Wastewater surveillance of dengue and chikungunya during the worst arbovirus epidemic in Brazil

This study evaluated wastewater-based epidemiology (WBE) for monitoring dengue virus (DENGV) and chikungunya virus (CKV) during Brazil's most severe arbovirus epidemic, focusing on the city of Belo Horizonte, Minas Gerais. From March 2022 to August 2024, 24-hour composite raw sewage samples were collected weekly from two major wastewater treatment plants, encompassing over 80% of the city's population. Viral RNA was quantified via RT-qPCR and positive samples underwent genome sequencing for genotype characterization. DENGV and CKV RNA were detected in over 90% of samples across both wastewater treatment plants (WWTPs), demonstrating sustained and widespread viral circulation throughout epidemic and inter-epidemic periods. Although CHIKV concentrations varied significantly across years, DENGV concentrations remained statistically stable, and no significant correlations were observed between wastewater viral loads and reported clinical cases. A considerable proportion of samples presented concentrations below the limit of quantification, indicating that while WBE is highly sensitive for qualitative detection of arboviruses, quantitative interpretation remains methodologically constrained. Sequencing confirmed the presence of DENGV-1 sorotype I and CKV genotype V, clustering with contemporaneous Brazilian strains and reflecting regional transmission dynamics. Wastewater-based modelling further suggested that reported clinical cases may substantially underestimate true infection burden, although quantitative estimates were highly sensitive to assumptions regarding viral shedding variability. These findings demonstrate that WBE provides a sensitive, non- invasive, population level approach for tracking arboviral circulation and viral diversity during large-scale outbreaks and could complement public health surveillance frameworks, especially in regions with limited diagnostic capacity or high levels of underreporting, to enhance epidemic response and control strategies.