SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
Preprint — published as 10.1073/pnas.2103154118
Abstract
To investigate the evolution of SARS-CoV-2 in the immune population, we co-incubated authentic virus with a highly neutralizing plasma from a COVID-19 convalescent patient. The plasma fully neutralized the virus for 7 passages, but after 45 days, the deletion of F140 in the spike N-terminal domain (NTD) N3 loop led to partial breakthrough. At day 73, an E484K substitution in the receptor-binding domain (RBD) occurred, followed at day 80 by an insertion in the NTD N5 loop containing a new glycan sequon, which generated a variant completely resistant to plasma neutralization. Computational modeling predicts that the deletion and insertion in loops N3 and N5 prevent binding of neutralizing antibodies. The recent emergence in the United Kingdom and South Africa of natural variants with similar changes suggests that SARS-CoV-2 has the potential to escape an effective immune response and that vaccines and antibodies able to control emerging variants should be developed. One Sentence Summary: Three mutations allowed SARS-CoV-2 to evade the polyclonal antibody response of a highly neutralizing COVID-19 convalescent plasma.
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Nine of the 17 strongest antibodies lost at least ten-fold potency against pseudoviruses with E484K.
“As seen in natural infection, a majority of the antibodies tested (9/17) were at least ten-fold less effective against pseudotyped viruses carrying the E484K mutation7,12,29.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [29]
Neutralizing human mAbs against SARS-CoV-2 RBD fall into four classes according to their RBD target regions.
“Human neutralizing monoclonal antibodies to the SARS-CoV-2 RBD can be categorized as belonging to 4 different classes based on their target regions on the RBD29.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [29]
Antibody-spike complexes bound RBD in several orientations, either up/down or only up, matching classes defined structurally in natural infection.
“Fab-S complexes exhibited multiple RBD-binding orientations recognizing either ‘up’/‘down’ (Fig 4a–j) or solely ‘up’ (Fig 4k–n) RBD conformations, consistent with structurally defined antibody classes from natural infection (Fig 4o)29.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [29]
Class 1 antibodies are resisted by A475V; class 2 by E484K and Q493R; class 3 by R346S, N439K, and N440K.
“A475V is resistant to class 1 antibodies (structurally defined as described29); E484K and Q493R are resistant to class 2 antibodies7,8,12,13,29,30,32,33; while R346S, N439K, and N440K are resistant to class 3 antibodies7,8,12,13,29,33.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [29]
Their epitopes overlap or lie near RBD positions K417, E484, and N501.
“These antibodies target epitopes that overlap or are closely associated with RBD residues K417, E484 and N501.”
From mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants (2021) · cites this paper as [29]
Licensed SARS-CoV-2 vaccines target the spike protein and have protection rates ranging from 62 to 95%.
“SARS-CoV-2 vaccines have recently been licensed that target the spike (S) protein, either using mRNA or adenovirus vector technology with protection rates ranging from 62 to 95%9–11.”
From Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies (2021) · cites this paper as [9]
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Self-citationOne-hit models for virus inactivation studies.
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“The main target of vaccines and mAbs is the SARS-CoV-2 spike protein (S-protein), a large class I trimeric fusion protein which plays a key role in viral pathogenesis (3, 5, 6).”
Molecular features of IGHV3-53-encoded antibodies elicited by SARS-CoV-2
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“This viral concentration is approximately three logs more than what is conventionally used in microneutralization assays (15-19).”
Self-citation
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SARS-CoV-2 variants, spike mutations and immune escape
Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., COVID-19 Genomics UK (COG-UK) Consortium, et al. (2021) · Nature Reviews Microbiology · doi:10.1038/s41579-021-00573-0 · Cited by 3,528 · see citing works
Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
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mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants
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“For example, mutations and deletions in the NTD can affect plasma antibody neutralization (Andreano et al., 2020; Kemp et al., 2020b; Liu et al., 2020a;McCarthy et al., 2020; Voss et al., 2020).”
InfluentialEvidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera
Zhou, D., Dejnirattisai, W., Supasa, P., Liu, C., Mentzer, A. J., Ginn, H. M., Zhao, Y., Duyvesteyn, H. M. E., Tuekprakhon, A., Nutalai, R., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.037 · Cited by 992 · see citing works
“Furthermore, serial passage of virus in sub-neutralizing concentrations of immune plasma led to the emergence of the deletion of F140 and the creation of a new N-linked glycosylation sequon in the NTD together with the E484K RBD mutation (Andreano et al., 2020).”
N-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 · see citing works
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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
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
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 · see citing works
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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
“E484K also emerged during passage with convalescent 35 plasma, leading to substantial drops in neutralization [9, 10].”
BackgroundStarr, T. N., Greaney, A. J., Dingens, A. S., & Bloom, J. D. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100255 · Cited by 470 · see citing works
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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
Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Greaney, A. J., Starr, T. N., Barnes, C. O., Weisblum, Y., Schmidt, F., Caskey, M., Gaebler, C., Cho, A., Agudelo, M., Finkin, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24435-8 · Cited by 433 · see citing works
The first 12 months of COVID-19: a timeline of immunological insights
Carvalho, T., Krammer, F., & Iwasaki, A. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00522-1 · Cited by 448 · see citing works
Structural 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
The variant gambit: COVID-19’s next move
Plante, J. A., Mitchell, B. M., Plante, K. S., Debbink, K., Weaver, S. C., & Menachery, V. D. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.02.020 · Cited by 328 · see citing works
“This change may correspond with improved binding to ACE2 but has also been associated with immune escape from both monoclonal antibodies and polyclonal sera (Starr et al., 2021; Andreano et al., 2020; Weisblum et al., 2020).”
BackgroundThe germinal centre B cell response to SARS-CoV-2
Laidlaw, B. J., & Ellebedy, A. H. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00657-1 · Cited by 250 · see citing works
Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail
Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00972-2 · Cited by 285 · see citing works
“A total of 386, 193, 47, or 7 heavy chain sequences for this SARS-CoV-2 reactive public clonotype was found in each donor or cord blood repertoire, respectively (Extended Data Fig.”
Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
Voss, W. N., Hou, Y. J., Johnson, N. V., Delidakis, G., Kim, J. E., Javanmardi, K., Horton, A. P., Bartzoka, F., Paresi, C., Tanno, Y., et al. (2021) · Science · doi:10.1126/science.abg5268 · Cited by 248 · see citing works
Self-citationGreaney, 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 · see citing works
“Notably, E484 is a site at which mutations have recently been demonstrated to reduce neutralization by several monoclonal antibodies and sera (Andreano et al., 2020; Greaney et al., 2020; Starr et al., 2020a; Weisblum et al., 2020).”
BackgroundResultInfluentialProlonged evolution of the human B cell response to SARS-CoV-2 infection
Sakharkar, M., Rappazzo, C. G., Wieland-Alter, W. F., Hsieh, C.-L., Wrapp, D., Esterman, E. S., Kaku, C. I., Wec, A. Z., Geoghegan, J. C., McLellan, J. S., et al. (2021) · Science Immunology · doi:10.1126/sciimmunol.abg6916 · Cited by 174 · see citing works
Self-citationExtremely potent human monoclonal antibodies from COVID-19 convalescent patients
Andreano, E., Nicastri, E., Paciello, I., Pileri, P., Manganaro, N., Piccini, G., Manenti, A., Pantano, E., Kabanova, A., Troisi, M., et al. (2021) · Cell · doi:10.1016/j.cell.2021.02.035 · Cited by 198 · see citing works
“Plasma from COVID-19 convalescent donors showing neutralization activity against SARS-CoV-2 (Andreano et al., 2020) were also assessed in this assay.”
BackgroundMethodInfluentialSelf-citationExperimental 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 190 · 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. L., Thomas, P., Graham, C., Seow, J., Lee, N., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108890 · Cited by 215 · see citing works
“Further studies to assess potential mutations before they arise should include those in the NTD, given the emerging importance of the NTD as a site for neutralizing antibodies (Andreano et al., 2020; Rosa et al., 2021).”
Kuzmina, A., Khalaila, Y., Voloshin, O., Keren‐Naus, A., Cohen, L. B., Raviv, Y., Shemer‐Avni, Y., Rosenberg, E., & Taube, R. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.03.008 · Cited by 172 · see citing works
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 · see citing works
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 188 · see citing works
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 · see citing works
“To understand the impact of the full constellation of mutations present in the S proteins of the aforementioned VOCs, we evaluated RBD-NP- andHexaPro S-elicited serum neutralizing activity against corresponding HIV and VSV pseudotyped variants (D614G GMT RBD-NP HIV 5 3 103 and VSV RBD-NP 6 3 102, respectively, and D61…”
BackgroundInfluentialSelf-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 201 · see citing works
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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 181 · see citing works
“An important question for vaccine application is whether the authentic virus, under the selective pressure of the polyclonal immune response in convalescent or vaccinated people, can evolve to escape herd immunity and antibody treatment [55].”
BackgroundSARS-CoV-2 one year on: evidence for ongoing viral adaptation
Peacock, T. P., Penrice-Randal, R., Hiscox, J. A., & Barclay, W. (2021) · Journal of General Virology · doi:10.1099/jgv.0.001584 · Cited by 149 · see citing works
(2021) · doi:10.1101/2021.02.27.433180 · Cited by 706 · see citing works
“…with the variants could be reflective of adaptation in terms of optimizing replication or binding to ACE2, but also reflective of adaptation to escape immune recognition by antibodies (Andreano et al., 2020; Starr et al., 2020; Wang et al., 2021a; Wang et al., 2021b; Zahradník et al., 2021).”
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 · see citing works
“E484K also emerged during passage with convalescent 35 plasma, leading to substantial drops in neutralization with convalescent plasma samples [12, 13].”
BackgroundSARS-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 · see citing works
Rates of SARS-CoV-2 transmission and vaccination impact the fate of vaccine-resistant strains
Rella, S. A., Kulikova, Y. A., Dermitzakis, E. T., & Kondrashov, F. A. (2021) · Scientific Reports · doi:10.1038/s41598-021-95025-3 · Cited by 136 · see citing works
Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules
Stravalaci, M., Pagani, I., Paraboschi, E. M., Pedotti, M., Doni, A., Scavello, F., Mapelli, S. N., Sironi, M., Perucchini, C., Varani, L., et al. (2022) · Nature Immunology · doi:10.1038/s41590-021-01114-w · Cited by 156 · see citing works
Self-citationFocosi, D., & Maggi, F. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2231 · Cited by 148 · see citing works
“Continuous passaging of SARS‐CoV‐2 in the presence of a CCP unit with nAb titre more than 1:10(4) led to ΔF140 at Day 45, followed by E484K at Days 73 and an insertion in the NTD: these accumulating mutations led to complete lack of neutralisation.(185) Accordingly, K417N, E484K and N501Y mutations were selected when…”
BackgroundN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
McCallum, M., Marco, A. D., Lempp, F., Tortorici, M. A., Pinto, D., Walls, A. C., Beltramello, M., Chen, A., Liu, Z., Zatta, F., et al. (2021) · doi:10.1101/2021.01.14.426475 · Cited by 901 · see citing works
“, 2021), the in vitro selection of SARS-CoV-2 S escape variants with NTD mutations that decrease the neutralization potency of COVID-19 convalescent patient sera (Andreano et al., 2020; Weisblum et al., 2020), and the escape mutants reported here.”
BackgroundTruong, T., Ryutov, A., Pandey, U., Yee, R., Goldberg, L., Bhojwani, D., Aguayo-Hiraldo, P. I., Pinsky, B. A., Pekosz, A. S., Shen, L., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103355 · Cited by 183 · see citing works
The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK
Hill, V., du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N. A. F., Gallagher, E., Groves, N., Jackson, B., et al. (2022) · Virus Evolution · doi:10.1093/ve/veac080 · Cited by 138 · see citing works
Nanobody cocktails potently neutralize SARS-CoV-2 D614G N501Y variant and protect mice
Pymm, P., Adair, A., Chan, L., Cooney, J. P., Mordant, F., Allison, C., Lopez, E., Haycroft, E., O, Neill, M., et al. (2021) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.2101918118 · Cited by 134 · see citing works
Evolutionary trajectory of SARS-CoV-2 and emerging variants
Singh, J., Pandit, P., McArthur, A. G., Banerjee, A., & Mossman, K. L. (2021) · Virology Journal · doi:10.1186/s12985-021-01633-w · Cited by 144 · see citing works
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2Preprint
Vanshylla, K., Cristanziano, V. D., Kleipass, F., Dewald, F., Schommers, P., Gieselmann, L., Gruell, H., Schlotz, M., Ercanoglu, M., Stumpf, R., et al. (2021) · bioRxiv · doi:10.1101/2021.01.26.428207 · Cited by 129 · see citing works
Graham, C., Seow, J., Huettner, I., Khan, H., Kouphou, N., Acors, S., Winstone, H., Pickering, S., Galão, R. P., Dupont, L., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.03.023 · Cited by 130 · see citing works
“More specifically, deletions in NTD have been associated with neutralization escape from mAbs (Andreano et al., 2020; Kemp et al., 2021; McCarthy et al., 2021; Wibmer et al., 2021).”
Zhang, Q., Ju, B., Ge, J., Chan, J. F., Cheng, L., Wang, R., Huang, W., Fang, M., Chen, P., Zhou, B., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24514-w · Cited by 112 · see citing works
Engineered ACE2 receptor therapy overcomes mutational escape of SARS-CoV-2
Higuchi, Y., Suzuki, T., Arimori, T., Ikemura, N., Mihara, E., Kirita, Y., Ohgitani, E., Mazda, O., Motooka, D., Nakamura, S., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24013-y · Cited by 126 · see citing works
Sapkal, G. N., Yadav, P. D., Ella, R., Deshpande, G. R., Sahay, R. R., Gupta, N., Vadrevu, K. M., Abraham, P., Panda, S., & Bhargava, B. (2021) · Journal of Travel Medicine · doi:10.1093/jtm/taab051 · Cited by 121 · see citing works
“in convalescent plasma, which was a serious concern.(9) Our study evidently highlighted comparable neutralization activity of vaccinated sera against the new UK variant as well as heterologous SARS-CoV-2 strains.”
ResultSARS-CoV-2 can recruit a heme metabolite to evade antibody immunity
Rosa, A., Pye, V. E., Graham, C., Muir, L., Seow, J., Ng, K., Cook, N., Rees-Spear, C., Parker, E., dos Santos, M. S., et al. (2021) · SciAdv · doi:10.1126/sciadv.abg7607 · Cited by 120 · see citing works
Kapłonek, P., Fischinger, S., Cizmeci, D., Bartsch, Y. C., Kang, J., Burke, J. S., Shin, S. A., Dayal, D., Martin, P., Mann, C. J., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.01.001 · Cited by 111 · see citing works
“Given the ability of VOCs to re-infect previously naturally immune individuals (Andreano et al., 2020; Wibmer et al., 2021; Planas et al., 2021a), we probed the impact of the recently emerging SARSCoV-2 VOCs on antibody binding and functional humoral immunity, induced by natural immunity or the mRNA-1273 vaccine, on b…”
Emerging SARS-CoV-2 Variants of Concern (VOCs): An Impending Global Crisis
Thye, A. Y.-K., Law, J. W., Pusparajah, P., Letchumanan, V., Chan, K., & Lee, L. (2021) · Biomedicines · doi:10.3390/biomedicines9101303 · Cited by 116 · see citing works
“Although some plasmas are unaffected by mutation at E484, many experiments showed that it reduces the neutralization potency of some human plasma by over 10-fold [117,140,142].”
BackgroundInfluentialMutations of SARS-CoV-2 spike protein: Implications on immune evasion and vaccine-induced immunity
Mengist, H. M., Kombe, A. J. K., Mekonnen, D. S., Abebaw, A., Getachew, M., & Jin, T. (2021) · Seminars in Immunology · doi:10.1016/j.smim.2021.101533 · Cited by 112 · see citing works
“developed resistance to neutralization [260].”
Concerns about SARS-CoV-2 evolution should not hold back efforts to expand vaccination
Cobey, S. E., Larremore, D. B., Grad, Y. H., & Lipsitch, M. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00544-9 · Cited by 118 · see citing works
“…spike protein are likely a major component of protection after either kind of exposure (Addetia et al. 2020; Zost et al. 2020; Steffen et al. 2020), and genetic variants that escape polyclonal sera after natural infection have already been identified (Weisblum et al. 2020; Andreano et al. 2020).”
BackgroundThe global epidemic of SARS‐CoV‐2 variants and their mutational immune escape
Tian, D., Sun, Y., Zhou, J., & Ye, Q. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27376 · Cited by 101 · see citing works
“this critical antigenic region and have the potential to obstruct or hide the binding to neutralizing epitopes, and could effectively eliminate the neutralization of some antibodies.(72) In addition, it is reported that Y141‐144del can enable the B.”
BackgroundJohn, G., Sahajpal, N., Mondal, A. K., Ananth, S., Williams, C., Chaubey, A., Rojiani, A. M., & Kolhe, R. B. (2021) · Current Issues in Molecular Biology · doi:10.3390/cimb43020061 · Cited by 123 · see citing works
“V2 variant, E484K, was identified in a preprint on 28 December 2020, as a possible mutation that could confer an immunological escape to SARS-CoV-2 [57].”
BackgroundMutations in SARS-CoV-2: Insights on structure, variants, vaccines, and biomedical interventions
Abulsoud, A. I., El‐Husseiny, H. M., El-Husseiny, A. A., El‐Mahdy, H. A., Ismail, A., Elkhawaga, S. Y., Khidr, E. G., Fathi, D., Mady, E. A., Najda, A., et al. (2022) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2022.113977 · Cited by 108 · see citing works
“The genuine virus’ ability to promote herd immunity and antibody treatment in convalescent or vaccinated individuals under discerning stress of the polyclonal immune response is an important concern for vaccine application [240].”
Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine–boosted nonhuman primates
Corbett, K. S., Gagné, M., Wagner, D. A., Connell, S. O., Narpala, S., Flebbe, D. R., Andrew, S. F., Davis, R. L., Flynn, B. J., Johnston, T. S., et al. (2021) · Science · doi:10.1126/science.abl8912 · Cited by 95 · see citing works
SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants
Srivastava, S., Banu, S., Singh, P., Sowpati, D. T., & Mishra, R. K. (2021) · Journal of Biosciences · doi:10.1007/s12038-021-00145-7 · Cited by 96 · see citing works
“It is of concern that this mutation can impact binding and can escape even a potent polyclonal serum targeting multiple neutralizing epitopes (Greaney et al. 2020; Andreano et al. 2020; Weisblum et al. 2020).”
BackgroundSignatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies
Alenquer, M., Ferreira, F., Lousa, D., Valério, M., Medina-Lopes, M., Bergman, M., Gonçalves, J., Demengeot, J., Leite, R. B., Lilue, J., et al. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009772 · Cited by 99 · see citing works
Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines?
Jia, Z.-X., & Gong, W. (2021) · Journal of Korean medical science · doi:10.3346/jkms.2021.36.e124 · Cited by 87 · see citing works
Villoutreix, B. O., Cálvez, V., Marcelin, A., & Khatib, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041695 · Cited by 88 · see citing works
“If the pathogenicity of the South African strain is higher than the reference strain, this could be due in part to an amino acid change at residue 484 which upon substitution seems to impede recognition by neutralizing antibodies [38,39].”
BackgroundSequence signatures of two public antibody clonotypes that bind SARS-CoV-2 receptor binding domain
Tan, T. J. C., Yuan, M., Kuzelka, K., Padron, G. C., Beal, J. R., Chen, X., Wang, Y., Rivera-Cardona, J., Zhu, X., Stadtmueller, B. M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24123-7 · Cited by 75 · 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.2021.07.027 · Cited by 78 · see citing works
“…VOCs/VOIs were already previously identified as resistant variants in vitro by using mAbs and convalescent or vaccine-elicited serum antibodies (Andreano et al., 2020; Baum et al., 2020b; Liu et al., 2021b; Weisblum et al., 2020), suggesting that the emergence of these VOCs/VOIs may result…”
Cheng, M. H., Krieger, J., Kaynak, B., Arditi, M., & Bahar, İ. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.10.426143 · Cited by 57 · see citing works
Ferrareze, P. A. G., Franceschi, V. B., Mayer, A. D. M., Caldana, G. D., Zimerman, R. A., & Thompson, C. E. (2021) · Infection, Genetics and Evolution · doi:10.1016/j.meegid.2021.104941 · Cited by 82 · see citing works
“, 2020) and the influence of different mutations in the effectiveness of COVID-19 vaccines and immunotherapies (Andreano et al., 2020; Pinto et al., 2020; Yu et al., 2020).”
Wyllie, D., Jones, H. E., Mulchandani, R., Trickey, A., Taylor-Phillips, S., Brooks, T., Charlett, A., Ades, A., EDSAB-HOME investigators, Moore, P., et al. (2020) · doi:10.1101/2020.11.02.20222778 · Cited by 96 · see citing works
Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein
Egeren, D. V., Novokhodko, A., Stoddard, M., Tran, U., Zetter, B. R., Rogers, M. S., Pentelute, B. L., Carlson, J. M., Hixon, M. S., Joseph‐McCarthy, D., et al. (2021) · PLoS ONE · doi:10.1371/journal.pone.0250780 · Cited by 90 · see citing works
“Evidence from multiple experimental studies showing that single RBD point mutations can lead to resistance [36] to neutralizing convalescent plasma from multiple donors [16,39,40] suggests that specific single mutants may be able to evade spike-targeting vaccinal immunity in many individuals and rapidly lead to spread…”
BackgroundRotondo, J. C., Martini, F., Maritati, M., Mazziotta, C., Mauro, G. D., Lanzillotti, C., Barp, N., Gallerani, A., Tognon, M. G., & Contini, C. (2021) · Viruses · doi:10.3390/v13091687 · Cited by 78 · see citing works
The role of B cells in COVID-19 infection and vaccination
Chen, S., Guan, F., Candotti, F., Benlagha, K., Câmara, N. O. S., Herrada, A. A., James, L. K., Lei, J., Miller, H., Kubo, M., et al. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.988536 · Cited by 74 · see citing works
Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail
Dong, J., Zost, S. J., Greaney, A. J., Starr, T. N., Dingens, A. S., Chen, E. C., Chen, R. E., Case, J. B., Sutton, R. E., Gilchuk, P., et al. (2021) · doi:10.1101/2021.01.27.428529 · Cited by 55 · see citing works
An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants
Tanaka, S., Nelson, G., Olson, C. A., Buzko, O. V., Higashide, W., Shin, A., Gonzalez, M. R., Taft, J. D., Patel, R. S., Buta, S., et al. (2021) · Scientific Reports · doi:10.1038/s41598-021-91809-9 · Cited by 64 · see citing works
Vega‐Magaña, N., Sánchez-Sánchez, R., Hernández‐Bello, J., Venancio-Landeros, A. A., Rodríguez, M. P., Vega-Zepeda, R. A., Galindo-Ornelas, B., Díaz-Sánchez, M., García‐Chagollán, M., Ojeda, G. M., et al. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.672562 · Cited by 67 · see citing works
Valdés-Balbín, Y., Santana-Mederos, D., Paquet, F., Fernández-Castillo, S., Climent, Y., Chiodo, F., Rodríguez, L., Ramírez, B. S., León, K., Hernández, T., et al. (2021) · ACS Central Science · doi:10.1021/acscentsci.1c00216 · Cited by 53 · see citing works
mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates
Corbett, K. S., Werner, A. P., Connell, S. O., Gagné, M., Lai, L., Moliva, J. I., Flynn, B. J., Choi, A., Koch, M., Foulds, K. E., et al. (2021) · Nature Immunology · doi:10.1038/s41590-021-01021-0 · Cited by 53 · see citing works
Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein
Wang, L., Wu, Y. L., Yao, S., Ge, H., Zhu, Y., Chen, K., Chen, W., Zhang, Y., Zhu, W. J., Wang, H., et al. (2021) · Acta Pharmacologica Sinica · doi:10.1038/s41401-021-00735-z · Cited by 75 · see citing works
SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives
Long, S. (2021) · Viruses · doi:10.3390/v13101923 · Cited by 63 · see citing works
Souza, P. F. N., Mesquita, F. P., Amaral, J. L., Landim, P. G. C., Lima, K. R. P., Costa, M. B., Farias, I. R., Belém, M. O., Pinto, Y. O., Moreira, H. H. T., et al. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.03.058 · Cited by 65 · see citing works
The ins and outs of SARS-CoV-2 variants of concern (VOCs)
Salehi-Vaziri, ., Fazlalipour, M., Khorrami, S. M. S., Azadmanesh, K., Pouriayevali, M. H., Jalali, T., Shoja, Z., & Maleki, A. (2022) · Archives of Virology · doi:10.1007/s00705-022-05365-2 · Cited by 58 · see citing works
Mohammad, T., Choudhury, A., Habib, I., Asrani, P., Mathur, Y., Umair, M., Anjum, F., Shafie, A., Yadav, D. K., & Hassan, M. I. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.765039 · Cited by 60 · see citing works
Onodera, T., Kita, S., Adachi, Y., Moriyama, S., Sato, A., Nomura, T., Sakakibara, S., Inoue, T., Tadokoro, T., Anraku, Y., et al. (2021) · Immunity · doi:10.1016/j.immuni.2021.08.025 · Cited by 59 · see citing works
“All of these VOCs possess the N501Y mutation in RBD, probably contributing to the enhanced transmissibility by increased ACE2 binding (Andreano et al., 2020).”
Israeli, M., Finkel, Y., Yahalom-Ronen, Y., Paran, N., Chitlaru, T., Israeli, O., Cohen-Gihon, I., Aftalion, M., Falach, R., Rotem, S., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29896-z · Cited by 46 · see citing works
SARS-CoV-2 variants and convalescent plasma: reality, fallacies, and opportunities
Casadevall, A., Henderson, J. P., Joyner, M. J., & Pirofski, L. (2021) · Journal of Clinical Investigation · doi:10.1172/jci148832 · Cited by 51 · see citing works
Rapid characterization of spike variants via mammalian cell surface display
Javanmardi, K., Chou, C., Terrace, C. I., Annapareddy, A., Kaoud, T. S., Guo, Q., Lutgens, J., Zorkic, H., Horton, A. P., Gardner, E. C., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.11.024 · Cited by 51 · see citing works
Emergence and outcomes of the SARS-CoV-2 ‘Marseille-4’ variant
Fournier, P., Colson, P., Levasseur, A., Devaux, C. A., Gautret, P., Bedotto, M., Delerce, J., Bréchard, L., Pinault, L., Lagier, J., et al. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.03.068 · Cited by 54 · see citing works
Fedry, J., Hurdiss, D. L., Wang, C., Li, W.-T., Obal, G., Drulyte, I., Du, W., Howes, S., van Kuppeveld, F. V., Förster, F. G., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf5632 · Cited by 50 · see citing works
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Focosi, D., Maggi, F., Franchini, M., McConnell, S. A., & Casadevall, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010029 · Cited by 59 · see citing works
“insertions (causing additional glycosylation sites [12]) or recurrently deleted regions (RDR) ∆HV69–70 (RDR1), ∆LGVY141–144 and ∆D146 (RDR2), ∆I210 (RDR3) and ∆AL243–244 (RDR4) [55]: RDR1, RDR2 and RDR4 correspond to NTD loops N2, N3 and N5, whereas RDR3 falls between N4 and N5.”
BackgroundPrecision therapeutic targets for COVID-19
Krumm, Z. A., Lloyd, G. M., Francis, C. P., Nasif, L. H., Mitchell, D. A., Golde, T. E., Giasson, B. I., & Xia, Y. (2021) · Virology Journal · doi:10.1186/s12985-021-01526-y · Cited by 55 · see citing works
“These variants have demonstrated varying degrees of immune escape, including from convalescent sera [88].”
BackgroundLim, C. T., Tan, K. W., Wu, M., Ulferts, R., Armstrong, L. A., Ozono, E., Drury, L. S., Milligan, J. C., Zeisner, T. U., Zeng, J., et al. (2021) · Biochemical Journal · doi:10.1042/bcj20210244 · Cited by 58 · see citing works
Resende, P. C., Naveca, F. G., Lins, R. D., Dezordi, F. Z., Ferraz, M. V. F., Moreira, E. G., Coêlho, D. F., Motta, F. C., Paixão, A. C. D., Appolinario, L., et al. (2021) · Virus Evolution · doi:10.1093/ve/veab069 · Cited by 46 · see citing works
“Moreover, in vitro co-incubation of SARS-CoV-2 with highly neutralizing plasma form COVID-19 convalescent patient, has revealed an incremental resistance to neutralization followed by the stepwise acquisition of indels at N3/N5 loops 31 .”
BackgroundNeutralization of UK-variant VUI-202012/01 with COVAXIN vaccinated human serumPreprint
Sapkal, G. N., Yadav, P. D., Ella, R., Deshpande, G. R., Sahay, R. R., Gupta, N., Mohan, V., Abraham, P., Panda, S., & Bhargava, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.26.426986 · Cited by 55 · see citing works
“escape of the UK-variant with E484K substitution, which was followed by an 11-amino-acid insertion in the NTD N5 loop (248aKTRNKSTSRRE248k) from high NAb in convalescent plasma, which was a serious concern pertaining to the potential efficacy of the vaccines.(7) Our study evidently highlighted comparable neutralizatio…”
ResultGarcía-Valtanen, P., Hope, C. M., Masavuli, M. G., Yeow, A. E. L., Balachandran, H., Mekonnen, Z. A., Al-Delfi, Z., Abayasingam, A., Agapiou, D., Stella, A. O., et al. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100651 · Cited by 42 · see citing works
He, C., Yang, H. J., He, X., Hong, W., Hong, L., Chen, Z., Shen, G., Yang, L., Li, J., Wang, Z., et al. (2021) · MedComm · doi:10.1002/mco2.72 · Cited by 43 · see citing works
Liu, H., Yuan, M., Huang, D.-L., Bangaru, S., Zhao, F.-Z., Lee, C. D., Peng, L., Barman, S., Zhu, X.-Y., Nemazee, D., et al. (2021) · Cell Host and Microbe · doi:10.1016/j.chom.2021.04.005 · Cited by 46 · see citing works
“…mutations in both human and mink populations give rise to concerns about viral escape from current vaccines and therapeutics in development (Andreano et al., 2020; Greaney et al., 2021a; Kemp et al., 2021; Mallapaty, 2020; Oude Munnink et al., 2021; Tegally et al., 2021; Voloch et al.,…”
BackgroundInfluentialAhmad, L. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.742167 · Cited by 46 · see citing works
Haslwanter, D., Dieterle, M. E., Wec, A. Z., O’Brien, C. M., Sakharkar, M., Florez, C., Tong, K., Rappazzo, C. G., Lasso, G., Vergnolle, O., et al. (2021) · mBio · doi:10.1128/mbio.02473-21 · Cited by 55 · see citing works
“described recently (32, 33), we observed that neutralization-escape rVSV-SARS2 mutants of the NTD-targeting MAb were resistant to neutralization by COVID-19 convalescent donor sera, suggesting that natural variants in the NTD could, at least in part, escape the antibody response.”
BackgroundSelf-citation
- Authors
- Andreano, E., Piccini, G., Licastro, D., Casalino, L., Johnson, N. V., Paciello, I., Monego, S. D., Pantano, E., Manganaro, N., Manenti, A., Manna, R., Casa, E., Hyseni, I., Benincasa, L., Montomoli, E., Amaro, R. E., McLellan, J. S., & Rappuoli, R.
- Publisher
- openRxiv
- Published
- 2020-12-28
- PMC
- PMC7781313
- References
- 56
- Type
- Preprint
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