Chikungunya has long been one of the major health problems facing all over the world and is caused by the virus CHIKV . The disease is transmitted by Aedes mosquitoes. Current outbreaks that occurred in Asian countries were unusual. A specific drug for Chikungunya has not been discovered yet.

The Objectives of the work were

  • phylogentic analysis of different strains of Chikungunya virus.
  • The identification of protein in the most mutated region in the genome of Chikungunya Virus.
  •  Homology modeling of the protein in that region and
  • The prediction of probable amino acid sequence of capsid protein of Chikungunya virus that could cause the next outbreak.

Phylogenetic analysis of Chikungunya virus proved that the virus originated from African strains  from where it spread to the rest of the world. Using multiple sequence alignment tools frequently mutating regions of the virus were located and a graph showing mutation frequencies was drawn. From the graph NS3 protease, Capsid protein, and E1 protein were identified as most mutated regions in the genome of Chikungunya virus. As Capsid protein of Chikungunya virus are antigenically important, homology modeling of that protein was done via the software Swiss PDB viewer. It is found that in Chikungunya, variations in genomic sequences do not cause much change in its corresponding amino acid regions. So it is evident that Chikungunya evolution has reached a steady state. Some possible amino acid sequences of the capsid protein of the evolving Chikungunya virus strain was predicted on the basis of relative mutabilities of the amino acid residues in the preceding sequence and using substitution matrices.< xml="true" ns="urn:schemas-microsoft-com:office:office" prefix="o" namespace="">