Geographic dispersion of Zika virus: a phylodynamic approach

S.G. Seabra, Kristof Theys, Pieter Libin, Anna Zhukova, Barney I Potter, Hanna Nebenzahl-Guimaraes, Alexander E Gorbalenya, Igor A Sidorov, Victor Pimentel, Marta Pingarilho, Ana Tereza R. Vasconcelos, Dellicoure, Simon , Ricardo Khouri, Gascuel, Olivier , AM Vandamme, Guy Baele, Lize Cuypers, AB Abecasis

Research output: Contribution to conferencePosterpeer-review


Zika virus (ZIKV), a mosquito-borne virus of the Flaviviridae family that induces microcephaly in newborns, caused a public health emergency of international concern in 2016 due to its rapid spread in the Americas. Although the overall number of ZIKV-related cases has declined sharply after 2016, the virus might still be circulating unnoticed. The virus was first isolated in 1947 in non-human primates in Africa and the first suggestion of inter-human transmission came from its detection in the antropophilic mosquito, Aedes aegypti, in 1966, in South-East Asia. The first reported outbreaks occurred in the Pacific islands of Micronesia in 2007. In 2013, in French Polynesia, an outbreak was associated with increased congenital and neurological syndromes, from where it radiated to the Americas. Following the American outbreaks, intensified surveillance efforts provided an opportunity to understand the patterns of genetic diversity, evolution and spread of ZIKV. We analyzed a curated dataset of 505 publicly available full-length coding region sequences with associated metadata that included geographical origin and collection date. Maximum likelihood tree reconstruction showed two main genetic clusters that separated the African from non-African sequences. We further examined the non-African (previously denominated “Asian”) cluster with a Bayesian model-based hierarchical clustering approach and identified substructures within it. We reported a genetic distance between Pre-American and American lineages of 5 %, while the distance between American subgroups was limited to ~0.5 %. This reduced genetic distance is expected from a very recent diversification. Ancestral character reconstruction indicated a spread from South-East Asia to Polynesia and from there reaching South America, particularly Brazil. Subsequently, multiple diversification events occurred in other South-Central American and Caribbean countries, giving rise to the North American cluster. The large number of low-frequency mutations that were detected in sequences originating from epidemic regions and that are distributed homogeneously across the genome, agrees with a demographic expansion scenario. We detected nine sites with evidence of positive selection that also harbored increased frequencies of alternative amino acids in particular clades, for example, the non-African clade, the Central American clade and the Caribbean/North American clade. When restricting the detection of selection to the period of the earlier expansion of ZIKV in the Americas, we were able to identify another two sites with evidence of selection. We were unable to find evidence of recombination within ZIKV. The genetic subgroups that we identified in this study are the basis for a proposal of a new nomenclature that will constitute a helpful framework for future studies on ZIKV genomic variation.
Original languageEnglish
Publication statusPublished - 2021
EventXVII ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology -
Duration: 16 Dec 202117 Dec 2021


ConferenceXVII ENBE Annual Meeting of the Portuguese Association for Evolutionary Biology


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