AntiViral Research Center, Department of Medicine, University of California San Diego, San Diego, CA 92103, USA.
Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
Viruses. 2019 Aug 29;11(9):798. doi: 10.3390/v11090798.
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.
基孔肯雅病毒（CHIKV）是一种虫媒黄病毒属的正粘病毒科，最近在美洲从来自两个大陆的亚洲和非洲谱系中出现。历史上，CHIKV 在全球范围内至少有四个谱系传播，具有地方性和流行的传播周期。为了了解最近的出现模式和 CHIKV 传播的现状，需要对病毒的遗传数据和元数据进行更新分析。在这里，我们利用许多最近测序的分离株的公开可用性，对 CHIKV 基因组进行了系统发育和比较基因组学筛选。基于这些新的数据和分析，我们从编码区的核苷酸序列中得出了一个修订的系统发育树。利用这个系统发育树，我们揭示了非洲存在几个以前被认为是单一谱系的不同谱系。同时，我们对 CHIKV 的非翻译区（UTR）进行了热力学建模，揭示了 3'UTR 中进化上保守的结构和非结构 RNA 元件。我们为亚洲 CHIKV 谱系中最近出现的美洲分离株的重复事件提供了证据，并提出了不同 CHIKV 谱系之间存在灵活的 3'UTR 结构的假设。
