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 |
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| Main Authors: | , , , |
| Format: | Journal Article |
| Language: | English |
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| ISSN: | 2073-4425, 2073-4425 |
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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. |
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| AbstractList | Chikungunya virus (CHIKV) is an emerging
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. 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. 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.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. |
| Author | Spicher, Thomas Delitz, Markus Wolfinger, Michael T. Schneider, Adriano de Bernardi |
| AuthorAffiliation | 1 Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria; a01346576@unet.univie.ac.at (T.S.); delitzm93@univie.ac.at (M.D.) 3 Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria 2 AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA; adebernardischneider@health.ucsd.edu |
| AuthorAffiliation_xml | – name: 1 Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria; a01346576@unet.univie.ac.at (T.S.); delitzm93@univie.ac.at (M.D.) – name: 3 Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria – name: 2 AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA; adebernardischneider@health.ucsd.edu |
| Author_xml | – sequence: 1 givenname: Thomas surname: Spicher fullname: Spicher, Thomas – sequence: 2 givenname: Markus orcidid: 0000-0001-6159-5819 surname: Delitz fullname: Delitz, Markus – sequence: 3 givenname: Adriano de Bernardi orcidid: 0000-0001-7487-266X surname: Schneider fullname: Schneider, Adriano de Bernardi – sequence: 4 givenname: Michael T. orcidid: 0000-0003-0925-5205 surname: Wolfinger fullname: Wolfinger, Michael T. |
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| CitedBy_id | crossref_primary_10_22579_20112629_789 crossref_primary_10_1099_jgv_0_001680 crossref_primary_10_3389_fmicb_2021_689979 crossref_primary_10_1099_jgv_0_001615 crossref_primary_10_1093_ve_veac051 |
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| Snippet | Chikungunya virus (CHIKV) is an emerging Alphavirus which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since... Chikungunya virus (CHIKV) is an emerging which causes millions of human infections every year. Outbreaks have been reported in Africa and Asia since the early... |
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| SubjectTerms | 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 |
| Title | Dynamic Molecular Epidemiology Reveals Lineage-Associated Single-Nucleotide Variants That Alter RNA Structure in Chikungunya Virus |
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