Phylogeny-aware linear B-cell epitope predictor detects targets associated with immune response to orthopoxviruses

Abstract

We introduce a phylogeny-aware framework for predicting linear B-cell epitope (LBCE)-containing regions within proteins. Our approach leverages evolutionary information by using a taxonomic scaffold to build models trained on hierarchically structured data. The resulting models present performance equivalent or superior to generalist methods, despite using simpler features and a fraction of the data volume required by current state-of-the-art predictors. This allows the utilization of available data for major pathogen lineages to facilitate the prediction of LBCEs for emerging infectious agents. We demonstrate the efficacy of our approach by predicting new LBCEs in the monkeypox (MPXV) and vaccinia viruses. Experimental validation of selected targets using sera from infected patients confirms the presence of LBCEs, including candidates for the differential serodiagnosis of recent MPXV infections. These results point to the use of phylogeny-aware predictors as a useful strategy to facilitate the targeted development of immunodiagnostic tools.

Publication DOI: https://doi.org/10.1093/bib/bbae527
Divisions: College of Engineering & Physical Sciences > School of Computer Science and Digital Technologies > Applied AI & Robotics
Funding Information: J.A. was supported by the EPSRC/UK (PhD fees and stipend). J.R.-C. was supported by the UK Medical Research Council (MR/T016019/1). The Brazilian authors would like to acknowledge the following sources of financial support: MCTI/Brazil (C\u00E2mara Pox, 4
Additional Information: Copyright © The Author(s) 2024. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords: Orthopoxvirus,Epitope prediction,Diagnostics,Machine Learning,Monkeypox Virus,Phylogeny-aware Methods,Humans,Vaccinia virus,Epitopes, B-Lymphocyte,Computational Biology,Phylogeny
Publication ISSN: 1477-4054
Last Modified: 28 Mar 2025 08:11
Date Deposited: 04 Dec 2024 17:05
Full Text Link:
Related URLs: https://academi ... bbae527/7877279 (Publisher URL)
http://www.scop ... tnerID=8YFLogxK (Scopus URL)
PURE Output Type: Article
Published Date: 2024-11
Published Online Date: 2024-11-06
Accepted Date: 2024-09-01
Authors: Campelo, Felipe (ORCID Profile 0000-0001-8432-4325)
de Oliveira, Ana Laura Grossi
Reis-Cunha, João
Fraga, Vanessa Gomes
Bastos, Pedro Henrique
Ashford, Jodie
Ekárt, Anikó (ORCID Profile 0000-0001-6967-5397)
Adelino, Talita Emile Ribeiro
Silva, Marcos Vinicius Ferreira
de Melo Iani, Felipe Campos
de Jesus, Augusto César Parreiras
Bartholomeu, Daniella Castanheira
de Souza Trindade, Giliane
Fujiwara, Ricardo Toshio
Bueno, Lilian Lacerda
Lobo, Francisco Pereira

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