Wastewater Surveillance for Pathogens Gains Momentum Worldwide

Wastewater surveillance systems that were launched during the pandemic proved invaluable for the early detection of SARS-CoV-2 and its variants [1]. Now, these systems are transitioning to broader, forward-looking programs, spurred on by global organizations such as the World Health Organization (WHO), which has established a global genomic surveillance strategy for pathogens with pandemic and epidemic potential, and the United Nations Environment Programme (UNEP), which supports wastewater surveillance and advocates for a systems-thinking approach to both environmental management and public health [2,3].

Several countries are showing leadership in this area, which is also known as wastewater-based epidemiology. For example:

In the United States, the Centers for Disease Control and Prevention (CDC) administers a National Wastewater Surveillance System (NWSS) that collects and displays wastewater data from communities across the nation, and it is currently testing for SARS-CoV-2, Influenza A, respiratory syncytial virus (RSV), and MPOX (previously known as monkeypox) [4].
The EU Wastewater Observatory for Public Health has expanded beyond COVID-19, and Finland is monitoring Influenza A, B, and RSV; Hungary is actively observing Influenza A; and Sweden is conducting surveillance for enteric and influenza viruses [5].
In Germany, the AMELAG project (Wastewater Monitoring for Epidemiological Situation Assessment) aims for the continuous monitoring of SARS-CoV-2 virus load in wastewater and is expanding wastewater-based monitoring into research of other pathogens or disease indicators [6].
South Africa is extending its research efforts in wastewater surveillance beyond COVID-19 with the planned inclusion of other vaccine-preventable diseases such as hepatitis A, hepatitis E, measles, rubella, and influenza A and B [7].
Korea’s new “Pandemic Influenza Preparedness and Response Plan” will increase the number of surveillance institutions from 300 to 1,000 and deploy predictive models that use genetic analysis and artificial intelligence (AI) [8].

Other regions are not as advanced. For instance, a study assessing capacity in low-resource settings across 13 countries in South and Southeast Asia showed pathogen genomics capacity exists, but use is limited and under-resourced [9].

A brief history of wastewater surveillance

The history of modern wastewater surveillance dates back to the 1940s when epidemiologists cultured wastewater to track polio outbreaks in the United States [10]. Forty years later, in the 1980s, researchers began monitoring Hepatitis A using hybridization with radioactive complementary DNA (cDNA) probes [11]. Then, in the 1990s, polymerase chain reaction (PCR) was introduced as the gold standard of wastewater pathogen detection [12]. Beginning in 2020, public health officials worldwide began using PCR to analyze wastewater for the SARS-CoV-2 virus, proving it a non-invasive and cost-effective way to monitor community health [13].

Why wastewater-based epidemiology is important

As climate change, urbanization, and global travel increase the risk of pathogen transmission, wastewater surveillance has become an essential tool for tracking disease prevalence, trends, and potential outbreaks. Wastewater-based epidemiology enables public health officials to identify and surveil infectious disease pathogens before cases are reported, and because both symptomatic and asymptomatic cases can be detected, it can provide the real-time data necessary for quick responses and informed public health decisions prior to spread of the pathogen. Wastewater surveillance also provides unbiased data, protection of the anonymity of individuals, the ability to quickly pivot, and a variety of scanning ranges, from broad to very targeted [14].

Based on these benefits, public health officials are using wastewater surveillance at sentinel sites (e.g., airports) to detect emerging threats, as well as in areas with limited healthcare access (e.g., rural, low-density areas), making it a valuable tool for global health surveillance and prevention efforts [15, 16].

Analytical methods for wastewater surveillance of pathogens

Several different analytical methods can be used for wastewater surveillance. Targeted approaches can identify known pathogens, while broader sequencing methodologies can be used to detect novel threats. The most common molecular detection methods are:

Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is considered the “gold standard” for wastewater-based epidemiology due to its sensitivity, reliability, and widespread availability. RT-qPCR uses pathogen-specific primers and probes, and qPCR arrays are ideal for gene expression profiling and verification applications that require the analysis of tens to thousands of targets [17].
Digital polymerase chain reaction (dPCR) is an advanced technique to detect and quantify DNA or RNA. Unlike conventional PCR, which provides relative quantification, dPCR offers absolute quantification by partitioning the sample into thousands (or more) of individual reactions, ensuring that each partition contains either zero or one target molecule. This enables highly sensitive and accurate detection of low-level targets in complex samples [18].
Next-generation sequencing (NGS) offers high-throughput, comprehensive sequencing of entire genomes or metagenomes from wastewater samples, allowing for broad surveillance of multiple pathogens and their variants in a community [19].
Sanger sequencing provides high-accuracy sequencing of DNA segments and is used for targeted surveillance of specific genetic regions; however, this method has a relatively low throughput and is not as suitable for large-scale pathogen monitoring [20].

Limitations to wastewater surveillance for pathogens

In its new Phase 2 report, the U.S. National Academies of Sciences, Engineering, and Medicine offers a detailed assessment of technical constraints associated with increasing the use of wastewater for the surveillance and prevention of infectious diseases [15]. In general terms, these limitations are related to sampling, testing, and data analysis and as the report points out, challenges like these create opportunities for the implementation of standardized protocols, guidelines, and quality control measures to help ensure consistency and comparability of results across different regions and laboratories. (For more detail, please see Increasing the Utility of Wastewater-based Disease Surveillance for Public Health Action: A Phase 2 Report [15].)

The growing need for wastewater-based epidemiology

The need for wastewater surveillance is growing globally due to research on emerging infectious diseases, as well as other mounting public health threats such as antimicrobial resistance and environmental contamination. Wastewater surveillance offers a non-invasive, cost-effective, scalable solution for monitoring entire populations and providing early warnings of outbreaks before clinical cases surge. It is an increasingly essential complement to other epidemiological tools, especially in areas with limited healthcare access or where testing infrastructure is insufficient.

To learn more, download our Application Note “Wastewater pathogen detection: optimizing efficiency with TaqMan Array Card.”

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