Identification of conserved linear epitopes in the SARS-CoV-2 receptor-binding region using monoclonal antibodies

Yujie Yang; Liling Zhou; Chuncong Mo; Longbo Hu; Zhichao Zhou; Ye Fan; Wenkuan Liu; Xiao Li; Rong Zhou; Xingui Tian

doi:10.1016/j.heliyon.2023.e16847

Identification of conserved linear epitopes in the SARS-CoV-2 receptor-binding region using monoclonal antibodies

Heliyon. 2023 Jun;9(6):e16847. doi: 10.1016/j.heliyon.2023.e16847. Epub 2023 Jun 3.

Authors

Yujie Yang¹, Liling Zhou¹, Chuncong Mo¹, Longbo Hu², Zhichao Zhou¹, Ye Fan¹, Wenkuan Liu¹, Xiao Li¹, Rong Zhou¹, Xingui Tian¹

Affiliations

¹ State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510182, China.
² State Key Laboratory of Respiratory Disease, Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, 511436, China.

Abstract

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused millions of cases of infections, leading to a global health emergency. The SARS-CoV-2 spike (S) protein plays the most important role in viral infection, and S1 subunit and its receptor-binding domain (RBD) are widely considered the most attractive vaccine targets. The RBD is highly immunogenic and its linear epitopes are important for vaccine development and therapy, but linear epitopes on the RBD have rarely been reported. In this study, 151 mouse monoclonal antibodies (mAbs) against the SARS-CoV-2 S1 protein were characterized and used to identify epitopes. Fifty-one mAbs reacted with eukaryotic SARS-CoV-2 RBD. Sixty-nine mAbs reacted with the S proteins of Omicron variants B.1.1.529 and BA.5, indicating their potential as rapid diagnostic materials. Three novel linear epitopes of RBD, R6 (³⁹¹CFTNVYADSFVIRGD⁴⁰⁵), R12 (⁴⁶³PFERDISTEIYQAGS⁴⁷⁷), and R16 (⁵¹⁰VVVLSFELLHAPAT⁵²³), were identified; these were highly conserved in SARS-CoV-2 variants of concern and could be detected in the convalescent serum of COVID-19 patients. From pseudovirus neutralization assays, some mAbs including one detecting R12 were found to possess neutralizing activity. Together, from the reaction of mAbs with eukaryotic RBD (N501Y), RBD (E484K), and S1 (D614G), we found that a single amino acid mutation in the SARS-CoV-2 S protein may cause a structural alteration, exerting substantial impact on mAb recognition. Our results could, therefore, help us better understand the function of the SARS-CoV-2 S protein and develop diagnostic tools for COVID-19.

Keywords: Epitope; Monoclonal antibody; Receptor-binding domain; SARS-CoV-2; Spike protein.