In Silico Characterization of Conserved Epitopes in Alphavirus E2 Proteins - A Promising Approach for Pan-vaccine Design

Sep 29, 2026

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Alphaviruses infect diverse hosts, creating growing public health risks, with arthritogenic Chikungunya virus (CHIKV) and encephalitogenic Eastern equine encephalitis virus (EEEV) notable for epidemic capacity and clinical severity. Licenced and effective vaccine models remain limited, motivating rational epitope design using immunoinformatics. This study applied the POA pipeline to prioritize predicted E2 epitopes from both viruses, selecting 39 conserved linear epitopes (8 B-cell, 2 T-cell, 29 Th-cell). The epitopes were evaluated for allergenicity, toxicity, and physicochemical features and mapped onto quasi-3-fold symmetry for accessibility in native quaternary context. Results support multiepitope pan-vaccine design targeting conserved antigenic regions with translational relevance, aligned with One Health. The POA pipeline is shared on GitHub.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages13

Reading Time33 min

AccessFree to download

Abstract

Introduction

Alphavirus epidemiology and vaccine challenges

Role of E2 glycoprotein and conserved epitopes

Pipeline overview and epitope mapping

This article is licensed under CC-BY 4.0 [http://pubs.acs.org/journal/acsodf](http://pubs.acs.org/journal/acsodf) Article In Silico Characterization of Conserved Epitopes in Alphavirus E2 Proteins: A Promising Approach for Pan-vaccine Design Ubiratan da Silva Batista, Ana Clara Gomes de Souza, Breno de Mello Silva, * and Ricardo Lemes Gonalves * Cite This: ACS Omega 2025, 10, 58856−58868 Read Online | | | | | | | | --- | --- | --- | --- | --- | --- | | ACCESS | Metrics & More | | Article Recommendations | | *sı Supporting Information | ABSTRACT: Alphaviruses infect a wide range of hosts, including humans and domestic animals, and they represent an increasing public health concern. Among them, arthritogenic Chikungunya virus (CHIKV) and encephalitogenic Eastern equine encephalitis virus (EEEV) stand out for their epidemic potential and clinical severity. Developing effective and licensed vaccine models against these viruses remains a significant challenge. Rational epitope design, supported by immunoinformatics, offers a promising route for nextgeneration effective vaccine development. In this study, we utilized the POA pipeline to assist in the selection and prioritization of predicted epitopes from the E2 glycoproteins of CHIKV and EEEV. A total of 39 conserved linear epitopes were selected, comprising 8 B-cell, 2 T-cell, and 29 Th-cell epitopes. These epitopes were characterized for allergenicity, toxicity, and physicochemical properties, including polarity and hydrogen-bonding potential. Structural mapping onto the quasi-3-fold (q3) symmetry unit enabled assessment of their solvent accessibility and spatial organization in the native quaternary context. Our result provides a basis for the rational design of a multiepitope vaccine targeting conserved antigenic regions in alphaviruses with high translational relevance. This integrative approach aligns with the One Health perspective, highlighting its potential for developing biotechnological solutions that address human, animal, and environmental health. The POA pipeline is available on GitHub ([https://github.com/UbiratanBatista/POA_Project](https://github.com/UbiratanBatista/POA_Project)). ■ INTRODUCTION Alphaviruses are emerging arboviruses of major public health concern, responsible for outbreaks that cause severe disease in both humans and animals worldwid.1 The genus Alphavirus (family Togaviridae) comprises 30 enveloped, singlestranded, positive-sense RNA viruses, which are broadly classified into arthritogenic and encephalitogenic groups based on clinical manifestations and epidemiological patterns. Chikungunya virus (CHIKV), an arthritogenic alphavirus, causes febrile illness, skin rashes, and debilitating polyarthritis.2 In contrast, eastern equine encephalitis virus (EEEV), a representative encephalitic alphavirus, is associated with acute and often fatal neurological disease.3 Both viruses exemplify the epidemic potential of alphaviruses and their capacity to cause large-scale outbreaks.4 Despite their clinical relevance,5,6 effective vaccines and antivirals for human use remain limited. To date, two vaccines against CHIKV infection have received regulatory approval,7,8 while additional candidates are progressing through advanced clinical evaluation. In contrast, vaccine development for other alphaviruses has lagged significantly.9, 10 For EEEV, for example, available licensed formulations are restricted to veterinary use in equines and typically elicit moderate immunogenicity, 10 requiring periodic booster doses to maintain protective titers.6,9 These gaps underscore the need for rational vaccine strategies designed to target both arthritogenic and encephalitic alphaviruses. The E2 structural glycoprotein plays a central role in alphavirus infectivity and immunogenicity, mediating receptor binding and entry into host cells. It is the primary target of neutralizing antibodies and thus represents a critical antigen for vacci

FAQs

What is the main goal of this study?

To characterize conserved linear epitopes in alphavirus E2 proteins using an immunoinformatics workflow, supporting rational pan-vaccine design targeting shared antigenic regions.

Which viruses and protein region were analyzed?

The study focused on the E2 glycoproteins of Chikungunya virus (CHIKV) and Eastern equine encephalitis virus (EEEV).

How were selected epitopes evaluated and mapped?

Selected B- and T-cell epitopes were assessed for allergenicity, toxicity, and physicochemical properties, then structurally mapped onto the quasi-3-fold symmetry unit to evaluate solvent accessibility and spatial organization.

Sep 29, 2026

Upload by Fahsai