Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

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dc.creatorSarah C. Hill
dc.creatorFlavia Cristina da Silva Sales
dc.creatorIray M. Rocco
dc.creatorAdriana Yumi Maeda
dc.creatorFernanda G. S. Vasami
dc.creatorLouis du Plessis
dc.creatorPaola P. Silveira
dc.creatorJaqueline G. de Jesus
dc.creatorJoshua Quick
dc.creatorNatália Coelho Couto de Azevedo Fernandes
dc.creatorJuliana M. Guerra
dc.creatorRenato de Souza
dc.creatorRodrigo A. Réssio
dc.creatorMarta Giovanetti
dc.creatorLuiz C. J. Alcantara
dc.creatorCinthya dos Santos Cirqueira Borges
dc.creatorJosué Díaz-Delgado
dc.creatorFernando Luiz de Lima Macedo
dc.creatorMaria do Carmo Timenetsky
dc.creatorRegiane de Paula
dc.creatorRoberta Spinola
dc.creatorJuliana Telles de Deus
dc.creatorJulien Thézé
dc.creatorLuís Filipe Mucci
dc.creatorRosa Maria Tubaki
dc.creatorRegiane Maria Tironi de Menezes
dc.creatorPatricia Locosque Ramos
dc.creatorAndre L. de Abreu
dc.creatorLaura N. Cruz
dc.creatorNick Loman
dc.creatorSimon Dellicour
dc.creatorOliver G. Pybus
dc.creatorEster C. Sabino
dc.creatorIngra Claro
dc.creatorNuno R. Faria
dc.creatorRenato Santana de Aguiar
dc.creatorLeandro Abade
dc.creatorFabiana dos Santos
dc.creatorMariana Sequetin Cunha
dc.creatorJuliana da Silva Nogueira
dc.date.accessioned2023-07-17T19:29:28Z
dc.date.accessioned2025-09-08T23:07:52Z
dc.date.available2023-07-17T19:29:28Z
dc.date.issued2020
dc.identifier.doihttps://doi.org/10.1371/journal.ppat.1008699
dc.identifier.issn1553-7374
dc.identifier.urihttps://hdl.handle.net/1843/56472
dc.languagepor
dc.publisherUniversidade Federal de Minas Gerais
dc.relation.ispartofPLOS Pathogens
dc.rightsAcesso Aberto
dc.subjectFebre amarela
dc.subjectBrasil - São Paulo
dc.subject.otherSão Paulo, Brazil
dc.subject.otherYellow fever virus (YFV)
dc.titleGenomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018
dc.typeArtigo de periódico
local.citation.epage18
local.citation.issue8
local.citation.spage1
local.citation.volume16
local.description.resumoSão Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.
local.identifier.orcidhttp://orcid.org/0000-0002-9048-0030
local.identifier.orcidhttps://orcid.org/0000-0002-8793-5479
local.identifier.orcidhttps://orcid.org/0000-0003-2195-9707
local.identifier.orcidhttp://orcid.org/0000-0002-3719-5505
local.identifier.orcidhttps://orcid.org/0000-0003-1216-5446
local.identifier.orcidhttps://orcid.org/0000-0003-2097-0429
local.identifier.orcidhttps://orcid.org/0000-0001-8317-0539
local.identifier.orcidhttps://orcid.org/0000-0002-1617-7340
local.identifier.orcidhttp://orcid.org/0000-0001-8188-9494
local.identifier.orcidhttp://orcid.org/0000-0002-7766-7597
local.identifier.orcidhttps://orcid.org/0000-0002-9688-5266
local.identifier.orcidhttps://orcid.org/0000-0002-1778-437X
local.identifier.orcidhttps://orcid.org/0000-0003-2726-4949
local.identifier.orcidhttps://orcid.org/0000-0001-5180-3717
local.identifier.orcidhttps://orcid.org/0000-0003-1751-4537
local.identifier.orcidhttps://orcid.org/0000-0001-8903-604X
local.identifier.orcidhttps://orcid.org/0000-0002-3059-0270
local.publisher.countryBrasil
local.publisher.departmentICA - INSTITUTO DE CIÊNCIAS AGRÁRIAS
local.publisher.initialsUFMG
local.url.externahttps://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008699

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