The recent re-emergence of yellow fever virus (YFV) in Brazil has raised serious concerns due to the virus' rapid dissemination in the southeastern region. To better understand YFV genetic diversity and dynamics during the recent outbreak in southeastern Brazil we generated 18 complete and near-complete genomes from the peak of the epidemic curve from non-human primates (NHPs) and human infected cases across Espírito Santo and Rio de Janeiro states. Genomic sequencing of 18 YFV genomes revealed the timing, source and likely routes of yellow fever virus transmission and dispersion during the one of the largest outbreaks ever registered in Brazil. We showed that the recent YFV epidemic spillover southwards several times from Minas Gerais to Espírito Santo and Rio de Janeiro states in 2016 to 2019. The quick production and analysis of data from portable sequencing could identify the corridor of spread of YFV.These findings reinforce that real-time and continued genomic surveillance strategies can assist in the monitoring and public health responses of arbovirus epidemics.

Yellow fever virus spread in Rio de Janeiro and Espírito Santo, 2016-2019: Phylodynamic assessment to improve intervention strategies