Summary
Yellow fever virus (YFV) causes substantial human morbidity and mortality in Brazil via zoonotic spillover from sylvatic cycles maintained in non-human primates (NHPs) and forest-canopy mosquitoes (Haemagogus and Sabethes). Because disease surveillance directly in wild NHP populations is challenging and subject to heterogeneous reporting, the environmental and ecological mechanics driving sylvatic outbreaks have remained poorly understood.
This study applied a multi-stage analytical framework integrating epidemiological, phylogenetic, demographic, and meteorological datasets from southeast Brazil between 2015 and 2019. Using EpiFusion joint inference models—which simultaneously condition on viral phylogenetic trees and epidemiological case incidence—the authors estimated YFV infection trajectories and the effective reproduction number (Rt) in NHPs, and fitted generalized additive models (GAMs) to evaluate associations with climatic anomalies and human spillover cases:
Tipping-Point Dynamics (Rt≈1.0): Across the study period, the effective reproduction number of YFV in NHPs hovered close to 1.0, demonstrating that minor shifts in transmission efficiency can spark explosive sylvatic outbreaks alongside large, unobserved wildlife transmission waves.
El Niño Climate Drivers: Medium- and long-term El Niño sea surface temperature (SST) anomalies emerged as strong predictors of NHP infection dynamics.
Predicting Human Spillover: Inferred NHP infection metrics correlated closely with subsequent human yellow fever incidence, providing a quantitative foundation for climate- and genomic-informed early warning and pre-emptive vaccination campaigns.
