Phylogenomics and genetic recombination detection among Matrix protein of Chandipura Virus genome: A computational approach
DOI:
https://doi.org/10.51976/zbve5y64Keywords:
Chandipura virus, matrix protein, phylogenetic analysis, Recombination detection, viral pathogenesisAbstract
Chandipura virus (CHPV), a negative-sense (-) single-stranded (ss) RNA virus of the family Rhabdoviridae and genus Vesiculovirus, is re-emerging as a neurotropic pathogen. This virus causes encephalitis outbreaks, which kill several children within 24 hours of being symptomatic. The latest outbreak in Gujarat state, between June and August 2024, showed the severity of CHPV infections, with a 33% case fatality rate. Even though CHPV is a public health threat, its matrix (M) protein's molecular evolution and functional dynamics are unknown. This work examines CHPV's M protein's evolutionary links and genetic recombination processes, which are essential for viral assembly and budding. Phylogenetic analysis employed the NJ method, incorporating M protein sequences from BLAST searching. By using the SDT, pairwise sequence comparisons and homology analyses revealed that the CHPV Indian isolate (NC020805) shares a nucleotide identity of 78% with Lyssavirus Duvenhage virus (LVDV, NC020810) and 72% with Rabies virus (ReV, NC001542). Further, the closest relative to the Indian CHPV isolate was identified as the Jurona virus (JuV, NC039206) by performing molecular evolution and phylogenetic analysis with the help of MEGA 11 software. Our result showed five genomic recombination events analyzed using RDP methods, demonstrating strong evidence of recombination in the cases of Event 2 and Event 4, which have exceptionally low p-values. In event 2, the recombinant sequence (NC039206) has a major parent NC020805 and minor parent NC034550, with major parent recombination regions 1-1169 and 1479-15347 and minor parent 1170-1478. In event 4, a recombinant sequence (NC039206), with NC020805 (Indian isolate) as the major parent and NC020807 as the minor parent, suggests a more reliable recombination detection. Compared to other Rhabdoviruses, the CHPV's M protein is non-conserved. This heterogeneity may affect CHPV's virulence and adaptability to viral evolution and infection processes. This study of the CHPV molecular phylogenomics and recombination, specifically in the M protein gene, will enhance our horizon of understanding of host-virus interaction, assembly, and pathogenesis. It will further assist in customized diagnostics, vaccinations, and therapeutic measures to mitigate future outbreaks.
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