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

• Published in: PLoS pathogens 2020-08, Vol.16 (8), p.e1008699-e1008699
• Main Authors: Hill, Sarah C, de Souza, Renato, Thézé, Julien, Claro, Ingra, Aguiar, Renato S, Abade, Leandro, Santos, Fabiana C P, Cunha, Mariana S, Nogueira, Juliana S, Salles, Flavia C S, Rocco, Iray M, Maeda, Adriana Y, Vasami, Fernanda G S, du Plessis, Louis, Silveira, Paola P, de Jesus, Jaqueline G, Quick, Joshua, Fernandes, Natália C C A, Guerra, Juliana M, Réssio, Rodrigo A, Giovanetti, Marta, Alcantara, Luiz C J, Cirqueira, Cinthya S, Díaz-Delgado, Josué, Macedo, Fernando L L, Timenetsky, Maria do Carmo S T, de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís F, Tubaki, Rosa Maria, de Menezes, Regiane M T, Ramos, Patrícia L, de Abreu, Andre L, Cruz, Laura N, Loman, Nick, Dellicour, Simon, Pybus, Oliver G, Sabino, Ester C, Faria, Nuno R
• Format: Article
• Language: English
• Subjects: Animals; Biology and Life Sciences; Brazil - epidemiology; Computer and Information Sciences; Disease Outbreaks; Dispersal; Dispersion; Earth Sciences; Ecology and Environmental Sciences; Epidemics; Fever; Genome, Viral; Genomes; Genomics; Health surveillance; Heterogeneity; Humans; Infections; Life Sciences; Medicine and Health Sciences; Mosquitoes; Municipalities; Outbreaks; People and places; Pest outbreaks; Phases; Phylogeny; Phylogeography; Population density; Primate Diseases - epidemiology; Primate Diseases - transmission; Primate Diseases - virology; Primates; Primates - virology; Public health; Software; Supervision; Surveillance; Vector-borne diseases; Viruses; Yellow Fever - epidemiology; Yellow Fever - transmission; Yellow Fever - veterinary; Yellow Fever - virology; Yellow fever virus - classification; Yellow fever virus - genetics; Yellow fever virus - isolation & purification; Zoology; Zoonoses - epidemiology; Zoonoses - transmission; Zoonoses - virology
• ISSN: 1553-7374; 1553-7366; 1553-7374
• DOI: 10.1371/JOURNAL.PPAT.1008699

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.