Exploring the impact of envelope protein mutations on Chikungunya virus epitopes: Analysis of virus samples from the Alagoas State outbreak, Brazil

Abstract

Objective: To investigate mutations in the Chikungunya (CHIKV) envelope genome region and evaluate their potential impact on B lymphocyte epitopes via in silico analysis.

Methods: E1, E2 and 6K protein genes were sequenced from viral RNA isolated from 13 CHIKV-positive serum samples from Alagoas State, Brazil, during the 2016 outbreak. Phylogenetic analysis, experimental epitope identification in the immune epitope database (IEDB) and in silico approaches were employed to predict the potential impact of the detected mutations.

Results: The sequences were clustered via phylogenetic analysis. The CHIKV isolates belong to the ECSA genotype, with 13 detected amino acid mutations. Five mutations are located on the surface of the viral particle in regions critical for cellular receptor interaction. Nine mutations are known experimentally validated epitopes for B and T cells. In B-cell epitope predictions, mutations affect sequences within three conformational epitopes in E2 and one in E1, as well as linear epitopes. Notably, the E2-G60D mutation found in the Alagoas strain has been previously reported to influence the vector competence of Aedes aegypti, the primary vector in Brazil.

Conclusions: Genomic surveillance and an in-depth understanding of viral mutations are crucial for adapting public health strategies and improving the outbreak response. These findings could have significant public health implications, such as the development of more effective vaccines, diagnostic tests, and antiviral therapies.

Keywords

Genomic variations / In silico analysis / Epitope prediction / Glycoprotein mutations

Conflict of interest statement

The authors declare that they have no conflicts of interest.

Funding

This study was supported by Decit/SCTIE-Ministério da Saúde, Conselho Nacional de Desenvolvimento Científico e Tecnológico(CNPq), Fundação de Amparo à Pesquisa do Estado de Alagoas(FAPEAL) and Secretaria de Estado da Saúde de Alagoas (SESAUAL)[PPSUS 60030 000841/2016].

Authors’ contributions

Concepts, design, experimental studies, data analysis and manuscript preparation: JTS. Experimental studies: MJTCCO, SJMS, JFGF and MCL. Experimental studies and manuscript editing: JAB. Manuscript review: ASJ. Concepts, design, experimental studies, data analysis and manuscript review: EJB and LA.

Publisher’s note

The Publisher of the Journal remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Edited by Zhang Q, Lei Y, Pan Y

Acknowledgments

We would like to thank all the technical support of the Laboratorio Central de Saude Publica do Estado de Alagoas (LACEN/AL), Maceio, Alagoas, Brazil, and Ana Rachel V. Lima from Laboratorio de Pesquisas em Virologia e Imunologia (LAPEVI).

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