Valnete das Graças Dantas Andrade, Talita Adelino, Vagner Fonseca, Keldenn Melo Farias Moreno, Luíz Marcelo Ribeiro Tomé, Luiz Augusto Pereira, Debora Glenda Lima de La‐Roque, Ana María Bispo de Filippis, Daniel Garkauskas Ramos, Dario Brock Ramalho, Kátia Cristina de Lima Furtado, Gleissy Adriane Lima Borges, Lívia Carício Martins, Lívia Carla Vinhal Frutuoso, Ludmila Oliveira Lamounier, Natália Rocha Guimarães, Patrícia Barros, Priscila Souza de Almeida, Paulo Eduardo de Souza da Silva, Rodrigo Giesbrecht Pinheiro, Rodrigo G. Stábeli, Shirley Moreira da Silva Chagas, Sílvia Helena Sousa Pietra Pedroso, Simone Kashima, Solange Gonçalves Penante, Marília Santini de Oliveira, Vinicius Lemes da Silva, Wesley C. Van Voorhis, Edward C. Holmes, José Lourenço, Felipe Campos de Melo Iani, Alberto Simões Jorge Júnior, Marta Giovanetti, Luiz Carlos Junior Alcantara
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. Yellow fever is a serious mosquito-borne disease that affects both people and animals in Brazil. Although vaccination has helped control past outbreaks, the virus continues to circulate in forested regions and sometimes spreads toward towns and cities, creating a risk for new epidemics. In this study, we monitored yellow fever activity in two parts of Brazil between 2023 and 2025: the Amazon region in the north and a southeastern region where past outbreaks occurred. We analyzed samples from people and monkeys to track how the virus is spreading over time and across different environments. We found ongoing virus circulation in both regions, showing that yellow fever can persist quietly and then reappear. Strengthening surveillance is essential to detect early warning signs and protect at-risk communities. Andrade, Adelino, Fonseca et al. used phylogenetic, phylogeographic, and temporal approaches to track yellow fever viral transmission across forestry, rural, and urban areas of Brazil. All genomes belong to the South American lineage, with one Amazon cluster showing hidden persistence and another in the southeast indicating reintroduction and sustained transmission.