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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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“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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]
In the citing paper
“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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BackgroundN-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
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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. W., Cook, N., Rees-Spear, C., Parker, E. L., dos Santos, M. S., et al. (2021) · Science Advances · doi:10.1126/sciadv.abg7607 · Cited by 142
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 121
“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 121
“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 115
“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 119
“…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 106
“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 131
“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 112
“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 98
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
“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 101
Will Mutations in the Spike Protein of SARS-CoV-2 Lead to the Failure of COVID-19 Vaccines?
Jia, Z., & Gong, W. (2021) · Journal of Korean Medical Science · doi:10.3346/jkms.2021.36.e124 · Cited by 94
Villoutreix, B. O., Cálvez, V., Marcelin, A., & Khatib, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22041695 · Cited by 89
“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
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
“…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
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
“, 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
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 91
“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 81
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 75
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
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 65
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
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
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 57
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 77
SARS-CoV-2 Subgenomic RNAs: Characterization, Utility, and Perspectives
Long, S. (2021) · Viruses · doi:10.3390/v13101923 · Cited by 67
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 67
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 61
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 61
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 61
“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
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 49
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 54
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 57
Fédry, J., Hurdiss, D. L., Wang, C., Li, W., Obal, G., Drulyte, I., Du, W., Howes, S. C., van Kuppeveld, F. J. M., Förster, F. G., et al. (2021) · Science Advances · doi:10.1126/sciadv.abf5632 · Cited by 54
Muñoz-Alía, M. Á., Nace, R. A., Zhang, L., & Russell, S. J. (2021) · Cell Reports Medicine · doi:10.1016/j.xcrm.2021.100225 · Cited by 60
Focosi, D., Maggi, F., Franchini, M., McConnell, S. A., & Casadevall, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms23010029 · Cited by 61
“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 58
“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
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 47
“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
“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 43
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
Liu, H., Yuan, M., Huang, D., Bangaru, S., Zhao, F., Lee, C.-C. D., Peng, L., Barman, S., Zhu, X., Nemazee, D. A., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.04.005 · Cited by 58
“…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
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
“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
Metadata
- 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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