Reemergence of yellow fever virus in forest and periurban settings in Brazil

Yellow fever virus remains a major public health threat in Brazil, where recent resurgence risks affecting both forest and periurban populations. Understanding viral movement across ecological settings is critical to support early detection and prevent outbreaks.

We performed genomic surveillance in two Brazilian states, a northern Amazon region and a southeastern region, between 2023 and 2025. Human and non-human primate samples were collected across forest, rural, and urban environments. Viral genomes were generated and analyzed using phylogenetic, phylogeographic, and temporal approaches to reconstruct viral transmission patterns.

Here, we show evidence of continued yellow fever virus circulation and diversification in distinct ecological settings. We generate 25 genomes from humans and non-human primates, including the first human-derived genomes from the Amazon region. All genomes fall within the South American lineage. We identify one cluster in the Amazon region consistent with undetected viral persistence and reemergence, and a second cluster in the southeast associated with reintroduction followed by sustained local transmission.

These findings demonstrate ongoing yellow fever virus activity in Brazil, with forest regions serving as reservoirs for reemergence and periurban areas supporting continued spread. Strengthened genomic and epizootic surveillance is required to detect viral expansion early and inform targeted prevention strategies across Brazil and the Americas.