Abstract
São Paulo (SP), a densely populated state in southeast Brazil that contains one of the world’s largest urban regions, has experienced its largest yellow fever virus (YFV) outbreak in decades. Surveillance in non-human primates (NHP) is important in order to detect YFV early during an epidemic or epizootic, to quantify the magnitude of the outbreak in NHP, and to evaluate the risk of YFV spillover infection in human populations. To better understand the genetic diversity and spatial distribution of YFV during the current outbreak in southeast Brazil, we generated 46 new virus genomes from YFV positive cases identified in 18 different municipalities in SP, mostly sampled from non-human primates between April 2017 and February 2018. Our data show that most NHP cases in São Paulo state were likely caused by the introduction of a single YFV lineage from Minas Gerais to São Paulo. Phylogenetic and phylogeographic analyses of these data indicate that YFV spread southwards from Minas Gerais into São Paulo state at a typical rate of <1km per day. These results shed light in the sylvatic transmission of yellow fever in highly fragmented forested regions in São Paulo state and highlight the importance of continued operational research and surveillance of zoonotic pathogens in sentinel populations.
Author’s Summary Since July 2016, the southeast region of Brazil has experienced the largest yellow fever virus (YFV) outbreak in decades. São Paulo is the most densely populated state in southeast Brazil. YFV is not normally present in São Paulo state and therefore a large proportion of the 18 million inhabitants of the state have not been vaccinated against YFV. The presence of YFV in São Paulo state therefore represents a serious threat to public health. In Brazil, YFV typically circulates among non-human primates, with cases in humans representing isolated ‘spillover’ events from this predominantly sylvatic cycle. Understanding the epidemiological dynamics and spread of YFV in primates is therefore critical for contextualising human cases, and guiding vaccination strategies that can better protect local human populations. Here, we analyse the geographic and temporal distribution of observed cases of YFV in non-human primates in São Paulo state. We generate sequence data from 46 YFV positive cases, and perform phylogenetic and phylogeographic analyses aimed at understanding the spatial spread of YFV in São Paulo state. We show that most cases in non-human primates in the São Paulo state were likely caused by a single introduction of YFV from Minas Gerais to São Paulo. Analyses of these data indicate that YFV spread southwards from Minas Gerais into São Paulo state at a typical rate of <1 km per day, consistent with a scenario of continued spread in non-human primates and sylvatic vectors across forested patches, with occasional spillover to unvaccinated human populations.
Article Summary Line Genomic surveillance of yellow fever in São Paulo during the yellow fever 2017-2018 epidemic reveals movement towards Atlantic coast.
