28 29 *Denotes equal contribution. 30 31 Corresponding author mailing address: doencasporvetor@ial.sp.gov.br and 32 nuno.faria@zoo.ox.ac.uk 33 34 Article Summary Line: Genomic surveillance of yellow fever in São Paulo during the yellow fever 35 2017-2018 epidemic reveals movement towards Atlantic coast. 36 37 Running title: Phylogeography of yellow fever virus in São Paulo 38 Keywords: Yellow fever, outbreak, Brazil 3 40 Abstract 41 São Paulo (SP), a densely populated state in southeast Brazil that contains one of the world's largest 42 urban regions, has experienced its largest yellow fever virus (YFV) outbreak in decades. 43 Surveillance in non-human primates (NHP) is important in order to detect YFV early during an 44 epidemic or epizootic, to quantify the magnitude of the outbreak in NHP, and to evaluate the risk of 45 YFV spillover infection in human populations. To better understand the genetic diversity and 46 spatial distribution of YFV during the current outbreak in southeast Brazil, we generated 46 new 47 virus genomes from YFV positive cases identified in 18 different municipalities in SP, mostly 48 sampled from non-human primates between April 2017 and February 2018. Our data show that 49 most NHP cases in São Paulo state were likely caused by the introduction of a single YFV lineage 50 from Minas Gerais to São Paulo. Phylogenetic and phylogeographic analyses of these data indicate 51 that YFV spread southwards from Minas Gerais into São Paulo state at a typical rate of <1km per 52 day. These results shed light in the sylvatic transmission of yellow fever in highly fragmented 53 forested regions in São Paulo state and highlight the importance of continued operational research 54 and surveillance of zoonotic pathogens in sentinel populations. 55 4 56 Author´s Summary 57 Since July 2016, the southeast region of Brazil has experienced the largest yellow fever virus (YFV) 58 outbreak in decades. São Paulo is the most densely populated state in southeast Brazil. YFV is not 59 normally present in São Paulo state and therefore a large proportion of the 18 million inhabitants of 60 the state have not been vaccinated against YFV. The presence of YFV in São Paulo state therefore 61 represents a serious threat to public health. In Brazil, YFV typically circulates among non-human 62 primates, with cases in humans representing isolated 'spillover' events from this predominantly 63 sylvatic cycle. Understanding the epidemiological dynamics and spread of YFV in primates is 64 therefore critical for contextualising human cases, and guiding vaccination strategies that can better 65 protect local human populations. Here, we analyse the geographic and temporal distribution of 66 observed cases of YFV in non-human primates in São Paulo state. We generate sequence data from 67 46 YFV positive cases, and perform phylogenetic and phylogeographic analyses aimed at 68 understanding the spatial spread of YFV in São Paulo state. We show that most cases in non-human 69 primates in the São Paulo state were likely caused by a sing...