Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture
Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To unders...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/11/9/798 |
| _version_ | 1818017741390479360 |
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| author | Adriano de Bernardi Schneider Roman Ochsenreiter Reilly Hostager Ivo L. Hofacker Daniel Janies Michael T. Wolfinger |
| author_facet | Adriano de Bernardi Schneider Roman Ochsenreiter Reilly Hostager Ivo L. Hofacker Daniel Janies Michael T. Wolfinger |
| author_sort | Adriano de Bernardi Schneider |
| collection | DOAJ |
| description | Chikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages. |
| first_indexed | 2024-04-14T07:30:54Z |
| format | Article |
| id | doaj.art-29a771e262d140ea91fd5afb457e6a00 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-04-14T07:30:54Z |
| publishDate | 2019-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-29a771e262d140ea91fd5afb457e6a002022-12-22T02:05:51ZengMDPI AGViruses1999-49152019-08-0111979810.3390/v11090798v11090798Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA ArchitectureAdriano de Bernardi Schneider0Roman Ochsenreiter1Reilly Hostager2Ivo L. Hofacker3Daniel Janies4Michael T. Wolfinger5AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USADepartment of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, AustriaAntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USADepartment of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, AustriaDepartment of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USADepartment of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, AustriaChikungunya virus (CHIKV), a mosquito-borne alphavirus of the family Togaviridae, has recently emerged in the Americas from lineages from two continents: Asia and Africa. Historically, CHIKV circulated as at least four lineages worldwide with both enzootic and epidemic transmission cycles. To understand the recent patterns of emergence and the current status of the CHIKV spread, updated analyses of the viral genetic data and metadata are needed. Here, we performed phylogenetic and comparative genomics screens of CHIKV genomes, taking advantage of the public availability of many recently sequenced isolates. Based on these new data and analyses, we derive a revised phylogeny from nucleotide sequences in coding regions. Using this phylogeny, we uncover the presence of several distinct lineages in Africa that were previously considered a single one. In parallel, we performed thermodynamic modeling of CHIKV untranslated regions (UTRs), which revealed evolutionarily conserved structured and unstructured RNA elements in the 3’UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3’UTR architecture among different CHIKV lineages.https://www.mdpi.com/1999-4915/11/9/798RNA virusevolutionepidemicsphylogeographysecondary structure |
| spellingShingle | Adriano de Bernardi Schneider Roman Ochsenreiter Reilly Hostager Ivo L. Hofacker Daniel Janies Michael T. Wolfinger Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture Viruses RNA virus evolution epidemics phylogeography secondary structure |
| title | Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture |
| title_full | Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture |
| title_fullStr | Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture |
| title_full_unstemmed | Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture |
| title_short | Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture |
| title_sort | updated phylogeny of chikungunya virus suggests lineage specific rna architecture |
| topic | RNA virus evolution epidemics phylogeography secondary structure |
| url | https://www.mdpi.com/1999-4915/11/9/798 |
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