The first signs of the latest waves of Covid-19 have often been detected in our sewers instead of nasal swabs.
But in the future, the potential for human waste to tell us what’s going on with our community’s health could extend far beyond the novel coronavirus.
“It was his coming out party. We realized the power of this pandemic,” John Dennehy, a biologist at the City University of New York who helped NYC’s sewage monitoring program, told me. “Now there is great interest in developing infrastructure to maintain this capacity beyond the pandemic.”
Wastewater monitoring is becoming more valuable right now, as conventional testing becomes less transparent. More and more people are using rapid home tests and might not report the results to a public health agency. This means that the number of positive cases reported by official sources might not provide a complete picture of what is happening with the pandemic.
But no matter how or if they test, infected people — whether they show symptoms or not — shed the virus when they go to the bathroom, leaving behind viral RNA that can be detected in sewage samples. This requires careful collection and testing, but sewage can provide a less biased view of viral trends in a given community.
Science has not yet reached the point where we can say that X amount of viral load in a community’s sewage means that Y number of people are infected in that community. Nevertheless, it is useful to know in which direction viral loads are changing. If they increase, even before the number of positive tests begins to increase, this could in theory allow public health authorities and the local health system to start preparing for an increase. If they go down, public health officials (and the general public) can be confident that any decrease in official case counts is real and not the byproduct of, say, less testing.
So far, health authorities have not used sewage levels to trigger a public health response – ordering people to mask up again once viral loads hit a certain level, for example. But experts say a more direct link between sewage monitoring and public health policies could be made in some places in the coming year.
Covid-19 has shown the value of wastewater monitoring in public health
The pandemic has revealed the potential for wastewater monitoring – and the shortcomings of current US infrastructure.
Dennehy told me his team in New York noticed an unusual iteration of the virus in November, but it wasn’t until South Africa announced the presence of the omicron variant in people there a month later. later that they realized they had seen the mutations that would soon trigger a new wave of infections around the world.
South Africa has been praised for its genomic surveillance system, which allowed it to be the first to identify omicron as a threat, even though, as the New York example shows, the variant was probably already present in other parts of the world. The United States, on the other hand, has lagged other countries for much of the pandemic in this work, and integrating wastewater into this monitoring system remains a work in progress.
Before the pandemic, the use of wastewater for disease surveillance was not unheard of, but it was generally limited to monitoring diseases like poliomyelitis, where the appearance of any amount of virus would be alarming.
Covid-19 has shown that sewage can provide an even more nuanced and varied picture of a community’s health. Since researchers showed the ability to detect the coronavirus in wastewater in early 2020, wastewater monitoring has spread around the world. More than 470 sites in the United States and nearly 3,400 sites worldwide report the amount of viruses they detect in the waste we empty.
Wastewater has its limitations, including challenges related to proper collection and adjusting the concentration of human waste in wastewater. Some rural areas have no community sanitation system, relying instead on septic tanks in individual houses, making large-scale monitoring impossible. In Montana, Wyoming, North and South Dakota, and Nebraska, only two wastewater sites are reporting their coronavirus levels to the CDC.
Establishing a strong wastewater monitoring program also requires political support and coordination between public health departments, environmental agencies and local water authorities, who may not be used to working together. .
Despite these obstacles, wastewater monitoring has become more integrated into the global response to the pandemic over time. And experts don’t expect it to stop there. They are already imagining how we might otherwise use all the information that can be gleaned from our waste to anticipate future outbreaks and target public health interventions.
“Most people think sewage testing isn’t going away,” Marc Johnson, a University of Missouri virologist who helped lead that state’s sewage monitoring program, told me. “It’s too good of a tool. It can give us an unbiased reading of a community’s health, without having to worry about patient confidentiality.
All the ways wastewater monitoring could help us improve public health
For the foreseeable future, sewage monitoring could help the country stay ahead of Covid-19. Not only can general trends – an increasing or decreasing amount of virus detected – give a warning of emerging or declining waves, but the sewage can also provide scientists with clues about new variants that may soon appear.
Once the wastewater is collected and sent to a laboratory, scientists perform the same type of test as that performed for an individual diagnostic PCR test. In addition to identifying whether or not the virus is present, the lab can also determine its quantity based on the number of test cycles it must run to detect it. (Fewer cycles means more viruses.)
Then, scientists can also take the sample and analyze the genetic makeup of the virus in it. If it is different from the most common variant at the time, it may be a sign that another variant is lurking with the potential to take over. Johnson said that in Missouri his team has seen variants of Covid-19 that have yet to be detected in humans. They may have found their way into the sewage system from animals, he told me, and we know that animal-to-human transmission is a way for the emergence of new variants.
American scientists are also starting to use wastewater in a more targeted way to fight Covid-19. Dennehy said a hospital in New York asked his team if they could start testing the sewage coming out of their facility specifically so they could get an early warning if the virus appeared more frequently in their patients and their staff. Ongoing diagnostic testing would be expensive to maintain, and this population-level surveillance would allow the hospital to institute more rigorous testing only when the viral load in the sewage suggests it is needed.
This kind of creative approach can also be applied to other public health issues.
Johnson described a similar proposal in Missouri prisons that want to monitor TB outbreaks. They requested that their wastewater be tested regularly for tuberculosis, which they could use to determine when to perform individual diagnostic tests, which are both expensive and logistically burdensome.
“They don’t have to waste money on testing when they know there’s nothing there,” he said.
Surveillance programs could also monitor other pathogens, such as influenza, hepatitis, and norovirus, for early warnings of emerging outbreaks. Julianne Nassif, a wastewater monitoring expert with the Association of Public Health Labs, said we could also monitor bacteria, viruses and other microbes that are resistant to current treatments. Public health officials could try to preempt an outbreak of antibiotic-resistant bacteria in a nursing home, for example, with information gleaned from sewage downstream.
Johnson imagined that communities were monitoring narcotics, in order to better tailor their public health campaigns. Wastewater could be tested to determine whether cocaine or opioid use is increasing at a given treatment plant. It could even determine what kind of opioids are being used, which could be helpful to health services. Widespread heroin use may require a different response than diverted prescription opioids or black market fentanyl.
The possibilities seem nearly endless, extending to research that could help us better understand human health. Dennehy described to me a hypothetical experiment that could be conducted with sewage monitoring, looking for viral markers associated with colon cancer. By comparing the results of a community with, say, a nearby nuclear power plant and another community elsewhere, we could better understand how the surrounding environment affects people’s health.
But for all of this potential to be realized, these efforts would require sustained support. The CDC has bet on the sewage boom, launching a national Covid-19 monitoring system in the fall of 2020. But dedicated investments in infrastructure and a workforce would be needed if the country were to start carrying out monitoring wastewater on a more permanent basis.
In general, the United States seems unwilling to make large investments in public health. Scientists working on these programs hope that the same cannot be said for wastewater monitoring, given the opportunities it presents.
“We learned a lot of hard-won lessons with the Covid pandemic. We got caught with our pants down at the start. A lot of things we did were too late,” Dennehy told me. “The hope is that we can remember those lessons for the next time it happens, which may not be so long.”