Wastewater-based surveillance as a proactive public health tool: Insights from SARS-CoV-2 monitoring in Kampala, Uganda (2023–2024)

Background Wastewater-based surveillance (WBS) offers a cost-effective, population-level complement to clinical testing for the early detection of infectious disease outbreaks; however, its adoption in low- and middle-income countries (LMICs) remains limited. To address this gap, we conducted a study in Kampala, Uganda, to quantify SARS-CoV-2 RNA in wastewater and evaluate its relationship with reported clinical cases, to strengthen community-level surveillance strategies. Methods We conducted a 15-month longitudinal study (March 2023–May 2024) at four wastewater collection sites in Kampala, Uganda. Samples were collected using Moore swabs, concentrated with Nanotrap® magnetic virus capture, and extracted with the Qiagen QIAamp Viral RNA Mini Kit. SARS-CoV-2 RNA was detected using the Life River Novel Coronavirus (2019-nCoV) Real-Time Multiplex RT-qPCR Kit. Pepper mild mottle virus (PMMoV) was included as an internal control. Results From 309 samples, wastewater signals closely mirrored clinical case trends and consistently preceded rises in COVID-19 test positivity by approximately two weeks. SARS-CoV-2 RNA was also detected during periods of low clinical positivity, indicating underreported or asymptomatic transmission. Viral concentrations varied across sites, reflecting differences in sewer infrastructure and sampling dynamics. Across all sites, the ORF1ab gene was the most reliably detected target. Conclusion WBS is feasible in resource-limited urban settings and can provide early warning of disease resurgence. By revealing hidden transmission and anticipating clinical trends, it strengthens epidemic preparedness and response. Implications This work establishes a scalable, low-cost surveillance strategy that can be expanded beyond COVID-19 to monitor multiple pathogens. The integration of WBS into national health systems in LMICs could transform proactive outbreak detection and inform public health decision-making.