Wastewater Surveillance Has Become a Critical Covid Tracking Tool, but Funding Is Inconsistent

Lambert here: Why would we be crazy enough to fund something that depends on public utilities like local water and sewer departments, doesn’t boost the pharmaceutical industry, doesn’t boost the insurance industry or hospitals, and might help prevent transmission? Think, people! NOTE The CDC map on wastewater I keep publishing is miserably inadequate, and doesn’t provide a check on case numbers in Florida, Texas, or California, which drive the national figures just now. (Granted, California coverage is merely weak, as opposed to being abysmal, like the two others.) Too bad there’s no DIY solution for wastewater, like Corsi-Rosenthal boxes, or CO2 meters.

By Lauren Sausser, who covers health care across the South as a member of KHN’s Southern Bureau. She is based in Charleston, where she previously spent nine years covering health care at The Post and Courier. She has received awards from the Association of Health Care Journalists, the Society of Professional Journalists, and other groups. In 2016, she was part of a team of reporters who were named finalists for the Pulitzer Prize for Breaking News. Originally published at Kaiser Health News.

To look at recent data posted on Clemson University’s covid-19 dashboard, one might assume that viral activity is low on the Upstate South Carolina college campus.

The dashboard, which relies on positive covid tests reported by local laboratories and on-campus medical offices, identified 34 positive cases among students during the third week of August and 20 cases the week before.

These numbers pale in comparison to those from eight months ago, when the omicron variant first surged in the U.S. and Clemson averaged hundreds of positive covid tests every day.

For those who rely on these kinds of dashboards to assess the risk of contracting covid, the recent data doesn’t paint the most accurate picture, said David Freedman, who chairs the university’s Department of Environmental Engineering and Earth Sciences. With the proliferation of at-home covid tests, only a small fraction of positive results are reported to public agencies. Many people with mild infections don’t test at all.

He said that better data can be found in samples collected from sewage water and that those have shown this summer’s viral activity is much higher than the number of reported cases suggests.

“In our area, the numbers are actually higher than at any time except for the [first] omicron surge,” said Freedman, who runs the department’s covid wastewater surveillance program. “And yet the case reports are often zero.”

Even though wastewater surveillance is proving to be the most accurate and economical way to gauge covid activity in communities across the country, Freedman and others say funding for this type of tracking hasn’t been consistent. And data collection is sometimes paused while wastewater researchers look for new ways to pay for the surveillance.

“For the wastewater data to be actionable, you have to observe it,” said Mariana Matus, CEO and co-founder of Biobot Analytics, which has a $10 million contract with the federal Centers for Disease Control and Prevention to run wastewater surveillance at more than 300 sites across the U.S. “The more that you observe, the easier it is to catch early changes and take action.”

Wastewater research isn’t new. The method was used in the 1940s to track polio outbreaks. Besides covid, the technique is being used to track the spread of monkeypox.

It involves collecting a wastewater sample, often at a treatment plant, concentrating it, and processing it so scientists can run an analysis — similar to a PCR nasal swab — able to detect genetic evidence of the covid virus, other infectious diseases, and even the presence of opioids.

Historically, wastewater samples have been collected to gauge community trends, such as the rise and fall of covid cases. More recently, though, research published by Freedman and others in the journal Lancet Planetary Health found that wastewater surveillance can be used to estimate the number of infected people in an area.

For much of the pandemic, covid numbers reported on a daily or weekly basis by state and local health departments moved in tandem with data collected by wastewater surveillance programs. Typically, when cases reported by the health departments increased so did the amount of covid detected in wastewater samples.

Covid-related hospitalization data is also useful in measuring community spread and gauging the severity of variants, but it is considered a lagging indicator, meaning the data tends to peak weeks after covid is already running rampant through a community, said Michael Sweat, director of the Center for Global Health at the Medical University of South Carolina, whose work focuses on covid forecasting.

By contrast, because people excrete the covid virus in feces before they show symptoms of illness, community-level infections can show up in wastewater sludge before case counts or hospitalizations start to rise.

Many scientists now consider wastewater surveillance a more precise way to track covid activity in real time. Without wastewater surveillance, “we just don’t have a very accurate read of things,” Sweat said.

And researchers say data collection is not expensive. According to Freedman, the program at Clemson costs $700 a week. Erin Lipp, who runs the wastewater surveillance lab at the University of Georgia in Athens, said covid testing costs about $900 a week.

According to a U.S. Government Accountability Office report published in April, countries could save millions or billions of dollars by using wastewater surveillance, but the potential cost savings remain unclear. A general lack of cost-benefit analyses makes determining how and when to use it difficult, the report said.

Yet some labs say the lack of a consistent and centralized source of funding raises questions about how — or if — communities can continue to carry out this work.

“When we started this, it was basically extra bits of money I could find,” said Lipp. Her lab has used CDC grant money over the past year to pay for surveillance, but the portion of funding dedicated to that testing is set to expire at the end of August. Donations will sustain the lab through September.

“I’m very hopeful we can find some way to keep it going,” said Lipp. She is concerned that her lab, for the first time during the pandemic, is seeing a disconnect between the covid spikes in wastewater and the spikes in clinical cases. “What we’re seeing is a huge undercount,” she said.

Wastewater surveillance sites often go “offline” for periods and then resume work later, said Colleen Naughton, an assistant professor of civil and environmental engineering at the University of California-Merced. She developed an online dashboard called CovidPoops19 that tracks wastewater surveillance efforts across the world.

Surveillance work can be intermittent, she explained, because funding comes from such a variety of sources, including governments, universities, and the private sector.

At the Plum Island Wastewater Treatment Plant in Charleston, South Carolina, wastewater surveillance was suspended for more than two months this year. The project was reinstated this summer when the state Department of Health and Environmental Control assumed control from the University of South Carolina.

“The academics that I know who have been doing this up to this point, we’re all facing similar levels of funding problems,” said Freedman, of Clemson University.

For much of the pandemic, Clemson paid for its wastewater surveillance. The program faced a funding shortfall earlier this year, but Freedman said his lab was never forced to suspend its surveillance. Before the money for his lab work ran out in May, Freedman turned to Biobot Analytics, which, in addition to the work it does for the CDC, analyzes wastewater samples for about 50 independent projects.

Biobot’s wastewater surveillance network is funded through venture capital investment, Matus said.

Regardless of the funding hurdles, wastewater surveillance is moving forward. Nationally, more wastewater research is being conducted now than ever before.

Although some researchers have had to look for alternative sources of funding this year, CDC spokesperson Jasmine Reed said that more than 1,000 CDC-funded surveillance sites are now operational across the U.S. The agency expects 200 more to start collecting data within the next few months.

That’s good news for researchers who want more data. But many will face a whole other hurdle in fighting the American public’s covid burnout, said Freedman.

“People don’t want to hear about it anymore,” he said. “But if you look at the national statistics, we’re averaging around 400 deaths per day. We can pretend it’s not happening, but the wastewater and the deaths are telling us a different story.”

KHN (Kaiser Health News) is a national newsroom that produces in-depth journalism about health issues. Together with Policy Analysis and Polling, KHN is one of the three major operating programs at KFF (Kaiser Family Foundation). KFF is an endowed nonprofit organization providing information on health issues to the nation.

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About Lambert Strether

Readers, I have had a correspondent characterize my views as realistic cynical. Let me briefly explain them. I believe in universal programs that provide concrete material benefits, especially to the working class. Medicare for All is the prime example, but tuition-free college and a Post Office Bank also fall under this heading. So do a Jobs Guarantee and a Debt Jubilee. Clearly, neither liberal Democrats nor conservative Republicans can deliver on such programs, because the two are different flavors of neoliberalism (“Because markets”). I don’t much care about the “ism” that delivers the benefits, although whichever one does have to put common humanity first, as opposed to markets. Could be a second FDR saving capitalism, democratic socialism leashing and collaring it, or communism razing it. I don’t much care, as long as the benefits are delivered. To me, the key issue — and this is why Medicare for All is always first with me — is the tens of thousands of excess “deaths from despair,” as described by the Case-Deaton study, and other recent studies. That enormous body count makes Medicare for All, at the very least, a moral and strategic imperative. And that level of suffering and organic damage makes the concerns of identity politics — even the worthy fight to help the refugees Bush, Obama, and Clinton’s wars created — bright shiny objects by comparison. Hence my frustration with the news flow — currently in my view the swirling intersection of two, separate Shock Doctrine campaigns, one by the Administration, and the other by out-of-power liberals and their allies in the State and in the press — a news flow that constantly forces me to focus on matters that I regard as of secondary importance to the excess deaths. What kind of political economy is it that halts or even reverses the increases in life expectancy that civilized societies have achieved? I am also very hopeful that the continuing destruction of both party establishments will open the space for voices supporting programs similar to those I have listed; let’s call such voices “the left.” Volatility creates opportunity, especially if the Democrat establishment, which puts markets first and opposes all such programs, isn’t allowed to get back into the saddle. Eyes on the prize! I love the tactical level, and secretly love even the horse race, since I’ve been blogging about it daily for fourteen years, but everything I write has this perspective at the back of it.


  1. ambrit

    “People don’t want to hear about it any more.”
    Blaming the victims here. The People have been “encouraged” to not want to hear about it. Most of the Establishment promoted propaganda seems to be of the “go back to work, “go back to the Mall,” sort of economics based exhortations. The Establishment has determined to prioritize “The Economy” above “The Public Health.” It is no wonder that the public acts as it does. The public is being manipulated to do so.
    I’ll go out on a limb here and suggest that the Public will pay attention to the Pandemic when the daily death count passes 2500 persons. Given how quickly this pathogen is mutating, such a surmise is well within the bounds of possibility.
    Stay safe.

    1. Lupana

      I was also thinking along this line but you said it all much better. Thank you.
      To further add to the confusion is the messaging regarding the Fall vaccines. All summer we’ve been told things like Covid is now more like a cold…No masks needed…Back to normal. This all with BA 5 running rampant. Now, the government is preparing to release vaccines to protect us from BA 5. How are they going to convince people to get a vaccine/booster for something they’ve been telling people all summer is fine to be around? I’m not sure what the message is anymore. Be scared but not too much ..?
      Personally, I keep it simple – mask indoors and stay outdoors as much as possible. Only family in the house.

      1. ambrit

        We’re in complete agreement with you about the ‘new’ social model. No trips to the mall, no cinema visits, no eating out, no sports involvement, etc. etc. Definitely no in home visits by “strangers.” Keeping “family” at bay might need to be prioritized if and when the “new” coronavirus variant comes around. [This is already almost non-existent.]
        I kid Phyl that we are the vanguard of a new social phenomenon; Urban Anchorites.
        Be you safe!

        1. Lupana

          I like the Anchorite – Much, much better than anti social recluse.. It gives my isolation a spiritual, intentional dimension

  2. GramSci

    I’ve been tracking local wastewater using Biobot Analytics since Lambert turned me on to it what? 18 months ago? Then, a few months back the following banner appeared on their web page:

    “U.S. Centers for Disease Control and Prevention Selects Biobot Analytics to Expand National Wastewater Monitoring”

    Since then, the data they post seems to have become even sparser and less timely.

    Ok, I’ve had federal grants. It takes a while to ramp up. And communities probably don’t like the gubmint getting into their sh!t in the first place. But why do the words “regulatory capture” come to mind?

  3. Ignacio

    This is indeed the only way to follow what is going on easily and fast. Covid reports, for instance in Spain only focus on >60 yo and while it is an indicator the presentation of the report is awful and you need to open several reports to see trends, while the web page showing wastewater results give you an instant picture that is more telling. Fortunately these days wastewater is showing mostly stable or diminishing Covid reads in Spain with a few local increases.

    Covid is turning to be a pension saver with more that 95% of deaths among >60% in Spain. Some collateral damage in younger cohorts particularly amongst those with complicating factors and apart from unreported malaises such as long Covid, extended brain fog, and many others. I wonder if or how many see this (saving in pensions) as a positive…

  4. Linda Amick

    by Public Health pronouncements Omicron is like a bad cold. Additionally there is NO early treatment protocols according to Public Health pronouncements.
    Therefore why test? The whole asymptomatic spread was debunked via a city in China of 10M people with only 300 iffy cases.
    Why run our lives continously by the spurious test results? It is beyond me.

  5. Nicola Avery

    Very interesting article and thanks for the link to CovidPoops. Can I also give a shoutout to John Snow who identified and mapped cholera in London sewage from wastewater. https://europepmc.org/article/PMC/PMC7150208
    Its really encouraging to see research growing. Funding massive challenge in UK because of Brexit, no EU Horizon option in sight amongst other problems. But we will get more done somehow.

  6. CanCyn

    Hoping sky net will allow 2 links in this post.
    Like Ambrit, Lupana and I am sure many others, we follow our own semi lockdown. Groceries and necessities are the only things shopped for – always masked. No dining out. Farmers market, parks and trails, biking, walking the dog for exercise. Hubby plays golf and masks in clubhouse. No houseguests. I monitor the Ontario Science table data because they monitor wastewater, supposedly at arms length from the provincial gov. (Take a large grain of salt with that one, I am very suspicious of the politics but that’s a digression for another post). They’ve gone from daily updates to monthly updates and soon will not be updated at all. This at a time when wastewater data is trending up in my neck of the woods and university students are returning and mask free public school starts soon. We are also a tourist area easily assessable to Americans. We had emergency depts close due to staff illness over the summer. But yeah, it’s over so no need to worry.
    I also monitor our local public health unit’s crappy site, previously daily updates, now weekly. I have no doubt soon to be not updated at all???

    I know more people who’ve had COVID this year than in the entire pandemic. Some recent and yet the majority seem to be on board the “it’s over” train. I am thrice vaccinated and don’t plan on another one anytime soon. I will continue my suburban anchorite (thanks Ambrit, that’s a keeper) lifestyle for now with no idea how I will know when it is safe to get on that train. Sigh

    1. ambrit

      You or your SO might want to cultivate a relationship with someone in a local Emergency Room. They will be the first to see direct evidence of a surge or more effectively evil mutation in the Dreaded Pathogen.
      May the contemplative life lift your spirits into the Infinite.
      Stay safe! Keep masking, no matter how much ‘pushback’ you get. (I am getting the Evil Eye a bit when I go shopping with my tastefully black mask as my preferred fashion accessory.)

      1. CanCyn

        Thanks Ambrit, that’s a good idea. I know a couple of retired nurses who would probably be able to use some connections to get intel but they’re both on the it’s over train. Sigh.
        I got quite the eye roll from a mask-less woman in the grocery store today. I didn’t look away, just smiled (letting it reach my eyes Lambert). Got a head shake and off she went. It did seem to me that there were more masks at both the market and the grocery store today than the last couple of weeks. But still not many.

        1. ambrit

          I keep noticing that the majority of persons I encounter who are wearing masks are, shall I say, in my demographic, ie. older persons. That group is the prime cohort for adverse outcomes arising from Covid infections. I read somewhere recently that the over 60 crowd (?) accounted for the vast majority of Covid caused deaths, so far.
          Someone else on this thread mentioned the fall cold and flu season approaching as having the promise of “naturally” increasing the proportion of the public that will wear masks. Let us hope so. Somebody has to perpetuate the species.

  7. Ignacio

    So it seems Omicron has displaced all the previous variants no near extinction. Difficult to say, or course, last Delta variant sequences were obtained until July in Africa according to Nextstrain dashboard. As a matter of fact, BA.4 and BA.5 being even more pathogenic/infectious that previous Omicron variants, and leaving a faint immune response, make it even more difficult the return of previous variants. Of course Omicron itself is already a source for lots of new mutants and sub-variants and it is already the most diverse clade. Last December/January, seeing Omicron biological and epidemiological data i stated that this was an important evolutionary change for Covid and Omicron would be the only lineage remaining. So far this looks OK as a prediction. A study by evolutionary modellers predicted that, after Omicron, a new independent lineage would take much longer to appear than previously and they delivered a statistical estimate centred in a period of 15 months (let’s say by March 2023). We will see what time brings. Of course this is only interesting and important for evolutionary studies and hypothesis and doesn’t say a single word on what future evolution will bring in terms of pathogenicity and virulence.

    It looks like most previous variants evolved in chronic infections according, for instance, as this study recently published concludes. Omicron might have evolved similarly but possibly from older, previously unidentified, ancestors. If this is going to happen again, the variants generated in a chronic infection will have it hard to equal or surpass the fitness that Omicron has reached. That is quite a challenge with BA.4 and BA.5 being probably the most infectious human virus ever identified.

  8. Thistlebreath

    The melancholy likelihood that institutions are now habituated to lying by omission leads me to think that we are caught in a mashup ‘Groundhog Day’ loop of John Cleese and Michael Palin eternally arguing whether or not a Norwegian Blue Parrot is, in fact, dead.

    “Gone to join the choir invisible” sums up the obvious.

    Wastewater sampling yields data that is irrefutably true. Minimizing, dismissing and denying it is not rational.

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