In-silico analysis of novel mutations identified in Chikungunya virus

Abstract

Chikungunya fever, caused by CHIKV transmitted by Aedes mosquitoes, poses a significant global health challenge. This study investigates novel Chikungunya Virus (CHIKV) identified mutations in Jeddah, Saudi Arabia, through in silico analyses. The study focused on mutations detected in the E1, capsid, and nsP3 regions of the CHIKV genome, employing molecular dynamics (MD) simulations and bioinformatic tools for analysis. Methods included sequencing the virus's whole genome and identifying rare mutations in the CHIKV strain from Jeddah (2021), homology modelling done to create three-dimensional structures of CHIKV proteins, and protein stability prediction conducted using various computational tools. MD simulation was utilised to analyse the stability of mutated proteins, comparing wild-type and mutated forms. The main findings revealed three significant mutations (E1:A249T, C: A147V, nsP3:V58I) that potentially affect the stability and function of their respective proteins. The analysis predicted these mutations to generally decrease the stability of the proteins. MD simulations indicated fluctuations and conformational changes in mutated proteins, suggesting altered dynamics and potentially impacting CHIKV's virulence and transmission. The study identified and analysed novel CHIKV mutations, offering insights into their potential impact on viral pathogenesis and highlighting the importance of monitoring viral evolution to manage and prevent outbreaks effectively.