Author Proof 1 10.2217/FVL.12.95 © 2012 Future Medicine Ltd ISSN 1746-0794 Future Virology part of Future Virol. (2012) 7(10), 1–14 Chikungunya virus (CHIKV) is an arthropod- borne virus. CHIKV transmission in humans is reported to be carried out by Aedes spp. (e.g. , Aedes albopictus) mosquitoes [1–3] . Clinical symp- toms of chikungunya infection are fever, rash, headache, joint pain or arthralgia, and muscle pain or myalgia [4–6] . The symptoms usually last between 1 and 10 days [4] . Several outbreaks in Africa, India and South-East Asia have been reported previously [7–9] . Recently, from 2004 until now, there have been reports of a reemerged CHIKV infec- tion in several geographic regions [10–14] . The first of its outbreaks was recorded in Kenya in 2004. Similar outbreaks in different islands (e.g., Comoros Islands, southwest Indian Ocean) were also filed in early 2005 [7,15–18] . In 2005–06 it broke out in a massive propor- tion of India. Molecular analysis of the strains isolated on islands in the Indian Ocean and in India revealed that the epidemic was caused by a central/east African genotypic variant of CHIKV [11,12,19–21] . Soon, a large number of travelers from industrialized countries became infected with CHIKV. Hence what started as a mere endemic spark became the equivalent of a global forest fire without much ado [22,23] . CHIKV is an alphavirus and belongs to the Togaviridae family [24] . It possesses a single- strand positive-sense RNA genome. Two of the proteins in CHIKV have been sequenced in abundance to characterize the envelope pro- teins CHIKV- E1 and E2 [24–26] . E1-targeted antibodies are more likely to cross-react with other alphaviruses and thus are nonspecific compared with E2-targeted antibodies [26,27] . Monoclonal antibody-associated competi- tive binding assays identified approximately seven epitopes on the E1 glycoproteins of Sindbis virus (SINV), Simian foamy virus (SFV), Western equine encephalitis virus, and Venezuelan equine encephalitis virus (VEEV). Epitopes for E1 proteins are mostly present on the surface of infected cells instead of the virion surface. In vitro analysis of antibody reactions to E1 include HI, neutralization of virus infec- tivity, and inhibition of fusion. The presence of different functionally distinct domains has been suggested based on this analysis [28–30] . Mapping monoclonal antibody binding sites to specific E1 sequences is always a challenge. One acid-exposed epitope involves E1–157 of SFV [31] . A neutralizing mAb distinguishes strains of SINV differing only at residues 72 A computational assay to design an epitope-based peptide vaccine against chikungunya virus Md Rezaul Islam 1 , M Sadman Sakib 1 & Aubhishek Zaman* 2 1 Department of Biochemistry & Molecular Biology, University of Dhaka, Dhaka, Bangladesh 2 Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh *Author for correspondence: aubhishek@gmail.com Aim: Chikungunya virus, an arthropod-borne alphavirus, belongs to the Togavirus family. Despite severe epidemic outbreaks on several occasions, not much progress has been made with regard to epitope-based drug design for chikungunya virus. In this study we performed a proteome-wide search to look for a conserved region among the available viral proteins, one which has the capacity to trigger a significant immune response. Materials & methods: The conserved region was analyzed by performing an alignment of sequences collected from sources from varied geographic locations and time periods. Subsequently, the immune parameters for the peptide sequences were determined using several in silico tools and immune databases. Results: Both T-cell immunity and B-cell immunity were checked for the peptides to ensure that they had the capacity to induce both humoral and cell-based immunity. Our study reveals a stretch of conserved region in glycoprotein E2; yet this peptide sequence could interact with as many as seven HLAs and showed population coverage as high as 73.46%. The epitope was further tested for binding against the HLA structure using in silico docking techniques to validate the binding cleft epitope interaction in detail. Conclusion: Although the study requires further in vivo screening, keeping in mind the consistency and reproducibility of the immune system at selecting and reacting to peptide epitopes, this study allows us to claim a novel peptide antigen target in E2 protein with good confidence. Keywords n chikungunya virus n CHIKV n E2 envelope protein n epitope-based drug design Preliminary Communication