Wastewater surveillance: a critical tool in pandemic management

Updated : Thu, September 29, 2022 @ 7:57 PM

As SARS-CoV-2 variants continue to threaten public health, officials are looking beyond clinical tests to track infection trends. Wastewater surveillance is one cost-effective, non-invasive method to help guide COVID-19 management. 

Wastewater surveillance involves sampling sewage to detect traces of SARS-CoV-2 nucleic acid shed in human waste. It's a valuable tool because it reduces direct interaction with infected patients, provides insight to the population who are presymptomatic or asymptomatic for COVID-19, while also offering some communities an indication of disease transmission that don’t otherwise have timely access to clinical testing. Wastewater surveillance is not a new method for monitoring pathogens. Still, innovative technology, including digital PCR platforms, make wastewater testing more user-friendly, cost-effective and reliable than it may have been in the past. 

History of wastewater surveillance

As early as the 1940s, researchers used cell-culture technology to monitor for polio and other viral pathogens in sewage.1 Scientists saw that an increase in symptomatic cases in the community resulted in a greater frequency and higher concentration of poliovirus in wastewater. They used that information to estimate the extent of infection and the ratio of symptomatic to asymptomatic infections in the community, based on shedding estimates from individual patients and examining wastewater profiles.2 

In the 1960s, scientists at Yale University sampled sewage to assess the efficacy of polio vaccination campaigns. Thirty-five years later, the Helsinki poliovirus experiment confirmed that wastewater surveillance is an effective method to monitor poliovirus vaccination programs. The researchers concluded that in a community of 10,000 residents, it was possible to detect just one person shedding the poliovirus by sampling wastewater.3  

In the 1980s, scientists turned to molecular techniques, including hybridisation with cDNA probes, to monitor sewage for hepatitis A. As genomic technology advanced in the 1990s, researchers adopted more sensitive polymerase chain reaction (PCR) methods to monitor wastewater for a host of pathogenic microorganisms. In 2013, sewage surveillance was credited for delivering early warning of hepatitis A virus and norovirus outbreaks in Sweden and preventing an outbreak of paralytic polio in Israel.1  

Monitoring wastewater to understand local SARS-CoV-2 trends

Evidence from around the world has shown that genetic traces of SARS-CoV-2 identified in wastewater correlate with COVID-19 disease trends among communities. Although SARS-CoV-2 is a respiratory virus, it has three critical features that make it an optimal candidate for wastewater surveillance. 

First, the virus is excreted in fecal matter in large amounts. Studies show that concentrations of viral RNA in feces vary among patients and throughout the illness, but the virus can be detected for up to several weeks over the course of infection.4 Second, SARS-CoV-2 infects some people asymptomatically, so undiagnosed populations benefit from the early detection available from wastewater surveillance systems. Finally, surveying the SARS-CoV-2 virus in wastewater results in actionable information that can make a difference in public health responses.wastewater-testing

Wastewater surveillance can be an effective tool to detect hot spots or high-risk areas for SARS-CoV-2 infection. It’s possible to collect wastewater from a specific street or building to get precise information about local disease trends. For example, a U.S. university used wastewater testing to effectively stop the spread of COVID-19 after SARS-CoV-2 was identified in samples collected from residence halls on campus.5 This type of monitoring doesn’t replace the need for other COVID-19 surveillance systems. It complements other tools by providing an efficient pooled community sample. Using wastewater surveillance, public health officials can collect data for communities where timely COVID-19 clinical testing is underutilized or unavailable.6

Digital PCR offers advantages for wastewater monitoring
As technology advances, researchers are looking at new ways to collect information from wastewater samples. Digital PCR (dPCR) is one tool that has proven effective for this application. It’s a simple way of quantifying nucleic acids that doesn’t require a standard curve as traditional qPCR methods do. One of the significant advantages dPCR has for wastewater monitoring for SARS-CoV-2 specifically is that it provides more consistency between labs because there’s no reliance on preparing the same standard curve across different facilities, with different limitations and preparation strategies. dPCR is well suited to monitor SARS-CoV-2 targets from wastewater samples because it overcomes variability, reduces the impact of many PCR inhibitors and eliminates the need for standard curves.7

Wastewater is a complex matrix that varies from site to site. With dPCR, scientists take what would be a standard qPCR reaction and split it up into thousands of reactions. These smaller reactions are fundamentally more tolerant to inhibitors than qPCR. Another advantage of dPCR is that it's very adaptable and offers flexibility for adding targets to an assay. Monitoring the prevalence of SARS-CoV-2 in wastewater gives researchers insight into what is happening within a community without relying on positive clinical tests. It's a precursor dataset that can serve as an early warning before hospitals begin to fill up. At the heart of it, dPCR is a simple qPCR reaction that has the power to deliver a lot more information.

Actionable information for COVID-19 response plans
Wastewater surveillance of SARS-CoV-2 offers many public health benefits. History has shown that sewage testing is an effective method for the early detection of diseases. It’s a cost-effective way to survey the transmission dynamics of local communities, even down to specific streets within a community or a specific residential building on a university campus.8 Samples can be collected from those who may not seek healthcare because they are either asymptomatic or lack access to adequate medical services. Coupled with clinical surveillance, standardised wastewater testing can be an effective indicator of changes in COVID-19 burden in a community. That information can help public health officials understand how hospital capacities could fluctuate, prepare plans for lockdowns and decide which neighbourhoods could benefit most from COVID-19 resources, including testing sites or vaccine clinics.



  1. Schmidt C. Watcher in the wastewater. Nat Biotechnol 38, 917–920. Published 2020. Accessed July 20, 2021. https://doi.org/10.1038/s41587-020-0620-2
  2. Metcalf TG, Melnick JL, Estes MK. Environmental virology: from detection of virus in sewage and water by isolation to identification by molecular biology—a trip of over 50 years. Annual review of microbiology. 49(1), 461-487. Published 1995. Accessed July 25, 2021. https://doi.org/10.1146/annurev.mi.49.100195.002333
  3. Goodridge L. Sewage surveillance: How scientists track and identify diseases like COVID-19 before they spread. The Conversation. Published 2020. Accessed July 20, 2021.  https://theconversation.com/sewage-surveillance-how-scientists-track-and-identify-diseases-like-covid-19-before-they-spread-148307
  4. Wölfel R., Corman VM, Guggemos W. et al. Virological assessment of hospitalized patients with COVID-2019. Nature 581, 465–469. Published 2020. Accessed July 21, 2021. https://doi.org/10.1038/s41586-020-2196-x
  5. Ellis R, McNabb N, Levenson E. 287 Utah State University students quarantined after Covid-19 found in wastewater from four dorms. CNN. Published 2020. Accessed July 22, 2021. https://www.cnn.com/2020/09/01/health/us-coronavirus-tuesday/index.html
  6. Centers for Disease Control and Prevention. National wastewater surveillance system (NWSS). Published 2021. Accessed July 18, 2021.  https://www.cdc.gov/healthywater/surveillance/wastewater-surveillance/wastewater-surveillance.html
  7. Abola P, host. The role of wastewater surveillance in the next phase of the COVID-19 pandemic. Countering COVID podcast, Biosearch Technologies. Published May 15, 2021. Accessed July 21, 2021. https://www.biosearchtech.com/covid-19/countering-covid-podcast/the-role-of-wastewater-surveillance-in-the-next-phase-of-the-covid-19-pandemic
  8. Larsen DA, Wigginton KR. Tracking COVID-19 with wastewater. Nat Biotechnol 38, 1151–1153. Published 2020. Accessed July 19, 2021. https://doi.org/10.1038/s41587-020-0690-1

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