Wastewater-based surveillance as a proactive public health tool: insights from SARS-CoV-2 monitoring in Kampala, Uganda (2023–2024)
Year: 2026
Type: article
Abstract: BACKGROUND: Wastewater-based surveillance offers a cost-effective, population-level complement to clinical testing for early detection of infectious disease outbreaks; however, its adoption in low- and middle-income countries remains limited. We conducted a study in Kampala, Uganda, to quantify SARS-CoV-2 RNA in wastewater and evaluate its association with reported clinical cases, thereby strengthening community-level surveillance strategies. METHODS: From March 2023 to May 2024, 244 wastewater samples were collected weekly from four wastewater treatment plants in the Kampala Metropolitan Area, Uganda. SARS-CoV-2 RNA was quantified by RT-qPCR targeting the ORF1ab, N, and E genes using the Novel Coronavirus (2019-nCoV) Real-Time Multiplex RT-PCR kit, with PMMoV as the process control. Concordance of gene detection was assessed using Cohen’s kappa and the proportion of samples in which all targets were detected. SARS-CoV-2 viral concentrations were reported as log₁₀ genomic copies per 100 mL. Facility-level weekly mean ORF1ab concentrations were aggregated into citywide medians and correlated with clinical positivity, with lead–lag analyses to evaluate spatiotemporal associations. RESULTS: Overall SARS-CoV-2 RNA detection was 88.5%, with higher positivity at the Nakivubo wastewater treatment plant inlets (1 and 2) and the Naalya wastewater stabilization pond (both 93.4%) than at the Bugolobi fecal sludge treatment plant (78.7%). All 3 gene targets were detected in 66.4% of samples, with stronger concordance between ORF1ab and E than between ORF1ab and N (κ = 0.68), and facility-specific variability in three-gene detection ranged from 57.4% to 70.5%. Wastewater viral dynamics were characterized by episodic surges rather than sustained peaks, with ORF1ab concentrations ranging from 2.97 to 11.87 log₁₀ GC/100 mL. While same-week wastewater–clinical correlations were weak, lead–lag analysis showed wastewater signals preceded clinical positivity by 2–5 weeks, with the strongest association at a 4-week lead. CONCLUSION: WBS provided early warning of SARS-CoV-2 transmission in Kampala, with clinical positivity preceded by up to 1 month. These findings support the integration of WBS into routine surveillance to enhance outbreak preparedness and response, particularly in resource-limited settings, and to inform public health decision-making. Besides COVID-19, WBS can also track multiple infectious diseases by detecting covert transmission patterns and predicting clinical trends.
Source: BMC Public Health
Authors: Andrew Nsawotebba, Susan Nabadda, Isaac Ssewanyana, Noah Hull, Valeria Nakintu, Innocent Morunyanga, Jordan Magala, Jonathan Kabazzi, Harris Onywera, Samuel Jefferson Mutyaba, Denis Smith Akejo, Caroline Makoha, Catherine Dambya, Godfrey Katumba, James Peter Eliku, Steven Ssekyondwa, Ronald Kasujja, Misaki Wayengera, Winnie Agwang, Ashley Bolding, Sulaiman Ikoba, Sarah Snyder, Vallence Uragiwenimana, Fatim Cham, Osborn Otieno, Alisen Ayitewala, Allan Muruta, Herbert Nabaasa, Charles Olaro, Diana Atwine, Jane Ruth Aceng
Institutions: Association of Public Health Laboratories, Ministry of Health, National Health Laboratory and Diagnostics Services, Government of Uganda, Africa Centres for Disease Control and Prevention, National Water and Sewerage Corporation, Ministry of Water and Environment, Uganda Virus Research Institute, Makerere University, World Health Organization - Uganda, Global Fund to Fight AIDS, Tuberculosis and Malaria
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $3,290
Award: G1295875944
OpenAlex ID: W7124981211