All Posts Global Health

Eyes Below the Surface: Wastewater Surveillance Pilot Program in Uganda Shows Potential for Future Pandemic Monitoring

Members of the wastewater surveillance team from APHL, the Central Public Health Laboratories of Uganda (CPHL) and the National Water and Sewage Corporation collect samples at the Nakivubo Treatment Plant Inlet 1, Kampala on March 31, 2023.

By Andrew Nsawotebba, technical consultant, APHL

On March 21, 2020, Uganda declared their first confirmed case of COVID-19. As of July 14, 2023, a total of 168,489 cases and 3,627 deaths had been reported in the country. Initially, prevalence estimates of COVID-19 in Uganda were strictly limited to clinical surveillance – cases diagnosed following a doctor or hospital visit. In coordination with the Global Fund, the Uganda Central Public Health Laboratories (CPHL) and the National Water and Sewage Corporation, APHL launched a pilot program to explore the feasibility of using wastewater-based epidemiology to monitor the COVID-19 rates in the country.

 In Uganda, SARS-CoV-2 epidemiology is monitored through laboratory testing of clinical cases, rapid antigen tests, COVID-19 hospital admissions, and COVID-19-related deaths. These data sources provide the country’s official incidence, hospitalization, and death rates. However, reporting of laboratory-confirmed cases of SARS-CoV-2 has limitations. Household transmission studies in Uganda have demonstrated that a large proportion of cases are asymptomatic or so mild as to not elicit clinic or pharmacy visits; additionally, many affected populations have limited access to clinical care. Further, there is increasing use of rapid antigen tests, which have lower sensitivity and specificity PCR testing. Results of rapid antigen testing are less likely to be reported to health authorities. Consequently, laboratory diagnoses are becoming less reflective of the true extent of the disease burden in the country. 

In November 2022, four wastewater treatment centers located in the Kampala Metropolitan area were selected as surveillance sites, each from the categories of conventional, compact and fecal sludge treatment plants (see map).

Map showing a proxy of viral load based on molecular testing at the different wastewater collection sites in Kampala, Uganda.
Map showing a proxy of viral load based on molecular testing at the different wastewater collection sites in Kampala, Uganda.

In 2023, Uganda began conducting regular monitoring of the concentrations of SARS-CoV-2 in wastewater through laboratory testing of samples collected at these sites. Moore swab preparation is carried out at the Central Emergency Response and Surveillance Laboratory – CPHL and testing is done at the Virology Laboratory – CPHL. Moore swabs are bundles of cotton gauze that are attached to a string and installed in wastewater streams; the swabs then filter and trap microorganisms in wastewater over a 24-hour period.

A total of 146 wastewater samples were collected from these four initial sites over a 30-week period. Fifty-eight percent (58%; n=85) of the samples were positive for SARS-CoV-2 nucleic acid. These results complement the patient-level clinical surveillance data. Between March and August of 2023, evidence from the Kampala Metropolitan area revealed that SARS-CoV-2 can be detected in wastewater prior to the increase of clinical cases, and longitudinal tracking of SARS-CoV-2 viral load in wastewater strongly correlates with the burden of clinically diagnosed cases (see graph).

Graph showing the trend of SARS-CoV-2 in wastewater compared to national clinical cases between March and August 2023.
Graph showing the trend of SARS-CoV-2 in wastewater compared to national clinical cases between March and August 2023.

Moving forward, APHL plans to technically support Uganda in broadening its geographical wastewater surveillance scope by identifying and incorporating additional high-risk sites for wastewater sampling and covering diverse geographical regions for a more comprehensive understanding of the distribution and prevalence of pathogens across the country. We additionally plan to support the country in expanding the scope of the surveillance to include pathogens beyond SARS-CoV-2, such as viral hemorrhagic fevers, adenovirus, dengue, polio and MERS and bacterial pathogens such as Mycobacterium tuberculosis, Salmonella spp., Shigella spp. and Vibrio cholerae. This expansion will help us obtain a more holistic picture of public health risks, a better understanding of transmission dynamics and more targeted interventions to improve health outcomes.

This pilot study shows that wastewater-based surveillance has the potential to be an economical and rapid alternative to case-based surveillance for COVID-19 and other infectious disease pathogens. The findings of this study will provide valuable insights for the future of implementing wastewater-based epidemiology and assist governments and policymakers in making informed public health decisions.

Surveillance through wastewater analysis offers numerous advantages, including:

  • Near real-time information on disease abundance, independent of healthcare seeking behaviors
  • High-sensitivity detection of mild and asymptomatic cases
  • Early warning of spikes in COVID-19 cases, so public health officials can act
  • Cost-effective means to survey entire communities

To learn more about our wastewater surveillance capacity, please see this one-pager on our website.

Leave a Comment

Subscribe to get updates delivered to your inbox.