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

Spicher, Thomas; Delitz, Markus; Schneider, Adriano de Bernardi; Wolfinger, Michael T.

doi:10.3390/genes12020239

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

by

Thomas Spicher

^1,†,

Markus Delitz

^1,†

,

Adriano de Bernardi Schneider

²

and

Michael T. Wolfinger

^1,3,*

¹

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria

²

AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA

³

Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria

^*

Author to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Genes 2021, 12(2), 239; https://doi.org/10.3390/genes12020239

Submission received: 14 January 2021 / Revised: 29 January 2021 / Accepted: 4 February 2021 / Published: 8 February 2021

(This article belongs to the Special Issue Quest for Conserved RNAs in Viral Genomes)

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Abstract

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.

Keywords: Chikungunya virus; molecular epidemiology; mutation; RNA structure

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MDPI and ACS Style

Spicher, T.; Delitz, M.; Schneider, A.d.B.; Wolfinger, M.T. Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus. Genes 2021, 12, 239. https://doi.org/10.3390/genes12020239

AMA Style

Spicher T, Delitz M, Schneider AdB, Wolfinger MT. Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus. Genes. 2021; 12(2):239. https://doi.org/10.3390/genes12020239

Chicago/Turabian Style

Spicher, Thomas, Markus Delitz, Adriano de Bernardi Schneider, and Michael T. Wolfinger. 2021. "Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus" Genes 12, no. 2: 239. https://doi.org/10.3390/genes12020239

APA Style

Spicher, T., Delitz, M., Schneider, A. d. B., & Wolfinger, M. T. (2021). Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus. Genes, 12(2), 239. https://doi.org/10.3390/genes12020239

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

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

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