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

Sao 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 Sao 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 spill over 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 Sao Paulo, we generated and analysed virus genomic data and epizootic case data from NHP in Sao Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in Sao Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in Sao 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 Sao 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 Sao 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 Sao Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in Sao Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.