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.
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The panel also included circulating variant residues K417N, Y453F, S477R, N501Y, and D614G, some linked to rapidly rising case counts.
“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]
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.
“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]
An A701V mutation in S2 is also observed at high frequencies in B.1.351, whereas deletions in residues 242 to 244 as well as R246I and L18F mutations in the NTD are present at lower frequencies.
“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]
The B.1.351 lineage is defined by the D80A and D215G mutations in the NTD; the K417N, E484K, and N501Y mutations in the RBD; and the D614G mutation in S1.
“the B.1.351 lineage, which is defined by the D80A (amino acid substitution from aspartic acid to alanine at position 80) and D215G mutations in the NTD; the K417N, E484K, and N501Y mutations in the RBD; and the D614G mutation in S1 (52, 56).”
From mRNA vaccination boosts cross-variant neutralizing antibodies elicited by SARS-CoV-2 infection (2021) · cites this paper as [52]
The NTD region itself does not appear to be the target of cross-nAbs elicited by infection or vaccination.
“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]
Further mutations in spike protein observed in other novel lineages appear to be driven by escape of the virus from the neutralising activity of public antibodies, indicating that prevention of transmission might be temporary as the virus adapts to natural or vaccine-induced immunity.
“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.”
The B.1.351 variant is characterized by three deleterious mutations at key antigenic sites in the RBD, including N501Y, K417N, and E484K.
“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]
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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 · see citing works
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 · see citing works
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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 · see citing works
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 · see citing works
Self-citationSensitivity 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 · see citing works
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“, 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 · see citing works
“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…”
mRNA 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 · see citing works
Preliminary Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.351 Variant
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“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 · 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
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 · see citing works
“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 539 · see citing works
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“…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 · see citing works
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 513 · see citing works
The neutralizing antibody, LY-CoV555, protects against SARS-CoV-2 infection in nonhuman primates
Jones, B. E., Brown-Augsburger, P., Corbett, K., Westendorf, K., Davies, J., Cujec, T., Wiethoff, C. M., Blackbourne, J., Heinz, B., Foster, D., et al. (2021) · Science Translational Medicine · doi:10.1126/scitranslmed.abf1906 · Cited by 420 · see citing works
“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 · see citing works
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“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 · see citing works
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“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 408 · see citing works
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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
“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 · see citing works
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“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 380 · 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
“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 334 · see citing works
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 · 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
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 326 · see citing works
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 345 · see citing works
SARS-CoV-2 escape <i>in vitro</i> 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 · 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
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 · see citing works
“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., Schmidt, F., Schaefer-Babajew, D. J., Wang, Z.-J., Lorenzi, J. C. C., Flyak, A., DeLaitsch, A. T., Huey-Tubman, K. E., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.07.008 · Cited by 256 · see citing works
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 · see citing works
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 214 · see citing works
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 262 · see citing works
“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 · see citing works
“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 341 · see citing works
“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 · 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
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
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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 · see citing works
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 210 · see citing works
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 223 · see citing works
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“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 · see citing works
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 · see citing works
“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.-X., Liu, Y., Tang, X.-J., & He, D.-H. (2021) · Frontiers in Public Health · doi:10.3389/fpubh.2021.775224 · Cited by 208 · 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
“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 · see citing works
“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 · see citing works
Experimental Evidence for Enhanced Receptor Binding by Rapidly Spreading SARS-CoV-2 Variants
Laffeber, C., de Koning, K., Kanaar, R., & Lebbink, J. (2021) · bioRxiv · doi:10.1016/j.jmb.2021.167058 · Cited by 195 · see citing works
The effect of spike mutations on SARS-CoV-2 neutralization
Rees-Spear, C., Muir, L., Griffith, S. A., Heaney, J., Aldon, Y., Snitselaar, J., Thomas, P., Graham, C., Seow, J., Lee, N.-Y., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108890 · Cited by 191 · see citing works
“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
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“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).”
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“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).”
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- 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 · 2018: 1 · 2017: 1 · 2015: 1 · 2014: 2 · 2013: 1 · 2012: 1
- 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
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