Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus

Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Amer...

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Published in:Genes Vol. 12; no. 2; p. 239
Main Authors: Spicher, Thomas, Delitz, Markus, Schneider, Adriano de Bernardi, Wolfinger, Michael T.
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 08.02.2021
MDPI
Subjects:
Africa
Arthropods
Asia
Chikungunya virus
data collection
Epidemics
Epidemiology
Genomes
humans
Internet
molecular epidemiology
monophyly
Mutation
Outbreaks
Pathogens
Phylogenetics
Phylogeny
Proteins
Ribonucleic acid
RNA
RNA viruses
Viruses
South America
Southeast Asia
Indian Ocean
Asia
Tanganyika
Africa
molecular epidemiology
mutation
RNA structure
Chikungunya virus
ISSN:2073-4425, 2073-4425
Online Access:Get full text
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Summary:Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early 1950s, from three CHIKV lineages: West African, East Central South African, and Asian Urban. As new outbreaks occurred in the Americas, individual strains from the known lineages have evolved, creating new monophyletic groups that generated novel geographic-based lineages. Building on a recently updated phylogeny of CHIKV, we report here the availability of an interactive CHIKV phylodynamics dataset, which is based on more than 900 publicly available CHIKV genomes. We provide an interactive view of CHIKV molecular epidemiology built on Nextstrain, a web-based visualization framework for real-time tracking of pathogen evolution. CHIKV molecular epidemiology reveals single nucleotide variants that change the stability and fold of locally stable RNA structures. We propose alternative RNA structure formation in different CHIKV lineages by predicting more than a dozen RNA elements that are subject to perturbation of the structure ensemble upon variation of a single nucleotide.
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These authors contributed equally to this work.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes12020239