Epitope mapping of SARS-CoV-2 Spike protein using naturally-acquired immune responses to develop monoclonal antibodies
Year: 2025
Type: article
Abstract: Background COVID-19 vaccination strategies are already available almost worldwide. However, it is also crucial to develop new therapeutic approaches, especially for vulnerable populations that may not fully respond to vaccination, such as the immunocompromised. In this project, we predicted 25 B-cell epitopes in silico in the SARS-CoV-2 spike protein and screened these against serum and plasma samples from 509 COVID-19 convalescent patients. The aim was to identify those epitopes with the highest IgG reactivity to produce monoclonal antibodies against them for COVID-19 treatment. Methods We implemented Brewpitopes, a computational pipeline based on B-cell epitope prediction tools, such as BepiPred v2.0 and Discotope v2.0, and a series of antibody-epitope accessibility filters. We mapped the SARS-CoV-2 spike (S) protein epitopes most likely to be recognized by human neutralizing antibodies. Linear and structural epitope predictions were included and were further refined considering accessibility factors influencing their binding to antibodies like glycosylation status, localization in the viral membrane and accessibility on the 3D-surface of S. Blood samples were collected from 509 COVID-19 patients prospectively recruited days after symptoms initiation, positive RT-qPCR or hospital/ICU discharge. Presence of IgG against SARS-CoV-2 was confirmed by lateral flow immunoassays. Epitopes immunogenicity was tested through the analysis of IgG levels and seropositivity in the convalescent serum and plasma samples and 126 pre-pandemic negative controls by Luminex to identify those with the highest reactivity. The seropositivity cut-offs for each epitope were calculated using a set of 126 pre-pandemic samples as negative controls (NC). Results Twenty-five SARS-CoV-2 spike epitopes were predicted in silico as potentially the most immunogenic. These were synthesized and tested in a multiplex immunoassay against sera/plasmas from convalescent COVID-19 patients (5.7% asymptomatic, 35.6% mild, 13.8% moderate, 23% severe and 22% unknown because of anonymous donation). Among the 25 epitopes tested, 3 exhibited significantly higher IgG reactivity compared to the rest. The proportion of seropositive patients towards these 3 epitopes, based on median fluorescence intensity (MFI or Log10 MFI) above that from NC, ranged between 11-48%. The two most immunogenic epitopes were selected and two monoclonal antibodies were produced. These two MAbs exhibited comparable levels of Spike protein affinity to commercialized MAbs. Conclusions Our data shows that the candidate spike epitopes predicted in silico are recognized by IgG present in convalescent serum and plasma. This evidence suggests that our computational and experimental pipeline is able to yield immunogenic epitopes against SARS-CoV-2 S. These epitopes are suitable for the development of novel antibodies for preventive or therapeutic approaches against COVID-19.
Source: Scientific Reports
Authors: Rubén López-Aladid, Leticia Bueno-Freire, Roc Farriol-Duran, Eduard Porta-Pardo, Ruth Aguilar, Marta Vidal, Alfons Jiménez, Roberto Cabrera, Nil Vázquez, Alexandre López-Gavín, Gemma Moncunill, Montserrat Carrascal, Teresa García, Miquel Lozano, Alberto L. García-Basteiro, Carlota Dobaño, Martalu D. Pazos, M.-Carmen Estevez, Laura M. Lechuga, Antoni Torres, Laia Fernández-Barat
Institutions: Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Hospital Clínic de Barcelona, Consorci Institut D'Investigacions Biomediques August Pi I Sunyer, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Fundació Clínic per a la Recerca Biomèdica, Barcelona Supercomputing Center, Barcelona Institute for Global Health, Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública, Centro de Investigación Biomédica en Red, Centro de Investigación Biomédica en Red Enfermedades Infecciosas, Consejo Superior de Investigaciones Científicas, Institut d'Investigacions Biomèdiques de Barcelona, Institut Català de Nanociència i Nanotecnologia, Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,690
Funders: Centres de Recerca de Catalunya, Institut Català de Nanociència i Nanotecnologia, European Commission, Generalitat de Catalunya, Institució Catalana de Recerca i Estudis Avançats, Sociedad Española de Neumología y Cirugía Torácica, Instituto de Salud Carlos III, Agencia Estatal de Investigación, NextGenerationEU
OpenAlex ID: W4410229945