Genomic surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018
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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Public Library of Science
2020
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| _version_ | 1826267312913645568 |
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| author | Hill, SC de Souza, R Thézé, J Claro, I Aguiar, RS Abade, L Santos, FCP Cunha, MS Nogueira, JS Salles, FCS Rocco, IM Maeda, AY Vasami, FGS du Plessis, L Silveira, PP de Jesus, JG Quick, J Fernandes, NCCA Guerra, JM Réssio, RA Giovanetti, M Alcantara, LCJ Cirqueira, CS Díaz-Delgado, J Macedo, FLL Timenetsky, MDCST de Paula, R Spinola, R Telles de Deus, J Mucci, LF Tubaki, RM de Menezes, RMT Ramos, PL de Abreu, AL Cruz, LN Loman, N Dellicour, S Pybus, OG Sabino, EC Faria, NR |
| author_facet | Hill, SC de Souza, R Thézé, J Claro, I Aguiar, RS Abade, L Santos, FCP Cunha, MS Nogueira, JS Salles, FCS Rocco, IM Maeda, AY Vasami, FGS du Plessis, L Silveira, PP de Jesus, JG Quick, J Fernandes, NCCA Guerra, JM Réssio, RA Giovanetti, M Alcantara, LCJ Cirqueira, CS Díaz-Delgado, J Macedo, FLL Timenetsky, MDCST de Paula, R Spinola, R Telles de Deus, J Mucci, LF Tubaki, RM de Menezes, RMT Ramos, PL de Abreu, AL Cruz, LN Loman, N Dellicour, S Pybus, OG Sabino, EC Faria, NR |
| author_sort | Hill, SC |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T20:52:15Z |
| format | Journal article |
| id | oxford-uuid:37feb4e8-3656-433e-b3bf-c08d3c4cde21 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T20:52:15Z |
| publishDate | 2020 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | oxford-uuid:37feb4e8-3656-433e-b3bf-c08d3c4cde212022-03-26T13:47:35ZGenomic surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:37feb4e8-3656-433e-b3bf-c08d3c4cde21EnglishSymplectic ElementsPublic Library of Science2020Hill, SCde Souza, RThézé, JClaro, IAguiar, RSAbade, LSantos, FCPCunha, MSNogueira, JSSalles, FCSRocco, IMMaeda, AYVasami, FGSdu Plessis, LSilveira, PPde Jesus, JGQuick, JFernandes, NCCAGuerra, JMRéssio, RAGiovanetti, MAlcantara, LCJCirqueira, CSDíaz-Delgado, JMacedo, FLLTimenetsky, MDCSTde Paula, RSpinola, RTelles de Deus, JMucci, LFTubaki, RMde Menezes, RMTRamos, PLde Abreu, ALCruz, LNLoman, NDellicour, SPybus, OGSabino, ECFaria, NRPaulo, 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. |
| spellingShingle | Hill, SC de Souza, R Thézé, J Claro, I Aguiar, RS Abade, L Santos, FCP Cunha, MS Nogueira, JS Salles, FCS Rocco, IM Maeda, AY Vasami, FGS du Plessis, L Silveira, PP de Jesus, JG Quick, J Fernandes, NCCA Guerra, JM Réssio, RA Giovanetti, M Alcantara, LCJ Cirqueira, CS Díaz-Delgado, J Macedo, FLL Timenetsky, MDCST de Paula, R Spinola, R Telles de Deus, J Mucci, LF Tubaki, RM de Menezes, RMT Ramos, PL de Abreu, AL Cruz, LN Loman, N Dellicour, S Pybus, OG Sabino, EC Faria, NR Genomic surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018 |
| title | 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_short | Genomic surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018 |
| title_sort | genomic surveillance of yellow fever virus epizootic in sao paulo brazil 2016 2018 |
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