Molecular genome tracking of East, Central and South African genotype of Chikungunya virus in South-east Asia between 2006 and 2009

Objective: To understand the epidemiology of the East, Central and South African (ECSA) genotype of Chikungunya virus (CHIKV) in terms of emerging and re-emerging infections, this study has been aimed at investigating the evolutionary parameters, genomic signatures and molecular tracking of the CHIKV ECSA genotype in South-east Asia and coastal areas of the Indian Ocean between 2006 and 2009 by using phylogenetic analysis and the Bayesian Markov Chain Monte Carlo (BMCMC) evolutionary estimation. Methods: Nearly complete genome sequences of 53 CHIKV isolates from all genotypes were subjected to phylogenetic analysis and evolutionary parameter estimation. The amino acids of 67 of ECSA genotype during 2006 to 2009 were compared for finding molecular signature tracking. The ECSA genotype signatures were visualized to find the possible transmission root was projected onto a geographic map. Results: Phylogenetic analysis showed the ECSA genotype was divided into 2 groups. The first group comprises viruses from India and Southeast Asian countries. The second group consists of strains typically circulating in Sri Lanka in 2008. The evolutionary parameters of these groups depicted the time of the most recent common ancestor at approximately 7.5 years ago. The genomic signatures revealed the positions of amino acid variation in each group. Conclusions: The molecular evolution projected onto a geographical map showed the routes of CHIKV transmission from 2006 to 2009. Molecular tracking will assist in understanding transmission routes, epidemiology and molecular evolution of CHIKV.