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Background <p>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.</p> Methods <p>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.</p> Results <p>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.</p> Conclusion <p>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.</p>

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

  • 期刊论文

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  • 发表日期：

    2026年1月20日

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  • 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

摘要

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.