Novel b-cell epitopes of non-neutralizing antibodies in the receptor-binding domain of the S-protein of SARS-CoV-2 with differing effects on the severity of the course of COVID-19

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription Access

Abstract

Antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (RBD of S-protein) contribute significantly to the humoral immune response during coronavirus infection (COVID-19) and after vaccination. The main focus of the study of the epitope composition of RBD is concentrated on the epitopes recognized by viral neutralizing antibodies. The role of antibodies that bind to RBD but are unable to neutralize the virus in the formation of the immune response remains unclear. In this investigation, the immunochemical properties of two mouse monoclonal antibodies RS17 and S11 against RBD were examined. Both antibodies were shown to have high affinity, but they did not neutralize the virus. The epitopes of these antibodies were localized using phage display: the epitope recognized by the RS17 antibody is located at the N-terminal site of RBD (348-SVYAVNRKRIS-358); the epitope recognized by the S11 antibody is inside the receptor-binding motif of RBD (452-YRLFRKSN-459). Three groups of sera were tested for antibodies competing with non-neutralizing antibodies S11 and RS17: 1) from unvaccinated volunteers, who did not suffer from COVID-19 previously; 2) from people who had had a mild form of COVID-19; 3) from people who had had a severe form of COVID-19. Antibodies competing with the S11 antibody were shown to occur with equal frequency in each of the serum groups studied. At the same time, the presence of antibodies competing with antibody RS17 in the sera was associated with the severity of COVID-19 and was significantly more frequent in the group of sera obtained from patients with severe COVID-19. In conclusion, despite the clear significance of anti-RBD antibodies for the formation of an effective immune response against SARS-CoV-2, it is important to analyze their viral neutralizing activity and to confirm the absence of negative features of obtained anti-RBD antibodies after vaccination.

About the authors

A. L Matveev

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

Email: guterus@gmail.com
630090 Novosibirsk, Russia

O. V Pyankov

State Research Center of Virology and Biotechnology “VECTOR”, Federal Service for the Oversight of Consumer Protection and Welfare

630559 Koltsovo, Novosibirsk region, Russia

Y. A Khlusevich

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

630090 Novosibirsk, Russia

O. V Tyazhelkova

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

630090 Novosibirsk, Russia

L. A Emelyanova

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

630090 Novosibirsk, Russia

A. M Timofeeva

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

630090 Novosibirsk, Russia

A. V Shipovalov

State Research Center of Virology and Biotechnology “VECTOR”, Federal Service for the Oversight of Consumer Protection and Welfare

630559 Koltsovo, Novosibirsk region, Russia

A. V Chechushkov

Federal State Public Scientific Institution “Institute of Chemical Biology and Fundamental Medicine”, Siberian Branch of the Russian Academy of Sciences

630090 Novosibirsk, Russia

N. S Zaitseva

FIC FTM

630117 Novosibirsk, Russia

References

  1. Kubiak, J. Z., and Kloc, M. (2023) Coronavirus Disease Pathophysiology: Biomarkers, Potential New Remedies, Comorbidities, Long COVID-19, Post Pandemic Epidemiological Surveillance, Int. J. Mol. Sci, 2023, 12236, doi: 10.3390/ijms241512236.
  2. Masters, P. S. (2006) The molecular biology of coronaviruses, Adv. Virus Res., 65, 193-292, doi: 10.1016/S0065-3527(06)66005-3.
  3. Jiang, S., Hillyer, C., Du, L. (2020) Neutralizing antibodies against SARS-CoV-2 and other human coronaviruses, Trends Immunol., 41, 355-359, doi: 10.1016/j.it.2020.03.007.
  4. Maier, H. J., Bickerton, E., and Britton, P. (2015) Coronaviruses: methods and protocols, Methods in Molecular Biology, 1282, 1-282, doi: 10.1007/978-1-4939-2438-7.
  5. Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., and Veesler, D. (2020) Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein, Cell, 181, 281-292.e6, doi: 10.1016/j.cell.2020.02.058.
  6. Guo, Y., Huang, L., Zhang, G., Yao, Y., Zhou, H., et al. (2021) A SARS-CoV-2 neutralizing antibody with extensive Spike binding coverage and modified for optimal therapeutic outcomes, Nat. Commun., 12, 2623, doi: 10.1038/s41467-021-22926-2.
  7. Sun, M., Liu, S., Wei, X., Wan, S., Huang, M., et al. (2021) Aptamer blocking strategy inhibits SARS-CoV-2 virus infection, Angew. Chem., 60, 10266-10272, doi: 10.1002/anie.202100225.
  8. Barh, D., Tiwari, S., Silva Andrade, B., Giovanetti, M., Almeida Costa, E., et al. (2020) Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain, F1000Res., 9, 576, doi: 10.12688/f1000research.24074.1.
  9. Chaouat, A. E., Achdout, H., Kol, I., Berhani, O., Roi, G., et al. (2021) SARS-CoV-2 receptor binding domain fusion protein efficiently neutralizes virus infection, PLoS Pathog., 17, e1010175, doi: 10.1371/journal.ppat.1010175.
  10. Nassar, M., Nso, N., Gonzalez, C., Lakhdar, S., Alshamam, M., et al. (2021) COVID-19 vaccine-induced myocarditis: case report with literature review, Diabetes Metab. Syndrome, 15, 102205, doi: 10.1016/j.dsx.2021.102205.
  11. Morgan, M. C., Atri, L., Harrell, S., Al-Jaroudi, W., Berman, A. (2022). COVID-19 vaccine-associated myocarditis, World J. Cardiol., 14, 382-391, doi: 10.4330/wjc.v14.i7.382.
  12. Wang, C., Li, W., Drabek, D., Okba, N. M. A., van Haperen, R., et al. (2020) A human monoclonal antibody blocking SARS-CoV-2 infection, Nat Commun., 4, 2251, doi: 10.1038/s41467-020-16256-y.
  13. Liu, L., Wang, P., Nair, M. S., Yu, J., Rapp, M., Wang, Q., Luo, Y., Chan, J. F., Sahi, V., Figueroa, A., Guo, X. V., Cerutti, G., Bimela, J., Gorman, J., Zhou, T., Chen, Z., Yuen, K. Y., Kwong, P. D., Sodroski, J. G., Yin, M. T., Sheng, Z., Huang, Y., Shapiro, L., and Ho, D. D. (2020) Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike, Nature, 584, 450-456, doi: 10.1038/s41586-020-2571-7.
  14. Deshpande, A., Harris, B. D., Martinez-Sobrido, L., Kobie, J. J., and Walter, M. R. (2021) Epitope classification and RBD binding properties of neutralizing antibodies against SARS-CoV-2 variants of concern, Front. Immunol., 12, 691715, doi: 10.3389/fimmu.2021.691715.
  15. Chen, Y., Zhao, X., Zhou, H., Zhu, H., Jiang, S., and Wang, P. (2023) Broadly neutralizing antibodies to SARS-CoV-2 and other human coronaviruses, Nat. Rev. Immunol., 23, 189-199, doi: 10.1038/s41577-022-00784-3.
  16. Shi, J., Zheng, J., Tai, W., Verma, A. K., Zhang, X., et al. (2022) A glycosylated RBD protein induces enhanced neutralizing antibodies against omicron and other variants with improved protection against SARS-CoV-2 infection, J. Virol., 96, e0011822, doi: 10.1128/jvi.00118-22.
  17. Timofeeva, A. M., Sedykh, S. E., Ermakov, E. A., Matveev, A. L., Odegova, E. I., et al. (2022) Natural IgG against S-protein and RBD of SARS-CoV-2 do not bind and hydrolyze DNA and are not autoimmune, Int. J. Mol. Sci., 23, 13681, doi: 10.3390/ijms232213681.
  18. Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., et al. (2020) Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 367, 1260-1263, doi: 10.1126/science.abb2507.
  19. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem., 72, 248-254, doi: 10.1006/abio.1976.9999.
  20. Matveev, A. L., Krylov, V. B., Emelyanova, L., Solovev, A. S., Khlusevich, Y. A., et al. (2018) Novel mouse monoclonal antibodies specifically recognize Aspergillus fumigatus galactomannan, PLoS One, 13, e0193938, doi: 10.1371/journal.pone.0193938.
  21. Levanov, L. N., Matveev, L. E., Goncharova, E. P., Lebedev, L. R., Ryzhikov, A. B., et al. (2010) Chimeric antibodies against tick-borne encephalitis virus, Vaccine, 28, 5265-5271, doi: 10.1016/j.vaccine.2010.05.060.
  22. Borgoyakova, M. B., Karpenko, L. I., Rudometov, A. P., Shanshin, D. V., Isaeva, A. A., Nesmeyanova, V. S., et al. (2021) Immunogenic properties of the DNA construct encoding the receptor-binding domain of the SARS-CoV-2 spike protein, Mol. Biol., 55, 889-898, doi: 10.1134/S0026893321050046.
  23. Reed, L. J., and Muench, H. (1938) A simple method of estimating fifty percent endpoints, Am. J. Hyg., 27, 493-497, doi: 10.1093/oxfordjournals.aje.a118408.
  24. Khlusevich, Y. A., Matveev, A. L., Baykov, I. K., Bulychev, L. E., Bormotov, N. I., et al. (2018) Phage display antibodies against ectromelia virus that neutralize variola virus: selection and implementation for p35 neutralizing epitope mapping, Antivir. Res., 152, 18-25, doi: 10.1016/j.antiviral.2018.02.006.
  25. Matveev, A. L., Krylov, V. B., Khlusevich, Y. A., Baykov, I. K., Yashunsky, D. V., et al. (2019) Novel mouse monoclonal antibodies specifically recognizing β-(1-3)-D-glucan antigen, PLoS One, 14, 4, e0215535, doi: 10.1371/journal.pone.0215535.
  26. Yang, M., Li, J., Huang, Z., Li, H., Wang, Y., et al. (2021) Structural basis of a human neutralizing antibody specific to the SARS-CoV-2 spike protein receptor-binding domain, Microbiol. Spectr., 9, e01352-21, doi: 10.1128/Spectrum.01352-21.
  27. Yuan, M., Huang, D., Lee, C. D., Wu, N. C., Jackson, A. M., Zhu, X., Liu, H., Peng, L., van Gils, M. J., Sanders, R. W., Burton, D. R., Reincke, S. M., Prüss, H., Kreye, J., Nemazee, D., Ward, A. B., and Wilson, I. A. (2021) Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants, Science, 373, 818-823, doi: 10.1126/science.abh1139.
  28. Khlusevich, Y. A., Matveev, A. L., Emelyanova, L. A., Goncharova, E. P., Golosova, N. N., et al. (2022) New p35 (H3L) epitope involved in vaccinia virus neutralization and its deimmunization, Viruses, 14, 1224, doi: 10.3390/v14061224.
  29. Bahnan, W., Wrighton, S., Sundwall, M., Bläckberg, A., Larsson, O., et al. (2022) Spike-dependent opsonization indicates both dose-dependent inhibition of phagocytosis and that non-neutralizing antibodies can confer protection to SARS-CoV-2, Front. Immunol., 12, e808932, doi: 10.3389/fimmu.2021.808932.

Supplementary files

Supplementary Files
Action
1. JATS XML
Download

Copyright (c) 2023 Russian Academy of Sciences