Fast surveillance response and genome sequencing reveal the circulation of a new Yellow Fever Virus sublineage in 2021, in Minas Gerais, Brazil

Yellow fever virus (YFV) exhibits a sylvatic cycle of transmission involving wild mosquitoes and non-human primates (NHP). In Brazil, YFV is endemic in the Amazon region, from where waves of epidemic expansion towards other Brazilian states eventually occur. During such waves, the virus usually follows the route from North to the Central-West and Southeast Brazilian regions. Amidst these journeys, outbreaks of Yellow Fever (YF) in NHPs, with spillovers to humans have been observed. In the present work, we describe a surveillance effort encompassing the technology of smartphone applications and the coordinated action of several research institutions and health services that succeeded in the first confirmation of YFV in NHPs in the state of Minas Gerais (MG), Southeast region, in 2021, followed by genome sequencing in an interval of only ten days. Samples from two NHPs (one of the species Alouatta caraya in the municipality of Icaraí de Minas and the other of the species Callithrix penicillata in the municipality of Ubaí) were collected and the presence of YFV was confirmed by RT-qPCR. We generated three near-complete by Nanopore sequencer MinION. Phylogenetic analysis revealed that all viral genomes recovered are equal and related to lineage South America 1, clustering with a genome detected in the Amazon region (Pará state) in 2017. These findings reveal the occurrence of a new wave of viral expansion in MG, six years after the beginning of the major outbreak in the state, between 2015-2018. No human cases were reported to date, showing the importance of coordinated work between local surveillance based on available technologies and support laboratories to ensure a quick response and implementation of contingency measures towards avoiding the occurrence of YF cases in humans.