Genetic characterization of chikungunya viruses isolated during the 2015-2017 outbreaks in different states of India, based on their E1 and E2 genes.

During 2015-2017, chikungunya virus (CHIKV) showed a resurgence in several parts of India with Karnataka, Maharashtra and New Delhi accounting for a majority of the cases. E2-E1 gene based characterization revealed Indian subcontinent sublineage strains possessing Aedes aegypti mosquito-adaptive mutations E1: K211E and E2:V264A, with the 211 site positively selected. Novel mutational sites E1: K16E/Q, E1: K132Q/T, E1: S355T, E2: C19R and E2:S185Y could be associated with epitopes or virulence determining domains. The study examines the role of host, vector and viral factors and fills gaps in our molecular epidemiology data for these regions which are known to possess a dynamic population.

Chikungunya phylogeography reveals persistent global transmissions of the Indian Ocean Lineage from India in association with mutational fitness.

Since the resurgence of chikungunya virus (CHIKV) in India in 2005, the Indian subcontinent sublineage of the Indian Ocean lineage (IOL) has continued transmission in India and also radiation from India causing additional outbreaks in surrounding countries. This study was undertaken for an in-depth understanding of the evolutionary dynamics of the IOL, the global transmission routes in the Indian context and possible association with mutational fitness. The whole genome sequencing of Indian isolates representing CHIKV outbreaks (2014-2018) from selected States of India was carried out, followed by phylogeography analysis of the IOL using the Bayesian Markov chain Monte Carlo method and selection pressure analysis. Phylogeography analysis of IOL strains revealed indigenous evolution in India at least at three time points, with specific mutations that conferred viral fitness in the Aedes vector species. Further dispersal of the strains from India was noted to neighbouring and distant countries with multiple exportations to Sri Lanka, Bangladesh and China. The study reveals India as an endemic reservoir for CHIKV and persistent global transmissions from India. Though natural selection does not appear to play a major role in establishment of the IOL, sustainable efforts towards vector control can help address the issues.