Global transmission and evolutionary dynamics of the Chikungunya virus

Abstract

Chikungunya virus (CHIKV) is a re-emerging pathogen of global importance. We attempted to gain an insight into the organisation, distribution and mutational load of the virus strains reported from different parts of the world. We describe transmission dynamics and genetic characterisation of CHIKV across the globe during the last 65 years from 1952 to 2017. The evolutionary pattern of CHIKV was analysed using the E1 protein gene through phylogenetic, Bayesian and Network methods with a dataset of 265 sequences from various countries. The time to most recent common ancestor of the virus was estimated to be 491 years ago with an evolutionary rate of 2.78 × 10−4 substitutions/site/year. Genetic characterisation of CHIKV strains was carried out in terms of variable sites, selection pressure and epitope mapping. The neutral selection pressure on the E1 gene of the virus suggested a stochastic process of evolution. We identified six potential epitope peptides in the E1 protein showing substantial interaction with human MHC-I and MHC-II alleles. The present study augments global epidemiological and population dynamics of CHIKV warranting undertaking of appropriate control measures. The identification of epitopic peptides can be useful in the development of epitope-based vaccine strategies against this re-emerging viral pathogen.

Molecular Epidemiology, Evolution and Reemergence of Chikungunya Virus in South Asia

“…Molecular evolutionary analysis confirmed the divergence of lineages from each other in previous studies and Nextstrain project and recently published phylogenies and evolutionary analysis ( de Bernardi Schneider et al, 2019 ; Deeba et al, 2020 ; Nextstrain, 2021 ; Spicher et al, 2021 ). The single nucleotide variants of CHIKV can change the stability and fold of locally stable RNA structures.…”

“…Another distinct lineage called Indian Ocean Lineage (IOL) evolved from ECSA lineage ( Schuffenecker et al, 2006 ; Presti et al, 2016 ; Silva and Dermody, 2017 ; Pyke et al, 2018 ) was detected after 2004. Phylogenetic and mutational analysis revealed the presence of Asian lineage, IOL and Africa and Asia lineages in South Asian countries in recent time ( Wahid et al, 2017 ; Deeba et al, 2020 ). Asian lineage was the most predominant during 1960s to 2000 in South Asian and South East Asian countries ( Yadav et al, 2003 ; Powers and Logue, 2007 ; Wimalasiri-Yapa et al, 2019 ).…”

“…Besides, ESCA, AUL, and AAL lineages are circulating in South Asia in a low frequency after 2005 outbreaks. Evolutionary analysis has revealed that during 2010 to 2020, outbreaks in Bangladesh, Bhutan, India, Pakistan, and Sri Lanka have been associated with ECSA-IOL lineage ( Powers and Logue, 2007 ; Wahid et al, 2017 ; Melan et al, 2018 ; Deeba et al, 2020 ). During 2017 outbreaks in Bangladesh, only the ECSA-IOL lineage was reported ( Supplementary Table 1 ).…”

“…The single nucleotide variants of CHIKV can change the stability and fold of locally stable RNA structures. Besides, the 3′ untranslated regions of CHIKV was found to contain non-structural RNA elements and evolutionary conserved regions ( de Bernardi Schneider et al, 2019 ; Deeba et al, 2020 ; Spicher et al, 2021 ). Difference among lineages and origin of one lineage from other can be traced by analyzing duplication events and changes of architecture in 3′UTR ( de Bernardi Schneider et al, 2019 ).…”

Caracterização imunogênica do domínio B recombinante da proteína E2 de Chikungunya expressa em Escherichia coli

“…Em 2004, o vírus reemergiu no Quênia e se espalhou para as Ilhas Comores, onde 5000 casos foram reportados (Sergon et al, 2007;Simon, Tolou e Jeandel, 2006 (Bonn, 2006;Schuffenecker et al, 2006 (Powers e Logue, 2007). Atualmente o CHIKV é considerado um patógeno global, circulando ou tendo circulado em aproximadamente 100 países (figura 1) (Deeba et al, 2016(Deeba et al, , 2020. (Nunes et al, 2015).…”