Comparative Molecular and Structural Characterisation of Chikungunya Virus Isolated Before and After 2006 Epidemics

Background: Chikungunya virus caused incapacitating infection during 2006 epidemics spanning 28 countries. The expansion of the disease and increased virulence resulted in neurological and ocular complications in the affected patients implicating changes in the structural and functional properties of the newly emerging strains of Chikungunya virus.

Objective: Hence the study was designed to understand the disparity between two strains isolated before and after 2006 epidemics by both in vitro and in silico approaches with respect to E1 gene.

Materials and Methods: Sequencing of E1 gene and phylogenetic analysis of the two strains were carried out followed by the determination of growth pattern. The impact of aminoacid substitutions on the structural properties of E1 protein between the strains of Chikungunya virus was identified by different Bioinformatic tools.

Results: Sequencing and Phylogenetic analysis revealed the two strains as Asian (isolated before 2006) and East Central South African (isolated after 2006). ECSA strain produced 1.5 fold log10 titre increased viral production than the Asian strain at the multiplicity of infection 1. Influence of aminoacid difference on the structure of E1 protein between two strains by Bioinformatic analysis had shown a change in the conformations by the loss of two intermolecular hydrogen bonds in 121 position in Asian strain and electrostatic differences in 211 positions between the two strains was also observed.

Conclusion: As the interacting aminoacid 121 and 211 position lies near the fusion loop hence the difference in aminoacid position between the two strains could better influence fusogenicity and stable trimer formation. This forms a preliminary insight on the impact of aminoacid substitutions on the structural properties of E1 protein between the strains of Chikungunya virus and further experimental investigations are warranted.