{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T00:55:42Z","timestamp":1784681742981,"version":"3.55.0"},"reference-count":86,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T00:00:00Z","timestamp":1567036800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u2019UTR. We provide evidence for duplication events in recently emerged American isolates of the Asian CHIKV lineage and propose the existence of a flexible 3\u2019UTR architecture among different CHIKV lineages.<\/jats:p>","DOI":"10.3390\/v11090798","type":"journal-article","created":{"date-parts":[[2019,8,29]],"date-time":"2019-08-29T11:26:22Z","timestamp":1567077982000},"page":"798","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7487-266X","authenticated-orcid":false,"given":"Adriano","family":"de Bernardi Schneider","sequence":"first","affiliation":[{"name":"AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1126-0513","authenticated-orcid":false,"given":"Roman","family":"Ochsenreiter","sequence":"additional","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7548-8624","authenticated-orcid":false,"given":"Reilly","family":"Hostager","sequence":"additional","affiliation":[{"name":"AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7132-0800","authenticated-orcid":false,"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Vienna, Austria"},{"name":"Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, W\u00e4hringerstra\u00dfe 29, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel","family":"Janies","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0925-5205","authenticated-orcid":false,"given":"Michael T.","family":"Wolfinger","sequence":"additional","affiliation":[{"name":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, 1090 Vienna, Austria"},{"name":"Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, W\u00e4hringerstra\u00dfe 29, 1090 Vienna, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2019,8,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.onehlt.2017.06.001","article-title":"Emerging arboviruses: Why today?","volume":"4","author":"Gould","year":"2017","journal-title":"ONE Health"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1006\/viro.1997.8907","article-title":"The Alphavirus 3\u2019-Nontranslated Region: Size Heterogeneity and Arrangement of Repeated Sequence Elements","volume":"240","author":"Pfeffer","year":"1998","journal-title":"Virology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"20140135","DOI":"10.1098\/rstb.2014.0135","article-title":"Climate change influences on global distributions of dengue and chikungunya virus vectors","volume":"370","author":"Campbell","year":"2015","journal-title":"Philos. 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