Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/37328
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dc.contributor.authorSeabra, Sofia G.-
dc.contributor.authorLIBIN, Pieter-
dc.contributor.authorTheys, Kristof-
dc.contributor.authorZhukova, Anna-
dc.contributor.authorPotter, Barney, I-
dc.contributor.authorNebenzahl-Guimaraes, Hanna-
dc.contributor.authorGorbalenya, Alexander E.-
dc.contributor.authorSidorov, Igor A.-
dc.contributor.authorPimentel, Victor-
dc.contributor.authorPingarilho, Marta-
dc.contributor.authorde Vasconcelos, Ana T. R.-
dc.contributor.authorDellicour, Simon-
dc.contributor.authorKhouri, Ricardo-
dc.contributor.authorGascuel, Olivier-
dc.contributor.authorVANDAMME, Annie-
dc.contributor.authorBaele, Guy-
dc.contributor.authorAbecasis, Ana B.-
dc.contributor.authorCUYPERS, Lize-
dc.date.accessioned2022-05-25T12:16:02Z-
dc.date.available2022-05-25T12:16:02Z-
dc.date.issued2022-
dc.date.submitted2022-05-17T12:10:38Z-
dc.identifier.citationVIRUS EVOLUTION, 8 (1) (Art N° veac029)-
dc.identifier.urihttp://hdl.handle.net/1942/37328-
dc.description.abstractThe Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized 'African' and 'Asian' genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.-
dc.description.sponsorshipThis research was supported in part by the European Union's Horizon 2020 research and innovation program ZIKAlliance (Agreement No 734548) and by Fundacao para a Ciencia e Tecnologia (FCT) through funds GHTM-UID/04413/2020. S.G.S. was funded by FCT, Portugal, through contrato-programa 1567 (CEECINST/00102/2018). K.T. was supported by a Fonds Wetenschappelijk Onderzoek post-doctoral grant. P.L. was supported by a doctoral (1S31916N) and post-doctoral grant (#1242021N) provided by the Fonds Wetenschappelijk Onderzoek and was also supported by funding from the Flemish Government under the `Onderzoeksprogramma Artificiele Intelligentie (AI) Vlaanderen' programme. P.L. also received funding from the research council of the Vrije Universiteit Brussel (OZR-VUB) via grant number OZR3863BOF. S.D. acknowledges funding from the Fonds de la Recherche Scientifique (FNRS, Belgium). S.D. and G.B. acknowledge support from the Research Foundation-Flanders (Fonds voor Wetenschappelijk Onderzoek-Vlaanderen, G098321N). B.P. and G.B. acknowledge support from the Internal Fondsen KU Leuven/Internal Funds KU Leuven (Grant No. C14/18/094). G.B. also acknowledges support from the Research Foundation-Flanders ('Fonds voor Wetenschappelijk Onderzoek-Vlaanderen,' G0E1420N).-
dc.language.isoen-
dc.publisherOXFORD UNIV PRESS-
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License-
dc.subject.otherZika virus; arbovirus; phylogeography; molecular epidemiology;-
dc.subject.otherevolutionary biology-
dc.titleGenome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal-
dc.typeJournal Contribution-
dc.identifier.issue1-
dc.identifier.volume8-
local.format.pages15-
local.bibliographicCitation.jcatA1-
dc.description.notesSeabra, SG (corresponding author), Univ Nova Lisboa UNL, Inst Higiene & Med Trop IHMT, Global Hlth & Trop Med GHTM, Rua Junqueira 100, P-1349008 Lisbon, Portugal.-
dc.description.notessgseabra@ihmt.unl.pt-
local.publisher.placeGREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND-
local.type.refereedRefereed-
local.type.specifiedArticle-
local.bibliographicCitation.artnrveac029-
dc.identifier.doi10.1093/ve/veac029-
dc.identifier.isiWOS:000788263700001-
local.provider.typewosris-
local.description.affiliation[Seabra, Sofia G.; Nebenzahl-Guimaraes, Hanna; Pimentel, Victor; Pingarilho, Marta; Abecasis, Ana B.] Univ Nova Lisboa UNL, Inst Higiene & Med Trop IHMT, Global Hlth & Trop Med GHTM, Rua Junqueira 100, P-1349008 Lisbon, Portugal.-
local.description.affiliation[Libin, Pieter J. K.] Vrije Univ Brussel, Dept Comp Sci, Artificial Intelligence Lab, B-1050 Brussels, Belgium.-
local.description.affiliation[Libin, Pieter J. K.; Theys, Kristof; Potter, Barney, I; Dellicour, Simon; Khouri, Ricardo; Vandamme, Anne-Mieke; Baele, Guy] Katholieke Univ Leuven, Dept Microbiol Immunol & Transplantat, Lab Clin & Epidemiol Virol, Rega Inst Med Res, Herestr 49,Box 1030, B-3000 Leuven, Belgium.-
local.description.affiliation[Libin, Pieter J. K.] Hasselt Univ, Data Sci Inst, I Biostat, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium.-
local.description.affiliation[Zhukova, Anna] Univ Paris Cite, Inst Pasteur, Unite Bioinformat Evolut, 25-28 Rue Dr Roux, F-75015 Paris, France.-
local.description.affiliation[Zhukova, Anna] Univ Paris Cite, Inst Pasteur, Bioinformat & Biostat Hub, 25-28 Rue Dr Roux, F-75015 Paris, France.-
local.description.affiliation[Gorbalenya, Alexander E.; Sidorov, Igor A.] Leiden Univ, Med Ctr, Dept Med Microbiol, Postbus 9600, NL-2300 RC Leiden, Netherlands.-
local.description.affiliation[Gorbalenya, Alexander E.] Lomonosov Moscow State Univ, Fac Bioengn & Bioinformat, Moscow 119899, Russia.-
local.description.affiliation[de Vasconcelos, Ana T. R.] Natl Lab Sci Comp, Av Getulio Vargas 333, BR-25651075 Petropolis, RJ, Brazil.-
local.description.affiliation[Dellicour, Simon] Univ Libre Bruxelles, Spatial Epidemiol Lab SpELL, CP 264-3,50 Av FD Roosevelt, B-1050 Brussels, Belgium.-
local.description.affiliation[Khouri, Ricardo] Fundacao Oswaldo Cruz MS, Inst Goncalo Moniz, BR-40296710 Salvador, BA, Brazil.-
local.description.affiliation[Gascuel, Olivier] Museum Natl Hist Nat, CNRS, UMR7205, Inst Systemat,Evolut,Biodivers,MNHN,SU,EPHE,UA, CP 50,45 Rue Buffon, F-75005 Paris, France.-
local.description.affiliation[Cuypers, Lize] Univ Hosp Leuven, Dept Lab Med, Herestr 49, B-3000 Leuven, Belgium.-
local.uhasselt.internationalyes-
item.contributorSeabra, Sofia G.-
item.contributorLIBIN, Pieter-
item.contributorTheys, Kristof-
item.contributorZhukova, Anna-
item.contributorPotter, Barney, I-
item.contributorNebenzahl-Guimaraes, Hanna-
item.contributorGorbalenya, Alexander E.-
item.contributorSidorov, Igor A.-
item.contributorPimentel, Victor-
item.contributorPingarilho, Marta-
item.contributorde Vasconcelos, Ana T. R.-
item.contributorDellicour, Simon-
item.contributorKhouri, Ricardo-
item.contributorGascuel, Olivier-
item.contributorVANDAMME, Annie-
item.contributorBaele, Guy-
item.contributorAbecasis, Ana B.-
item.contributorCUYPERS, Lize-
item.validationecoom 2023-
item.fullcitationSeabra, Sofia G.; LIBIN, Pieter; Theys, Kristof; Zhukova, Anna; Potter, Barney, I; Nebenzahl-Guimaraes, Hanna; Gorbalenya, Alexander E.; Sidorov, Igor A.; Pimentel, Victor; Pingarilho, Marta; de Vasconcelos, Ana T. R.; Dellicour, Simon; Khouri, Ricardo; Gascuel, Olivier; VANDAMME, Annie; Baele, Guy; Abecasis, Ana B. & CUYPERS, Lize (2022) Genome-wide diversity of Zika virus: Exploring spatio-temporal dynamics to guide a new nomenclature proposal. In: VIRUS EVOLUTION, 8 (1) (Art N° veac029).-
item.accessRightsOpen Access-
item.fulltextWith Fulltext-
crisitem.journal.eissn2057-1577-
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