature · doi:10.1038/s41586-020-2180-5 · Cited by 5,983
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J., Abfalterer, W., Hengartner, N., Giorgi, E. E., Bhattacharya, T., Foley, B., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.043 · Cited by 4,281
Structural basis of receptor recognition by SARS-CoV-2
Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., Geng, Q., Auerbach, A., & Li, F. (2020) · Nature · doi:10.1038/s41586-020-2179-y · Cited by 3,661
Nextstrain: real-time tracking of pathogen evolutionPreprint
Hadfield, J., Megill, C., Bell, S. M., et al. (2017) · bioRxiv · doi:10.1101/224048 · Cited by 3,172
Nextstrain: real-time tracking of pathogen evolution
Hadfield, J., Megill, C., Bell, S. M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T., & Neher, R. A. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty407 · Cited by 3,154
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
A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology
Rambaut, A., Holmes, E. C., O’Toole, Á., Hill, V., McCrone, J. T., Ruis, C., du Plessis, L., & Pybus, O. G. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0770-5 · Cited by 2,543
Research works printed but not linked: 1
- 2020, SARS-CoV-2 seroprevalence in the Cape Town Metropolitan sub-districts after the peak of infections, NICD COVID-19 Special Public Health Surveillance Bulletin, 18, 1
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
Estimated 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 2,581
“068) 23 (18-28) 37 (29-46) UK sequence separate-slopes binomial GLMM (1|LTLA/OBS) + REGION * DATE London B.”
BackgroundInfluentialAntibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Wang, P., Nair, M. S., Liu, L., Iketani, S., Luo, Y., Guo, Y., Wang, M., Yu, J., Zhang, B., Kwong, P. D., et al. (2021) · Nature · doi:10.1038/s41586-021-03398-2 · Cited by 2,312
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., et al. (2021) · Nature · doi:10.1038/s41586-021-03324-6 · Cited by 1,343
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.003 · Cited by 1,178
“…tend to have the largest effect on plasma antibody binding to the RBD, and our neutralization assays (Figures 5A and 5D Brazil) (Faria et al., 2021; Tegally et al., 2020; Voloch et al., 2020); another mutation at the same site (E484Q) has also been found in a smaller number of human isolates…”
InfluentialSARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01285-x · Cited by 1,147
“N501Y has been shown to increase affinity for the human ACE2 receptor, which together with the repeated and independent evolution of 501Y containing lineages 25,26,31 , strongly argues for enhanced transmissibility of these new variants.”
Self-citationN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., De Marco, A., Lempp, F. A., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · Cell · doi:10.1016/j.cell.2021.03.028 · Cited by 901
“1 lineages initially identified in South Africa and Brazil (Tegally et al., 2020), would escape S2L28-mediated neutralization.”
Resurgence of COVID-19 in Manaus, Brazil, despite high seroprevalence
Sabino, E. C., Buss, L. F., Carvalho, M. P. S., Prete, C. A., Crispim, M. A. E., Fraiji, N. A., Pereira, R. H. M., Parag, K. V., da Silva Peixoto, P., Kraemer, M. U. G., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00183-5 · Cited by 758
Prospective mapping of viral mutations that escape antibodies used to treat COVID-19
Starr, T. N., Greaney, A. J., Addetia, A., Hannon, W. W., Choudhary, M. C., Dingens, A. S., Li, J. Z., & Bloom, J. D. (2021) · Science · doi:10.1126/science.abf9302 · Cited by 743
Liu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.014 · Cited by 725
“a combination of at least two neutralizing antibodies (Baum et al., 2020; Du et al., 2020; 316 Greaney et al., 2020; Group et al., 2020; Li et al., 2020; Weisblum et al., 2020).”
BackgroundFiolet, T., Kherabi, Y., MacDonald, C.-J., Ghosn, J., & Peiffer-Smadja, N. (2022) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2021.10.005 · Cited by 911
Sensitivity of infectious SARS-CoV-2 B.1.1.7 and B.1.351 variants to neutralizing antibodies
Planas, D., Bruel, T., Grzelak, L., Guivel-Benhassine, F., Staropoli, I., Porrot, F., Planchais, C., Buchrieser, J., Rajah, M. M., Bishop, E., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01318-5 · Cited by 697
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
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., et al. (2021) · doi:10.1101/2021.01.19.21249840 · Cited by 729
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies
Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., Kemp, S. A., Bassi, J., Pinto, D., Silacci-Fregni, C., et al. (2021) · Nature · doi:10.1038/s41586-021-03412-7 · Cited by 728
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Network for Genomic Surveillance in South Africa, Cele, S., COMMIT-KZN Team, Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., et al. (2021) · Nature · doi:10.1038/s41586-021-03471-w · Cited by 651
Self-citationXie, X., Liu, Y., Liu, J., Zhang, X., Zou, J., Fontes-Garfias, C. R., Xia, H., Swanson, K. A., Cutler, M., Cooper, D., et al. (2021) · Nature Medicine · doi:10.1038/s41591-021-01270-4 · Cited by 628
Self-citationThomson, 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
“, 2021) including one variant carrying three simultaneous RBM mutations (K417N, E484K, and N501Y) (Tegally et al., 2020).”
InfluentialEmary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., Blane, B., Bonsall, D., Cicconi, P., Charlton, S., et al. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00628-0 · Cited by 603
“However, it should be noted that further mutations in spike protein observed in other novel lineages 7,8 appear to be driven by escape of the virus from the neutralising activity of public antibodies, 40,41 indicating that prevention of transmission might be temporary as the virus adapts to natural…”
Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant
Shinde, V., Bhikha, S., Hoosain, Z., Archary, M., Bhorat, Q., Fairlie, L., Lalloo, U., Masilela, M. S. L., Moodley, D., Hanley, S., et al. (2021) · doi:10.1101/2021.02.25.21252477 · Cited by 625
“351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K, with the latter two having particular functional impact.(12,14,16,17) The N501Y mutation is known to increase binding affinity of the spike protein to the human angiotensin-converting enzym…”
BackgroundInfluentialEfficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant
Shinde, V., Bhikha, S., Hoosain, Z., Archary, M., Bhorat, Q., Fairlie, L., Lalloo, U., Masilela, M. S. L., Moodley, D., Hanley, S., et al. (2021) · New England Journal of Medicine · doi:10.1056/nejmoa2103055 · Cited by 625
Self-citationmRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection
Stamatatos, L., Czartoski, J., Wan, Y.-H., Homad, L. J., Rubin, V., Glantz, H., Neradilek, M., Seydoux, E., Jennewein, M. F., MacCamy, A. J., et al. (2021) · Science · doi:10.1126/science.abg9175 · Cited by 557
Estimated 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
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
Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
McCarthy, K. R., Rennick, L. J., Nambulli, S., Robinson-McCarthy, L. R., Bain, W. G., Haidar, G., & Duprex, W. P. (2021) · Science · doi:10.1126/science.abf6950 · Cited by 535
“351 (28), first reported in the United Kingdom 159 and South Africa, have deletions in RDRs 1/2 and 4, respectively.”
BackgroundSystems vaccinology of the BNT162b2 mRNA vaccine in humans
Arunachalam, P. S., Scott, M. K. D., Hagan, T., Li, C., Feng, Y., Wimmers, F., Grigoryan, L., Trisal, M., Edara, V. V., Lai, L., et al. (2021) · Nature · doi:10.1038/s41586-021-03791-x · Cited by 572
Wu, K., Werner, A. P., Moliva, J. I., Koch, M., Choi, A., Stewart-Jones, G. B. E., Bennett, H., Boyoglu-Barnum, S., Shi, W., Graham, B. S., et al. (2021) · doi:10.1101/2021.01.25.427948 · Cited by 419
“…in South Africa (B.1.351 lineage) has raised concerns due to their increased rates of transmission as well as their potential to circumvent immunity elicited by natural infection or vaccination (Volz et al., 2021; Tegally et al., 2020; Wibmer et al., 2021; Wang et al., 2021; Collier et al., 2021).”
BackgroundInfluentialStarr, T. N., Greaney, A. J., Dingens, A. S., & Bloom, J. (2021) · bioRxiv · doi:10.1101/2021.02.17.431683 · Cited by 477
SARS-CoV-2 variants and ending the COVID-19 pandemic
Fontanet, A. L., Autran, B., Lina, B., Kiény, M. P., Karim, S. S. A., & Sridhar, D. (2021) · The Lancet · doi:10.1016/s0140-6736(21)00370-6 · Cited by 535
The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates
Jones, B. E., Brown‐Augsburger, P., Corbett, K. S., Westendorf, K., Davies, J., Cujec, T. P., Wiethoff, C. M., Blackbourne, J. L., Heinz, B. A., Foster, D., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abf1906 · Cited by 546
“351 includes two other mutations at important residues in the RBD, K417N and E484K, of which only E484 falls within the epitope of LY-CoV555 (39).”
BackgroundSixteen 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
Self-citationShen, X., Tang, H., McDanal, C., Wagh, K., Fischer, W., Theiler, J., Yoon, H., Li, D., Haynes, B. F., Sanders, K. O., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.002 · Cited by 378
“Newer variants carry multiple spike mutations (Naveca et al., 2021; Rambaut et al., 2020; Tegally et al., 2020) that are a potential concern for immune escape.”
InfluentialGenomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil
Voloch, C. M., da Silva Francisco, R., de Almeida, L. G. P., Cardoso, C. C., Brustolini, O. J., Gerber, A. L., Guimarães, A. P. D. C., Mariani, D., da Costa, R. M., Ferreira, O. C., et al. (2021) · Journal of Virology · doi:10.1128/jvi.00119-21 · Cited by 372
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
“Since the start of the outbreak, circulating SARS-CoV-2 field strains have acquired genetic changes that facilitate transmission (Avanzato et al., 2020; Choi et al., 2020; Hou et al., 2020; Kemp et al., 2020; McCarthy et al., 2020; Plante et al., 2020; Rambaut et al., 2020; Tegally et al., 2020).”
The 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 427
Frampton, D., Rampling, T., Cross, A., Bailey, H., Heaney, J., Byott, M., Scott, R., Sconza, R., Price, J., Margaritis, M., et al. (2021) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(21)00170-5 · Cited by 397
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 389
“1 lineages (10, 11), which may have decreased sensitivity to natural and/or vaccineacquired immunity (12–14).”
BackgroundStructural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants
Yuan, M., Huang, D., Lee, C.-C. D., Wu, N. C., Jackson, A. M., Zhu, X., Liu, H., Peng, L., van Gils, M. J., Sanders, R. W., et al. (2021) · doi:10.1101/2021.02.16.430500 · Cited by 364
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
“1 strains are able to overcome previous immunity to SARS-CoV2 [5, 6], yet the evidence has been somewhat mixed.”
BackgroundTesting at scale during the COVID-19 pandemic
Mercer, T. R., & Salit, M. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00360-w · Cited by 399
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
“While the Beta and Gamma variants were able to outcompete Alpha in South Africa and Brazil, respectively, Gamma only reached a maximum prevalence of 8% in the United States in May 2020 and Beta circulated at a prevalence of 1% (Fig.”
InfluentialDispinseri, S., Secchi, M., Pirillo, M. F., Tolazzi, M., Borghi, M., Brigatti, C., Angelis, M. L. D., Baratella, M., Bazzigaluppi, E., Venturi, G., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-22958-8 · Cited by 338
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
Adjuvanting a subunit COVID-19 vaccine to induce protective immunity
Arunachalam, P. S., Walls, A. C., Golden, N., Atyeo, C. G., Fischinger, S., Li, C., Aye, P. P., Navarro, M. J., Lai, L., Edara, V. V., et al. (2021) · Nature · doi:10.1038/s41586-021-03530-2 · Cited by 317
SARS-CoV-2 501Y.V2 escapes neutralization by South African COVID-19 donor plasma
Wibmer, C. K., Ayres, F., Hermanus, T., Madzivhandila, M., Kgagudi, P., Oosthuysen, B., Lambson, B. E., de Oliveira, T., Vermeulen, M., van der Berg, K., et al. (2021) · doi:10.1101/2021.01.18.427166
Self-citationA Comprehensive Review of the Global Efforts on COVID-19 Vaccine Development
Li, Y., Tenchov, R., Smoot, J., Liu, C., Watkins, S., & Zhou, Q. A. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00120 · Cited by 349
Immune correlates of protection by mRNA-1273 vaccine against SARS-CoV-2 in nonhuman primates
Corbett, K. S., Nason, M. C., Flach, B., Gagne, M., O’Connell, S., Johnston, T. S., Shah, S. N., Edara, V. V., Floyd, K., Lai, L., et al. (2021) · Science · doi:10.1126/science.abj0299 · Cited by 286
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N. V., Paciello, I., Monego, S. D., Pantano, E., Manganaro, N., Manenti, A., et al. (2020) · doi:10.1101/2020.12.28.424451
“The recent isolation of SARS-CoV-2 variants in the United Kingdom and South Africa with deletions in or near the NTD loops shows that what we describe here can occur in the human population.”
SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2
Amanat, F., Thapa, M., Lei, T., Ahmed, S. M. S., Adelsberg, D. C., Carreño, J. M., Strohmeier, S., Schmitz, A. J., Zafar, S., Zhou, J. Q., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.005 · Cited by 273
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
Infection- and vaccine-induced antibody binding and neutralization of the B.1.351 SARS-CoV-2 variant
Edara, V. V., Norwood, C., Floyd, K., Lai, L., Davis-Gardner, M. E., Hudson, W. H., Mantus, G., Nyhoff, L. E., Adelman, M. W., Fineman, R., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.009 · Cited by 224
“In particular, the emergence of the B.1.351 variant, which was originally identified in South Africa, includes several mutations within the structural and nonstructural proteins (Tegally et al., 2020).”
InfluentialMuecksch, F., Weisblum, Y., Barnes, C. O., Schmidt, F., Schaefer-Babajew, D. J., Wang, Z., Lorenzi, J. C. C., Flyak, A. I., DeLaitsch, A. T., Huey‐Tubman, K. E., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.07.008 · Cited by 279
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) · doi:10.1101/2021.03.07.21252647 · Cited by 651
Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes
Saad-Roy, C. M., Morris, S. E., Metcalf, C. J. E., Mina, M. J., Baker, R. E., Farrar, J., Holmes, E. C., Pybus, O. G., Graham, A. L., Levin, S. A., et al. (2021) · Science · doi:10.1126/science.abg8663 · Cited by 221
Bovornkitti, S. (2021) · SpringerBriefs in Microbiology · doi:10.1007/978-3-030-87324-0_6 · Cited by 244
Emerging SARS-CoV-2 Variants and Impact in Global Vaccination Programs against SARS-CoV-2/COVID-19
Gómez, C. E., Perdiguero, B., & Estéban, M. (2021) · Vaccines · doi:10.3390/vaccines9030243 · Cited by 267
“However, the high number of mutations accumulated within two of the most immunodominant regions of S protein, such as the NTD and the RBD domains, suggests that it could also be originated as an escape variant to neutralization [28].”
BackgroundCopin, R., Baum, A., Wloga, E., Pascal, K. E., Giordano, S., Fulton, B. O., Zhou, A., Negron, N., Lanza, K., Chan, N., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.002 · Cited by 212
“We hypothesized that this noncompeting antibody combination would retain its potency as the virus evolves in the human population and safeguard against selection of escape mutants following treatment (Baum et al., 2020a; Tegally et al., 2020) With the recent rise in rapidly emerging variants, we are able to test this…”
SARS-CoV-2 501Y.V2 variants lack higher infectivity but do have immune escape
Li, Q., Nie, J., Wu, J., Zhang, L., Ding, R., Wang, H., Zhang, Y., Li, T., Liu, S., Zhang, M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.042 · Cited by 346
“Compared against the S protein of the 614G virus shows that 501Y.V2-3’s S protein contains 8 mutations: four are located at the NTD (L18F, D80A, D215G, and Del242-244), three are in the viral RBD (K417N, E484K, and N501Y), and one is in the S2 region (A701V) (Tegally et al., 2020a).”
BackgroundInfluentialBal, A., Destras, G., Gaymard, A., Stefic, K., Marlet, J., Eymieux, S., Regue, H., Semanas, Q., d’Aubarede, C., Billaud, G., et al. (2021) · Eurosurveillance · doi:10.2807/1560-7917.es.2021.26.3.2100008 · Cited by 212
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
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
Cathcart, A. L., Havenar‐Daughton, C., Lempp, F. A., Ma, D., Schmid, M., Agostini, M. L., Guarino, B., di Iulio, J., Rosen, L. E., Tucker, H., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.09.434607 · Cited by 210
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2
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, et al. (2021) · Wellcome Open Research · doi:10.12688/wellcomeopenres.16661.1 · Cited by 192
Self-citationWaves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe
Thakur, V., Bhola, S., Thakur, P., Patel, S. K. S., Kulshrestha, S., Ratho, R. K., & Kumar, P. (2022) · Infection · doi:10.1007/s15010-021-01734-2 · Cited by 195
van der Wijst, M. G. P., Vazquez, S. E., Hartoularos, G. C., Bastard, P., Grant, T., Bueno, R., Lee, D. S., Greenland, J. R., Sun, Y., Perez, R. K., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abh2624 · Cited by 226
Greaney, A. J., Loes, A. N., Crawford, K. H. D., Starr, T. N., Malone, K. D., Chu, H. Y., & Bloom, J. D. (2021) · doi:10.1101/2020.12.31.425021 · Cited by 1,178
“The site where mutations tend to have the largest effect on binding and neutralization is E484, which unfortunately is a site where mutations are present in several emerging SARS-CoV-2 lineages (Tegally et al., 2020; Voloch et al., 2020) .”
BackgroundInfluentialCohen, M. S., Nirula, A., Mulligan, M. J., Novak, R. M., Marovich, M., Yen, C., Stemer, A., Mayer, S. M., Wohl, D., Brengle, B., et al. (2021) · JAMA · doi:10.1001/jama.2021.8828 · Cited by 193
Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, BrazilPreprint
Faria, N., Mellan, T., Whittaker, C., et al. (2021) · medRxiv · doi:10.1101/2021.02.26.21252554 · Cited by 207
“In late 2020, two SARS-CoV-2 lineages of concern were discovered through genomic surveillance, both characterised by sets of significant mutations: lineage B.1.351, first reported in South Africa ( 12 ) and lineage B.1.1.7, detected in the United Kingdom ( 13 ) .”
InfluentialSelf-citationThe Disease Severity and Clinical Outcomes of the SARS-CoV-2 Variants of Concern
Lin, L., Liu, Y., Tang, X., & He, D. (2021) · Frontiers in Public Health · doi:10.3389/fpubh.2021.775224 · Cited by 239
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
“Members of Brazil-UK CADDE Genomic Network: Flavia Cristina da Silva Sales, Mariana Severo Ramundo, Darlan S. Candido, Camila Alves Maia Silva, Mariana Cardoso de Pinho, Thais de Moura Coletti, Pâmela dos Santos Andrade, Leandro Menezes de Souza, Esmênia Coelho Rocha, Ana Carolina Gomes Jardim, Erika Manuli, Nelson G…”
BackgroundMethodInfluentialSelf-citationTheoretical basis for stabilizing messenger RNA through secondary structure design
Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab764 · Cited by 197
“351 (47), which present 10, 10, and 12 amino acid changes compared to S-2P, respectively (Protein sequences listed in Table S2).”
mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
(2021) · doi:10.1101/2021.01.15.426911 · Cited by 1,354
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants
Laffeber, C., de Koning, K., Kanaar, R., & Lebbink, J. H. G. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167058 · Cited by 194
The effect of spike mutations on SARS-CoV-2 neutralization
Rees-Spear, C., Muir, L., Griffith, S. A., Heaney, J., Aldon, Y., Snitselaar, J. L., Thomas, P., Graham, C., Seow, J., Lee, N., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108890 · Cited by 221
“However, new variants of SARS-CoV-2 have begun to emerge (Kemp et al., 2020; Oude Munnink et al., 2021; Tegally et al., 2020; Welkers et al., 2021).”
Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution
Amicone, M., Borges, V., Alves, M. J., Isidro, J., Zé‐Zé, L., Duarte, S., Vieira, L., Guiomar, R., Gomes, J. P., & Gordo, I. (2022) · Evolution Medicine and Public Health · doi:10.1093/emph/eoac010 · Cited by 217
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N. V., Paciello, I., Monego, S. D., Pantano, E., Manganaro, N., Manenti, A., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2103154118 · Cited by 429
Public health actions to control new SARS-CoV-2 variants
Grubaugh, N. D., Hodcroft, E. B., Fauver, J. R., Phelan, A. L., & Cevik, M. (2021) · Cell · doi:10.1016/j.cell.2021.01.044 · Cited by 147
“In late 2020, genomic surveillance in South Africa revealed a new SARSCoV-2 variant (designated B.1.351 or 501Y.V2) associated with a concerning rise in local COVID-19 cases (Tegally et al., 2020).”
BackgroundInfluentialNelson, G., Buzko, O. V., Spilman, P., Niazi, K. R., Rabizadeh, S., & Soon‐Shiong, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.13.426558 · Cited by 180
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 infection in humans
Vanshylla, K., Di Cristanziano, V., Kleipass, F., Dewald, F., Schommers, P., Gieselmann, L., Gruell, H., Schlotz, M., Ercanoglu, M. S., Stumpf, R., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.04.015 · Cited by 153
Immune Evasion of SARS-CoV-2 Emerging Variants: What Have We Learnt So Far?
Lazarević, I., Pravica, V., Miljanovic, D., & Cupic, M. D. (2021) · Viruses · doi:10.3390/v13071192 · Cited by 193
Walls, A. C., Miranda, M. C., Schäfer, A., Pham, M. N., Greaney, A., Arunachalam, P. S., Navarro, M.-J., Tortorici, M. A., Rogers, K., O’Connor, M. A., et al. (2021) · Cell · doi:10.1016/j.cell.2021.09.015 · Cited by 185
“2 (delta) that originated in the UK, South Africa, the USA, Brazil, and India, respectively (Davies et al., 2020; Deng et al., 2021; Faria et al., 2021; McCallum et al., 2021b; Tegally et al., 2020).”
MacLean, O. A., Lytras, S., Weaver, S., Singer, J. B., Boni, M. F., Lemey, P., Pond, S. L. K., & Robertson, D. L. (2021) · PLoS Biology · doi:10.1371/journal.pbio.3001115 · Cited by 227
Self-citationThe SARS-CoV-2 mutations versus vaccine effectiveness: New opportunities to new challenges
Malik, J. A., Ahmed, S., Aroosa, M., Shinde, M., Bender, O., Alshammari, F., Ansari, M., & Anwar, S. (2022) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.12.014 · Cited by 206
Proteolytic activation of SARS‐CoV‐2 spike protein
Takeda, M. (2021) · Microbiology and Immunology · doi:10.1111/1348-0421.12945 · Cited by 194
High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants
Fontenele, R. S., Kraberger, S. J., Hadfield, J., Driver, E. M., Bowes, D. A., Holland, L. A., Faleye, T. O. C., Adhikari, S., Kumar, R., Inchausti, R., et al. (2021) · Water Research · doi:10.1016/j.watres.2021.117710 · Cited by 167
Emerging SARS-CoV-2 variants expand species tropism to murines
Shuai, H., Chan, J. F., Yuen, T. T., Yoon, C., Hu, J., Wen, L., Hu, B., Yang, D., Wang, Y., Hou, Y., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103643 · Cited by 166
Tauzin, A., Nayrac, M., Benlarbi, M., Gong, S. Y., Gasser, R., Beaudoin-Bussières, G., Brassard, N., Laumaea, A., Vézina, D., Prévost, J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.06.001 · Cited by 193
“Some harbor specificmutations in S that are associated with increased transmissibility and/or immune evasion (Davies et al., 2020; Sabino et al., 2021; Tegally et al., 2020; Volz et al., 2021).”
SARS‐CoV‐2 Alpha, Beta, and Delta variants display enhanced Spike‐mediated syncytia formation
Rajah, M. M., Hubert, M., Bishop, E., Saunders, N., Robinot, R., Grzelak, L., Planas, D., Dufloo, J., Gellenoncourt, S., Bongers, A., et al. (2021) · The EMBO Journal · doi:10.15252/embj.2021108944 · Cited by 192
Effects of SARS-CoV-2 variants on vaccine efficacy and response strategies
Bian, L., Gao, F., Zhang, J., He, Q., Mao, Q., Xu, M., & Liang, Z. (2021) · Expert Review of Vaccines · doi:10.1080/14760584.2021.1903879 · Cited by 183
“South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay [7].”
BackgroundInfluentialSARS-CoV-2 Viral Variants—Tackling a Moving Target
Mascola, J. R., Graham, B. S., & Fauci, A. S. (2021) · JAMA · doi:10.1001/jama.2021.2088 · Cited by 163
Neutralization of N501Y mutant SARS-CoV-2 by BNT162b2 vaccine-elicited sera
Xie, X., Zou, J., Fontes-Garfias, C. R., Xia, H., Swanson, K. A., Cutler, M., Cooper, D., Menachery, V. D., Weaver, S., Dormitzer, P. R., et al. (2021) · doi:10.1101/2021.01.07.425740 · Cited by 143
Self-citationStructural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants
Cai, Y., Zhang, J., Xiao, T., Lavine, C. L., Rawson, S., Peng, H., Zhu, H., Anand, K., Tong, P., Gautam, A. K., et al. (2021) · Science · doi:10.1126/science.abi9745 · Cited by 222
“28 lineage in Brazil within a period of several months (3-5).”
BackgroundEmergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York
Annavajhala, M. K., Mohri, H., Wang, P., Nair, M., Zucker, J. E., Sheng, Z., Gomez-Simmonds, A., Kelley, A. L., Tagliavia, M., Huang, Y., et al. (2021) · doi:10.1101/2021.02.23.21252259
“Each reaction plate included 8 control wells, 5x106 and 5x103 copies of 413 WA-1 (wild type), UK variant and South African variant, which were generated by PCR to match 414 the variant sequences, and 2 wells with water as no template controls (NTC).”
BackgroundInfluential(2021) · doi:10.1101/2021.02.27.433180 · Cited by 706
“%) are conserved within the B.1.351 variant, 509 (97.3”
InfluentialMolecular insights into receptor binding of recent emerging SARS-CoV-2 variants
Han, P., Su, C., Zhang, Y., Bai, C., Zheng, A., Qiao, C., Wang, Q., Niu, S., Chen, Q., Zhang, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26401-w · Cited by 166
Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma
Cele, S., Gazy, I., Jackson, L., Hwa, S.-H., Tegally, H., Lustig, G., Giandhari, J., Pillay, S., Wilkinson, E., Naidoo, Y., et al. (2021) · doi:10.1101/2021.01.26.21250224 · Cited by 651
“The combination3 of mutations in the 501Y.V2 variant first detected in South Africa include the N501Y,4 K417N, and E484K mutations in the receptor binding domain (RBD) as well as muta-5 tions in the N-terminal domain (NTD).”
BackgroundInfluentialSelf-citationLubinski, B., Fernandes, M. H. V., Frazier, L. E., Tang, T., Daniel, S., Diel, D. G., Jaimes, J. A., & Whittaker, G. R. (2021) · iScience · doi:10.1016/j.isci.2021.103589 · Cited by 209
Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy
Ramesh, S., Govindarajulu, M., Parise, R. S., Neel, L. T., Shankar, T., Patel, S., Lowery, P., Smith, F., Dhanasekaran, M., & Moore, T. (2021) · Vaccines · doi:10.3390/vaccines9101195 · Cited by 157
SARS-CoV-2 evolution and vaccines: cause for concern?
Williams, T., & Burgers, W. A. (2021) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(21)00075-8 · Cited by 163
Metadata
- Authors
- Tegally, H., Wilkinson, E., Giovanetti, M., Iranzadeh, A., Fonseca, V., Giandhari, J., Doolabh, D., Pillay, S., San, E. J., Msomi, N., Mlisana, K., von Gottberg, A., Walaza, S., Allam, M., Ismail, A., Mohale, T., Glass, A. J., Engelbrecht, S., Van Zyl, G., Preiser, W., Petruccione, F., Sigal, A., Hardie, D., Marais, G., Hsiao, M., Korsman, S., Davies, M.-A., Tyers, L., Mudau, I., York, D., Maslo, C., Goedhals, D., Abrahams, S., Laguda-Akingba, O., Alisoltani-Dehkordi, A., Godzik, A., Wibmer, C. K., Sewell, B. T., Lourenço, J., Alcantara, L. C. J., Pond, S. L. K., Weaver, S., Martin, D., Lessells, R. J., Bhiman, J. N., Williamson, C., & de Oliveira, T.
- Affiliations
- University of KwaZulu-Natal (ZA)
- Universidade Federal de Minas Gerais (BR)
- University of Cape Town (ZA)
- National Health Laboratory Service (ZA)
- University of the Witwatersrand (ZA)
- Stellenbosch University (ZA)
- National Institute for Theoretical Physics (ZA)
- Max Planck Institute for Infection Biology (DE)
- Molecular Diagnostics Services (ZA)
- University of the Free State (ZA)
- Walter Sisulu University (ZA)
- University of California, Riverside (US)
- University of Oxford (GB)
- Temple University (US)
- Centre for the AIDS Programme of Research in South Africa (ZA)
- ORCID
- Tegally, Houriiyah
- Wilkinson, Eduan
- Giovanetti, Marta
- Iranzadeh, Arash
- Fonseca, Vagner
- Giandhari, Jennifer
- Pillay, Sureshnee
- Msomi, Nokukhanya
- Mlisana, Koleka
- Walaza, Sibongile
- Allam, Mushal
- Ismail, Arshad
- Mohale, Thabo
- Glass, Allison J
- Engelbrecht, Susan
- Preiser, Wolfgang
- Petruccione, Francesco
- Sigal, Alex
- Hardie, Diana
- Marais, Gert
- Hsiao, Marvin
- Korsman, Stephen
- Davies, Mary-Ann
- Tyers, Lynn
- Maslo, Caroline
- Goedhals, Dominique
- Laguda-Akingba, Oluwakemi
- Godzik, Adam
- Wibmer, Constantinos Kurt
- Sewell, Bryan Trevor
- Lourenço, José
- Pond, Sergei L Kosakovsky
- Weaver, Steven
- Martin, Darren
- Lessells, Richard J
- Bhiman, Jinal N
- Williamson, Carolyn
- de Oliveira, Tulio
- Venue
- Nature
- Publisher
- openRxiv
- Published
- 2020-12-22
- Volume
- 592
- Issue
- 7854
- Pages
- 438-443
- ISSN
- 0028-0836 (ISSN-L)
- OpenAlex
- W3135383916
- Cited by
- 2,535
- References
- 39
- Citations by year
- 2026: 52 · 2025: 105 · 2024: 167 · 2023: 308 · 2022: 738 · 2021: 1136 · 2020: 13
- FWCI
- 185.77
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nd)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Arca - Repositório Institucional da Fiocruz (submittedVersion, other-oa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- Department of Science and Innovation, South Africa
- South African Medical Research Council
- Medical Research Council
- 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, Beta variant, variants of concern, spike protein mutations, receptor binding domain, K417N, E484K, N501Y, viral evolution, transmissibility, immune evasion, South Africa, Eastern Cape, Nelson Mandela Bay
- MeSH terms
- COVID-19, SARS-CoV-2, DNA Mutational Analysis, Humans, Models, Molecular, Mutation, Phylogeny, Selection, Genetic, South Africa, Time Factors, Evolution, Molecular, Genetic Fitness, Immune Evasion, Phylogeography, Spike Glycoprotein, Coronavirus
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
