{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T23:30:24Z","timestamp":1789428624742,"version":"build-2803163510"},"reference-count":62,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2022,9,23]],"date-time":"2022-09-23T00:00:00Z","timestamp":1663891200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosntds.org"],"crossmark-restriction":false},"short-container-title":["PLoS Negl Trop Dis"],"abstract":"<jats:p>From 2016 to 2019, the largest outbreak caused by the Yellow Fever virus (YFV) in the 21<jats:sup>st<\/jats:sup> century in the Americas occurred in southeastern Brazil. A sylvatic cycle of transmission was reported near densely populated areas, such as the large metropolitan area of the city of S\u00e3o Paulo. Here, we describe the origin, spread, and movement of the YFV throughout the state of S\u00e3o Paulo. Whole-genome sequences were obtained from tissues of two patients who died due to severe yellow fever, during 2018\u20132019. Molecular analysis indicated that all analyzed tissues were positive for YFV RNA, with the liver being the organ with the highest amount of viral RNA. Sequence analysis indicates that genomes belonged to the South American genotype I and were grouped in the epidemic clade II, which includes sequences from the states of Goi\u00e1s, Minas Gerais, and S\u00e3o Paulo of previous years. The analysis of viral dispersion indicates that the outbreak originated in Goi\u00e1s at the end of 2014 and reached the state of S\u00e3o Paulo through the state of Minas Gerais after 2016. When the virus reached near the urban area, it spread towards both the east and south regions of the state, not establishing an urban transmission cycle in the metropolitan region of S\u00e3o Paulo. The virus that moved towards the east met with YFV coming from the south of the state of Rio de Janeiro, and the YFV that was carried to the south reached the Brazilian states located in the south region of the country.<\/jats:p>","DOI":"10.1371\/journal.pntd.0010705","type":"journal-article","created":{"date-parts":[[2022,9,23]],"date-time":"2022-09-23T17:35:00Z","timestamp":1663954500000},"page":"e0010705","update-policy":"https:\/\/doi.org\/10.1371\/journal.pntd.corrections_policy","source":"Crossref","is-referenced-by-count":9,"title":["Phylogeographic patterns of the yellow fever virus around the metropolitan region of S\u00e3o Paulo, Brazil, 2016\u20132019"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2102-631X","authenticated-orcid":true,"given":"Marielton dos Passos","family":"Cunha","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6659-7186","authenticated-orcid":true,"given":"Amaro Nunes","family":"Duarte-Neto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7708-1406","authenticated-orcid":true,"given":"Shahab Zaki","family":"Pour","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"B\u00e1rbara Brito de Souza","family":"Pereira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8719-2508","authenticated-orcid":true,"given":"Yeh-Li","family":"Ho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2280-642X","authenticated-orcid":true,"given":"Beatriz","family":"Perondi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3188-8044","authenticated-orcid":true,"given":"Jaques","family":"Sztajnbok","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5285-4460","authenticated-orcid":true,"given":"Venancio Avancini Ferreira","family":"Alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luiz Fernando Ferraz","family":"da Silva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9073-9989","authenticated-orcid":true,"given":"Marisa","family":"Dolhnikoff","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paulo Hil\u00e1rio Nascimento","family":"Saldiva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8167-0625","authenticated-orcid":true,"given":"Paolo Marinho de Andrade","family":"Zanotto","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,9,23]]},"reference":[{"key":"pntd.0010705.ref001","first-page":"649","article-title":"Flavivirus Genome Organization, Expression, and Replication.","volume":"44","author":"TJ Chambers","year":"1990","journal-title":"Annu Rev."},{"key":"pntd.0010705.ref002","doi-asserted-by":"crossref","first-page":"e75","DOI":"10.1371\/journal.ppat.0030075","article-title":"Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas.","volume":"3","author":"JE Bryant","year":"2007","journal-title":"PLoS Pathog."},{"key":"pntd.0010705.ref003","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.jcv.2014.08.030","article-title":"Yellow fever.","volume":"64","author":"TP Monath","year":"2015","journal-title":"J Clin Virol."},{"key":"pntd.0010705.ref004","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1146\/annurev.ento.52.110405.091454","article-title":"Yellow Fever: A Disease that Has Yet to be Conquered","volume":"52","author":"ADT Barrett","year":"2007","journal-title":"Annu Rev Entomol"},{"key":"pntd.0010705.ref005","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1073\/pnas.93.2.548","article-title":"Population dynamics of flaviviruses revealed by molecular phylogenies","volume":"93","author":"A Zanotto PM de","year":"1996","journal-title":"Proc Natl Acad Sci"},{"key":"pntd.0010705.ref006","first-page":"1","article-title":"Genomic and phylogenetic characterization of Brazilian Yellow Fever virus strains","author":"MRT Nunes","year":"2012","journal-title":"J Virol"},{"key":"pntd.0010705.ref007","first-page":"218","article-title":"Haemagogus leucocelaenus and Haemagogus janthinomys are the primary vectors in the major yellow fever outbreak in Brazil, 2016\u20132018. 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