Volume 91, Issue 8 pp. 1021-1031
RESEARCH ARTICLE

SARS-CoV-2 neutralizing antibody epitopes are overlapping and highly mutated which raises the chances of escape variants and requires development of broadly reactive vaccines

Jeswin Joseph

Jeswin Joseph

Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India

Contribution: Writing - original draft, Formal analysis, Data curation, Methodology

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Sukhada Darpe

Sukhada Darpe

Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India

Contribution: Formal analysis, Software

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Grishma Kulkarni

Grishma Kulkarni

Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India

Contribution: Formal analysis, Software

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V. Stalin Raj

Corresponding Author

V. Stalin Raj

Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, India

Correspondence

V. Stalin Raj, Virology Scientific Research (VSR) Laboratory, School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, India.

Email: [email protected]

Contribution: Conceptualization, Funding acquisition, Writing - original draft, Writing - review & editing, Supervision, Resources

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First published: 13 March 2023

Abstract

The rapid adaptation of SARS-CoV-2 within the host species and the increased viral transmission triggered the evolution of different SARS-CoV-2 variants. Though numerous monoclonal antibodies (mAbs) have been identified as prophylactic therapy for SARS-CoV-2, the ongoing surge in the number of SARS-CoV-2 infections shows the importance of understanding the mutations in the spike and developing novel vaccine strategies to target all variants. Here, we report the map of experimentally validated 74 SARS-CoV-2 neutralizing mAb binding epitopes of all variants. The majority (87.84%) of the potent neutralizing epitopes are localized to the receptor-binding domain (RBD) and overlap with each other, whereas limited (12.16%) epitopes are found in the N-terminal domain (NTD). Notably, 69 out of 74 mAb targets have at least one mutation at the epitope sites. The potent epitopes found in the RBD show higher mutations (4-10aa) compared to lower or modest neutralizing antibodies, suggesting that these epitopes might co-evolve with the immune pressure. The current study shows the importance of determining the critical mutations at the antibody recognition epitopes, leading to the development of broadly reactive immunogens targeting multiple SARS-CoV-2 variants. Further, vaccines inducing both humoral and cell-mediated immune responses might prevent the escape of SARS-CoV-2 variants from neutralizing antibodies.

CONFLICT OF INTEREST STATEMENT

The authors declare no conflicts of interests.

DATA AVAILABILITY STATEMENT

Data available upon request.

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