Pathogen Sequence Signature Analysis


Chikungunya virus (CHIKV) is an arbovirus (arthropod-borne virus) which is a member of the Alphavirus genus belonging to the Togaviridae family, vectored by Aedes mosquitoes to humans in tropical and subtropical regions of Africa and Asia. CHIKV has a single-stranded, positive-sense RNA genome of 12 kb and causes chikungunya fever (CHIK), a febrile illness associated with severe arthralgia and rash; the name is derived from a Bantu language word describing the severe arthriticsigns,which can persist for years. CHIKV is transmitted to humans mainly by Aedes (Ae.) aegypti and Ae. albopictus mosquitoes. The phylogenetic analysis of CHIKV based on E1 gene sequences identified three geographically associated genotypes: the West African (WAf), East/Central/South African (ECSA), and Asian genotypes. More recent analyses indicate that the recent Indian Ocean and Indian strains form a monophyletic group within the ECSA lineage. However, most CHIKV phylogenetic studies have utilized only partial sequences from the envelope glycoprotein E1 gene, preventing arobust assessment of some of the relationships among strains and of their evolutionary dynamics.

Genes of Chikungunya

Name Description
E1The viral spike proteins facilitate attachment to cell surfaces and viral entry into the cells. The E1 envelope protein is a class II fusion protein that mediates low pH-triggered membrane fusion during virus infection.
E2The envelope glycoprotein E2 form heterodimeric spikes on the virion surface. The glycoprotein E2 binds to cellular receptors in order to enter the host cell through receptor-mediated endocytosis.
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