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.
Highlights
Academic Editor: Antonio CaruzReceived: 14 January 2021Accepted: 4 February 2021Published: 8 February 2021Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.Chikungunya virus (CHIKV) is an arthropod-borne Alphavirus of the family Togaviridae that causes millions of human infections every year, in tropic and subtropic regions
In Africa, CHIKV occurs in an enzootic, sylvatic cycle involving nonhuman primates as hosts, while in Asia, CHIKV is mainly maintained in an urban cycle with direct human–mosquito–human transmission [3]
To better understand the evolutionary traits associated with functional RNA conservation among different lineages, we set out to use the CHIKV molecular epidemiology data to study the impact of lineage-associated sequence variability on viral RNA structure
Summary
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations. Following the Indian Ocean islands outbreak, CHIKV spread independently into the Indian Subcontinent and Southeast Asia [9]. Following the 2005 La Réunion outbreak, and the subsequent emergence of CHIKV in India, the existence of a fourth separate lineage, termed Indian Ocean Lineage (IOL), has been proposed [15]. Haiti [19] (South American Lineage, SAL), and the East African Lineage (EAL) gave rise to the IOL The latter is predominantly found on the Asian continent, except for travel-related cases in which CHIKV has been imported to Europe and North America [3,20,21]. The AUL, is considered a sister clade to all ECSA-derived lineages and has been circulating in Southeast Asia before spreading into Central America and many South. South America, at the time CHIKV was mislabeled as another febrile disease, dengue [25]
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