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

São 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 outbr...

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Autores principales:	Sarah C Hill, Renato de Souza, Julien Thézé, Ingra Claro, Renato S Aguiar, Leandro Abade, Fabiana C P Santos, Mariana S Cunha, Juliana S Nogueira, Flavia C S Salles, Iray M Rocco, Adriana Y Maeda, Fernanda G S Vasami, Louis du Plessis, Paola P Silveira, Jaqueline G de Jesus, Joshua Quick, Natália C C A Fernandes, Juliana M Guerra, Rodrigo A Réssio, Marta Giovanetti, Luiz C J Alcantara, Cinthya S Cirqueira, Josué Díaz-Delgado, Fernando L L Macedo, Maria do Carmo S T Timenetsky, Regiane de Paula, Roberta Spinola, Juliana Telles de Deus, Luís F Mucci, Rosa Maria Tubaki, Regiane M T de Menezes, Patrícia L Ramos, Andre L de Abreu, Laura N Cruz, Nick Loman, Simon Dellicour, Oliver G Pybus, Ester C Sabino, Nuno R Faria
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2020
Materias:	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/2532b45a09204bba9fc562e7a49009c3
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spelling	oai:doaj.org-article:2532b45a09204bba9fc562e7a49009c32021-12-02T19:59:43ZGenomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.1553-73661553-737410.1371/journal.ppat.1008699https://doaj.org/article/2532b45a09204bba9fc562e7a49009c32020-08-01T00:00:00Zhttps://doi.org/10.1371/journal.ppat.1008699https://doaj.org/toc/1553-7366https://doaj.org/toc/1553-7374São 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.Sarah C HillRenato de SouzaJulien ThézéIngra ClaroRenato S AguiarLeandro AbadeFabiana C P SantosMariana S CunhaJuliana S NogueiraFlavia C S SallesIray M RoccoAdriana Y MaedaFernanda G S VasamiLouis du PlessisPaola P SilveiraJaqueline G de JesusJoshua QuickNatália C C A FernandesJuliana M GuerraRodrigo A RéssioMarta GiovanettiLuiz C J AlcantaraCinthya S CirqueiraJosué Díaz-DelgadoFernando L L MacedoMaria do Carmo S T TimenetskyRegiane de PaulaRoberta SpinolaJuliana Telles de DeusLuís F MucciRosa Maria TubakiRegiane M T de MenezesPatrícia L RamosAndre L de AbreuLaura N CruzNick LomanSimon DellicourOliver G PybusEster C SabinoNuno R FariaPublic Library of Science (PLoS)articleImmunologic diseases. AllergyRC581-607Biology (General)QH301-705.5ENPLoS Pathogens, Vol 16, Iss 8, p e1008699 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5
spellingShingle	Immunologic diseases. Allergy RC581-607 Biology (General) QH301-705.5 Sarah C Hill Renato de Souza Julien Thézé Ingra Claro Renato S Aguiar Leandro Abade Fabiana C P Santos Mariana S Cunha Juliana S Nogueira Flavia C S Salles Iray M Rocco Adriana Y Maeda Fernanda G S Vasami Louis du Plessis Paola P Silveira Jaqueline G de Jesus Joshua Quick Natália C C A Fernandes Juliana M Guerra Rodrigo A Réssio Marta Giovanetti Luiz C J Alcantara Cinthya S Cirqueira Josué Díaz-Delgado Fernando L L Macedo Maria do Carmo S T Timenetsky Regiane de Paula Roberta Spinola Juliana Telles de Deus Luís F Mucci Rosa Maria Tubaki Regiane M T de Menezes Patrícia L Ramos Andre L de Abreu Laura N Cruz Nick Loman Simon Dellicour Oliver G Pybus Ester C Sabino Nuno R Faria Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
description	São 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.
format	article
author	Sarah C Hill Renato de Souza Julien Thézé Ingra Claro Renato S Aguiar Leandro Abade Fabiana C P Santos Mariana S Cunha Juliana S Nogueira Flavia C S Salles Iray M Rocco Adriana Y Maeda Fernanda G S Vasami Louis du Plessis Paola P Silveira Jaqueline G de Jesus Joshua Quick Natália C C A Fernandes Juliana M Guerra Rodrigo A Réssio Marta Giovanetti Luiz C J Alcantara Cinthya S Cirqueira Josué Díaz-Delgado Fernando L L Macedo Maria do Carmo S T Timenetsky Regiane de Paula Roberta Spinola Juliana Telles de Deus Luís F Mucci Rosa Maria Tubaki Regiane M T de Menezes Patrícia L Ramos Andre L de Abreu Laura N Cruz Nick Loman Simon Dellicour Oliver G Pybus Ester C Sabino Nuno R Faria
author_facet	Sarah C Hill Renato de Souza Julien Thézé Ingra Claro Renato S Aguiar Leandro Abade Fabiana C P Santos Mariana S Cunha Juliana S Nogueira Flavia C S Salles Iray M Rocco Adriana Y Maeda Fernanda G S Vasami Louis du Plessis Paola P Silveira Jaqueline G de Jesus Joshua Quick Natália C C A Fernandes Juliana M Guerra Rodrigo A Réssio Marta Giovanetti Luiz C J Alcantara Cinthya S Cirqueira Josué Díaz-Delgado Fernando L L Macedo Maria do Carmo S T Timenetsky Regiane de Paula Roberta Spinola Juliana Telles de Deus Luís F Mucci Rosa Maria Tubaki Regiane M T de Menezes Patrícia L Ramos Andre L de Abreu Laura N Cruz Nick Loman Simon Dellicour Oliver G Pybus Ester C Sabino Nuno R Faria
author_sort	Sarah C Hill
title	Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
title_short	Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
title_full	Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
title_fullStr	Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
title_full_unstemmed	Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.
title_sort	genomic surveillance of yellow fever virus epizootic in são paulo, brazil, 2016 - 2018.
publisher	Public Library of Science (PLoS)
publishDate	2020
url	https://doaj.org/article/2532b45a09204bba9fc562e7a49009c3
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Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018.

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