{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,4]],"date-time":"2026-03-04T06:21:43Z","timestamp":1772605303791,"version":"3.50.1"},"reference-count":41,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T00:00:00Z","timestamp":1608681600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["213589\/Z\/18\/Z"],"award-info":[{"award-number":["213589\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>Zika virus (ZIKV) became a worldwide public health emergency after its introduction in the Americas. Brazil was implicated as central in the ZIKV dispersion, however, a better understanding of the pathways the virus took to arrive in Brazil and the dispersion within the country is needed. An updated genome dataset was assembled with publicly available data. Bayesian phylogeography methods were applied to reconstruct the spatiotemporal history of ZIKV in the Americas and with more detail inside Brazil. Our analyses reconstructed the Brazilian state of Pernambuco as the likely point of introduction of ZIKV in Brazil, possibly during the 2013 Confederations Cup. Pernambuco played an important role in spreading the virus to other Brazilian states. Our results also underscore the long cryptic circulation of ZIKV in all analyzed locations in Brazil. Conclusions: This study brings new insights about the early moments of ZIKV in the Americas, especially regarding the Brazil-Haiti cluster at the base of the American clade and describing for the first time migration patterns within Brazil.<\/jats:p>","DOI":"10.3390\/v13010012","type":"journal-article","created":{"date-parts":[[2020,12,23]],"date-time":"2020-12-23T12:19:51Z","timestamp":1608725991000},"page":"12","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["New Insights on the Zika Virus Arrival in the Americas and Spatiotemporal Reconstruction of the Epidemic Dynamics in Brazil"],"prefix":"10.3390","volume":"13","author":[{"given":"Larissa Catharina","family":"Costa","sequence":"first","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4413-193X","authenticated-orcid":false,"given":"Rafael Valente","family":"Veiga","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7167-8754","authenticated-orcid":false,"given":"Juliane Fonseca","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1594-2311","authenticated-orcid":false,"given":"Moreno S.","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Oswaldo Cruz Foundation, Porto Velho 76812-245, Rond\u00f4nia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9323-1400","authenticated-orcid":false,"given":"Roberto F. S.","family":"Andrade","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Physics Institute, Federal University of Bahia, Salvador 40210-340, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4797-908X","authenticated-orcid":false,"given":"Enny S.","family":"Paix\u00e3o","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3318-3408","authenticated-orcid":false,"given":"Maria Gl\u00f3ria","family":"Teixeira","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Collective Health Institute, Federal University of Bahia, Salvador 40110-040, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7275-4280","authenticated-orcid":false,"given":"Maria da Concei\u00e7\u00e3o N.","family":"Costa","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Collective Health Institute, Federal University of Bahia, Salvador 40110-040, Bahia, Brazil"}]},{"given":"Luciana L.","family":"Cardim","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"given":"Eduardo H.","family":"Carmo","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Collective Health Institute, Federal University of Bahia, Salvador 40110-040, Bahia, Brazil"}]},{"given":"Wanderson K.","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Ministry of Defense Hospital das Armed Forces, Technical Directorate of Education and Research, Brasilia 70675-731, Federal District, Brazil"}]},{"given":"Jos\u00e9 \u00cd. K.","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3172-9684","authenticated-orcid":false,"given":"Qeren H. R. F.","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0215-4930","authenticated-orcid":false,"given":"Maur\u00edcio L.","family":"Barreto","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"},{"name":"Collective Health Institute, Federal University of Bahia, Salvador 40110-040, Bahia, Brazil"}]},{"given":"Artur T. L.","family":"Queiroz","sequence":"additional","affiliation":[{"name":"Center of Data and Knowledge Integration for Health (CIDACS), Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 41745-715, Bahia, Brazil"}]},{"given":"Tiago","family":"Gr\u00e4f","sequence":"additional","affiliation":[{"name":"Gon\u00e7alo Moniz Institute, Oswaldo Cruz Foundation, Salvador 40296-710, Bahia, Brazil"}]}],"member":"1968","published-online":{"date-parts":[[2020,12,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1016\/0035-9203(52)90042-4","article-title":"Zika virus (I). Isolations and serological specificity","volume":"46","author":"Dick","year":"1952","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/0035-9203(54)90006-1","article-title":"Zika virus: A report on three cases of human infection during an epidemic of jaundice in Nigeria","volume":"48","author":"Macnamara","year":"1954","journal-title":"Trans. R. Soc. Trop. Med. Hyg."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2536","DOI":"10.1056\/NEJMoa0805715","article-title":"Zika virus outbreak on Yap Island, federated states of Micronesia","volume":"360","author":"Duffy","year":"2009","journal-title":"N. Engl. J. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"20720","DOI":"10.2807\/1560-7917.ES2014.19.9.20720","article-title":"Zika virus infection complicated by Guillain-Barre syndrome\u2013case report, French Polynesia, December 2013","volume":"19","author":"Oehler","year":"2014","journal-title":"Eurosurveillance"},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Pyke, A.T., Daly, M.T., Cameron, J.N., Moore, P.R., Taylor, C.T., Hewitson, G.R., Humphreys, J.L., and Gair, R. (2014). Imported Zika virus infection from the Cook Islands into Australia, 2014. PLoS Curr., 6.","DOI":"10.1371\/currents.outbreaks.4635a54dbffba2156fb2fd76dc49f65e"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1007\/s00705-015-2695-5","article-title":"A report on the outbreak of Zika virus on Easter Island, South Pacific, 2014","volume":"161","author":"Tognarelli","year":"2016","journal-title":"Arch. Virol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"381","DOI":"10.3201\/eid2102.141553","article-title":"Co-infection with Zika and dengue viruses in 2 patients, New Caledonia, 2014","volume":"21","author":"Calvez","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1412","DOI":"10.3201\/eid2008.140302","article-title":"Zika virus infection after travel to Tahiti, December 2013","volume":"20","author":"Maagard","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1126\/science.aaf5036","article-title":"Zika virus in the Americas: Early epidemiological and genetic findings","volume":"352","author":"Faria","year":"2016","journal-title":"Science"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Pettersson, J.H.-O., Eldholm, V., Seligman, S.J., Lundkvist, \u00c5., Falconar, A.K., Gaunt, M.W., Musso, D., Nougair\u00e8de, A., Charrel, R., and Gould, E.A. (2016). How did Zika virus emerge in the Pacific Islands and Latin America?. MBio, 7.","DOI":"10.1128\/mBio.01239-16"},{"key":"ref_11","first-page":"E4334","article-title":"Spread of Zika virus in the Americas","volume":"114","author":"Zhang","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/nature22401","article-title":"Establishment and cryptic transmission of Zika virus in Brazil and the Americas","volume":"546","author":"Faria","year":"2017","journal-title":"Nature"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2303","DOI":"10.1017\/S0950268817001200","article-title":"On the origin and timing of Zika virus introduction in Brazil","volume":"145","author":"Massad","year":"2017","journal-title":"Epidemiol. Infect."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.3201\/eid2110.150847","article-title":"Zika virus outbreak, bahia, brazil","volume":"21","author":"Campos","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1590\/0074-02760150192","article-title":"First report of autochthonous transmission of Zika virus in Brazil","volume":"110","author":"Zanluca","year":"2015","journal-title":"Mem. Inst. Oswaldo Cruz"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nature22402","article-title":"Zika virus evolution and spread in the Americas","volume":"546","author":"Metsky","year":"2017","journal-title":"Nature"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1016\/j.chom.2018.04.017","article-title":"Genomic epidemiology reconstructs the introduction and spread of Zika virus in Central America and Mexico","volume":"23","author":"Li","year":"2018","journal-title":"Cell Host Microbe"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/j.meegid.2019.04.006","article-title":"Time-scaled phylogeography of complete Zika virus genomes using discrete and continuous space diffusion models","volume":"73","author":"Ebranati","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/nature22400","article-title":"Genomic epidemiology reveals multiple introductions of Zika virus into the United States","volume":"546","author":"Grubaugh","year":"2017","journal-title":"Nature"},{"key":"ref_20","unstructured":"World Health Organization (2020, December 21). WHO Statement on the First Meeting of the International Health Regulations (2005) (IHR 2005) Emergency Committee on Zika Virus and Observed Increase in Neurological Disorders and Neonatal Malformations; 2016. Available online: http:\/\/www.who.int\/mediacentre\/news\/statements\/2016\/1st-emergency-committee-zika\/en."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"601","DOI":"10.2105\/AJPH.2016.303113","article-title":"The epidemic of Zika virus\u2013related microcephaly in Brazil: Detection, control, etiology, and future scenarios","volume":"106","author":"Teixeira","year":"2016","journal-title":"Am. J. Public Health"},{"key":"ref_22","first-page":"135","article-title":"Sistema de informa\u00e7\u00e3o de agravos de notifica\u00e7\u00e3o em sa\u00fade (Sinan): Desafios no desenvolvimento de um sistema de informa\u00e7\u00e3o em sa\u00fade","volume":"13","author":"Laguardia","year":"2004","journal-title":"Epidemiol. Servi\u00e7os Sa\u00fade"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: Improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"3276","DOI":"10.1093\/bioinformatics\/btu531","article-title":"AliView: A fast and lightweight alignment viewer and editor for large datasets","volume":"30","author":"Larsson","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"vew007","DOI":"10.1093\/ve\/vew007","article-title":"Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)","volume":"2","author":"Rambaut","year":"2016","journal-title":"Virus Evol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"vey016","DOI":"10.1093\/ve\/vey016","article-title":"Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10","volume":"4","author":"Suchard","year":"2018","journal-title":"Virus Evol."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/molbev\/msj021","article-title":"Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences","volume":"23","author":"Shapiro","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Drummond, A.J., Ho, S.Y.W., Phillips, M.J., and Rambaut, A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol., 4.","DOI":"10.1371\/journal.pbio.0040088"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/molbev\/mss265","article-title":"Improving Bayesian population dynamics inference: A coalescent-based model for multiple loci","volume":"30","author":"Gill","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Lemey, P., Rambaut, A., Drummond, A.J., and Suchard, M.A. (2009). Bayesian phylogeography finds its roots. PLoS Comput. Biol., 5.","DOI":"10.1371\/journal.pcbi.1000520"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using Tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"2167","DOI":"10.1093\/molbev\/msw082","article-title":"SpreaD3: Interactive visualization of spatiotemporal history and trait evolutionary processes","volume":"33","author":"Bielejec","year":"2016","journal-title":"Mol. Biol. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Miller, M.A., Pfeiffer, W., and Schwartz, T. (2010, January 14). Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Proceedings of the 2010 gateway computing environments workshop (GCE), New Orleans, LA, USA.","DOI":"10.1109\/GCE.2010.5676129"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Oliveira, J.F., Rodrigues, M.S., Skalinski, L.M., Santos, A.E.S., Costa, L.C., Cardim, L.L., Paix\u00e3o, E.S., Costa, M.d.C.N., Oliveira, W.K., and Barreto, M.L. (2020). Interdependence between confirmed and discarded cases of dengue, chikungunya and Zika viruses in Brazil: A multivariate time-series analysis. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0228347"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/S0140-6736(17)31368-5","article-title":"Infection-related microcephaly after the 2015 and 2016 Zika virus outbreaks in Brazil: A surveillance-based analysis","volume":"390","author":"Carmo","year":"2017","journal-title":"Lancet"},{"key":"ref_38","first-page":"6941735","article-title":"Revisiting key entry routes of human epidemic Arboviruses into the mainland Americas through large-scale Phylogenomics","volume":"2018","author":"Campos","year":"2018","journal-title":"Int. J. Genom."},{"key":"ref_39","first-page":"1085","article-title":"Zika virus, French polynesia, South pacific, 2013","volume":"20","author":"Roche","year":"2014","journal-title":"Emerg. Infect. Dis."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2275","DOI":"10.1016\/j.celrep.2020.01.085","article-title":"Genomic and epidemiological surveillance of Zika virus in the Amazon region","volume":"30","author":"Giovanetti","year":"2020","journal-title":"Cell Rep."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Lowe, R., Barcellos, C., Brasil, P., Cruz, O.G., Hon\u00f3rio, N.A., Kuper, H., and Carvalho, M.S. (2018). The Zika virus epidemic in Brazil: From discovery to future implications. Int. J. Environ. Res. Public Health, 15.","DOI":"10.3390\/ijerph15010096"}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/1\/12\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T10:49:00Z","timestamp":1760179740000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/13\/1\/12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,12,23]]},"references-count":41,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2021,1]]}},"alternative-id":["v13010012"],"URL":"https:\/\/doi.org\/10.3390\/v13010012","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,12,23]]}}}