How sewage monitoring could help prevent future outbreaks

A community’s wastewater holds clues to its COVID-19 burden. During the pandemic, sewage monitoring has become an increasingly popular way to try to understand local infection trends.

Microbiologists Susan De Long and Carol Wilusz met and became wastewater experts in April 2020 when a local group of wastewater treatment plant operators asked them to develop and deploy a test to detect SARS-CoV-2 in samples from Colorado sewers. De Long is an environmental engineer who studies beneficial bacteria. Wilusz’s expertise is in RNA biology. Here they describe how wastewater monitoring works and what it could do in a post-pandemic future.

How is wastewater monitored for SARS-CoV-2?

Wastewater monitoring takes advantage of the fact that many human pathogens and products of human drug metabolism are found in urine, feces, or both. The SARS-CoV-2 virus that causes COVID-19 appears in surprisingly large amounts in the feces of infected people, even though it is not a major route of disease transmission.

To determine if pathogens are present, we must first collect a representative sample of wastewater, either directly from the sewer or at the point where what engineers call “the influent” enters a station. purification. We can also use solids that have settled in the wastewater.

Technicians must then remove large particles of feces and concentrate any microbes or viruses. The next step is to extract their nucleic acids, the DNA or RNA that contains the genetic information of the pathogens.

The sequences contained in DNA or RNA act as unique barcodes for the pathogens present. For example, if we detect genes unique to SARS-CoV-2, we know that the coronavirus is in our sample. We use PCR-based approaches, similar to those used in clinical diagnostic tests, to detect and quantify SARS-CoV-2 sequences.

More detailed characterization of the nucleic acid sequence can provide information about viral strains, for example, it can identify variants like omicron BA.2.

More than 800 sites that span populations of varying sizes are reporting COVID-19 wastewater numbers to the CDC. [Image: CDC COVID Data Tracker]

Many state agencies, like the Colorado Department of Public Health and Environment, and cities, like Tempe, Arizona, have their own dashboards for reporting data. Some companies performing wastewater testing also report data on their own dashboards.

In our view, the NWSS represents an exciting first step in monitoring population health through wastewater. Similar systems are in place in other countries, including Australia and New Zealand.

What does wastewater data really show?

Levels of SARS-CoV-2 in sewage from large populations are an excellent indicator of the level of infection in a community. The system automatically monitors everyone who lives in the sewer basin (the community area served by a sewage collection system), so it is anonymous, unbiased and fair. It is important to note that it is also impossible to trace the infection back to a particular person, household or neighborhood without taking additional samples.

Wastewater monitoring does not rely on the availability of clinical tests or on who reports their test results. It also detects asymptomatic and pre-symptomatic cases of COVID-19; this is essential because people who are infected but do not feel sick can still spread COVID-19.

In our view, sewage testing is increasingly important as more and more COVID-19 tests are performed at home. And because vaccination has also led to milder, asymptomatic cases of COVID-19, people can become infected without getting tested at all. These factors mean that clinical case data is less informative than at the start of the pandemic, while sewage data remains a consistent indicator of community infection level.

So far, you cannot accurately predict the number of infected individuals in a community based on the level of virus in its wastewater. A person’s stage of infection, how their body reacts to the virus, the virus variant, the distance between a person and where the sewage sample was taken, even the weather can all affect the quantities of SARS-CoV-2 measured in wastewater.

But scientists can infer relative changes in infection rates. Watching viral levels rise and fall in sewage provides insight into whether cases are rising or falling in the community as a whole.

Since SARS-CoV-2 can be detected in wastewater days or even weeks before outbreaks occur, wastewater surveillance can provide an early warning that public health measures may be warranted. . And signal trends are important; if you know the levels are increasing, now may be a good time to reinstate a mask mandate or recommend working from home. Currently, public health officials use wastewater surveillance data along with other information such as test positivity rates and the number of clinical cases and hospitalizations in the community to take this type of decisions.

Sequencing data can also help detect new variants and monitor their levels, allowing public health responses to take into account the characteristics of the variant present.

In small populations, such as college dorms and nursing homes, sewage monitoring may detect small numbers of infected people. This may sound the alarm that targeted clinical testing is needed to identify infected people to isolate. Early detection, targeted testing and quarantine are effective in preventing outbreaks. Rather than using clinical tests for routine surveillance, administrators can reserve disruptive clinical tests for times when SARS-CoV-2 is detected in wastewater.

What will monitoring look like in the future?

Widespread and routine use of sewage monitoring would give public health officials access to information about levels of a range of potential infections in American communities. This data could guide decisions about where to provide additional resources to communities, such as holding testing or vaccination clinics in places where infection is on the rise. It could also help determine when interventions such as masking or school closures are needed.

In the best-case scenario, wastewater monitoring could catch a new virus when it first arrives in a new area; an early shutdown in the very localized area could potentially prevent a future pandemic. Interestingly, researchers detected SARS-CoV-2 in archived sewage samples collected before anyone was diagnosed with COVID-19. If wastewater surveillance had been part of the public health infrastructure established at the end of 2019, it could have provided an earlier warning that SARS-CoV-2 was becoming a global threat.

For now, however, setting up and operating a national wastewater monitoring system, especially one that includes building-level monitoring at key locations, is still too costly and demanding. labor.

Ongoing research and development efforts attempt to simplify and automate wastewater sampling. On the analytical side, adapting PCR and sequencing technologies to detect other pathogens, including novel pathogens, will be essential to take full advantage of such a system. Ultimately, wastewater monitoring could help support a future in which pandemics are far less deadly and have less social and economic impact.


Susan De Long is an associate professor of civil and environmental engineering at Colorado State University. Carol Wilusz is a professor of microbiology, immunology and pathology at Colorado State University.

Comments are closed.