LAUSR

Chikungunya, a mosquito‐borne disease caused by Chikungunya virus (CHIKV), continues to be a significant public health problem in India. In 2016, 56 000 cases were reported from India, the largest number since the reemergence of CHIKV in this region in 2006. In the present study, using molecular and phylogenetic methods, the circulating strains from southern India during 2015‐2016 were characterized in the context of circulating Asian strains. Partial envelope gene (E1) sequencing was performed on 20 serum samples positive for CHIKV by a reverse transcription‐polymerase chain reaction. Phylogenetic analysis showed that all the sequences in this study belonged to the East Central South African (ECSA) genotype and clustered together with other strains from India. Bayesian phylogenetic analysis revealed that the sequences from the study grouped into two different subclades. The estimate of divergence times suggests that subclades of the ECSA genotype, share a common ancestor approximately 4 to 12 years ago. Six nonsynonymous mutations—K211E, M269V, D284E, V322A, I317V and V220I were noted in E1. In conclusion, this study revealed the cocirculation of distinct subclades within the ECSA genotype of CHIKV in South India during 2015‐2016. The I317V mutation in E1 has only been described in recent CHIKV strains from north‐central India and Bangladesh. This study highlights the need for continued molecular surveillance to identify the emergence of novel strains and unique mutations in CHIKV with epidemic potential.