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

## TL;DR

This study identifies conserved immune targets in alphaviruses to design a universal vaccine, using computational methods and structural analysis.

## Contribution

A novel integrative pipeline (POA) for epitope selection and characterization in alphavirus E2 proteins is introduced.

## Key findings

- 39 conserved linear epitopes were identified, including B-cell, T-cell, and Th-cell epitopes.
- Epitopes were evaluated for allergenicity, toxicity, and structural accessibility for vaccine design.
- The approach supports a One Health strategy for biotechnological solutions targeting alphaviruses.

## 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 next-generation 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).