Evolutionary characterization of full length e2 gene of Chikungunya virus by phylogenetic, bayesian and network analyses

Chikungunya virus (CHIKV) is the re-emerging arthropod borne pathogen that is responsible for numerous epidemics across the globe. We studied evolutionary dynamics of 101 global full length E2 gene sequences of CHIKV that were reported during 1963 to 2017 using phylogenetic, Bayesian, Network, selection pressure and entropy analyses. Further, we also investigated local evolutionary dynamics encompassing Bayesian skyline plot, N- and O-linked glycosylation, and mutations of selected Indian strains. The evolutionary analysis clustered the study sequences in to East Central African (ECSA), Asian and West African genotypes. The ECSA is the most commonly reported genotype from different part of the world including India. The ECSA genotype clustered into ECSAI, ECSAII and ECSAIII subgroups. The tMRCA (time to most recent common ancestor) of CHIKV was estimated to be 582 year with a mean nucleotide substitution rate (substitution per site per year) of 2.87×10⁻⁴. Selection pressure identified 4 positively selected sites and Shannon entropy revealed 42 variable positions in the analyzed region suggesting probable variation at these positions. The BSP plot of Indian strains showed a nearly constant phase of CHIKV cases till year 2000 followed by a slight decrease. Subsequently, a sudden increase in the virus population was reported due to the 2005-06 CHIKV epidemic that was followed by stable virus population during 2007-2017. The mutations and N- and O-linked glycosylation sites were also analyzed for the Indian strains. Further, comprehensive full genome analyses from different parts of the globe are needed to delineate the evolutionary trajectory of Chikungunya, re-emerging viral pathogen.