Earlier this year, the Department of Homeland Security’s science and technology arm announced that it had joined a coalition of federal agencies, led by the Centers for Disease Control National’s Wastewater Surveillance System, whose goal is to “better understand the spread of the (COVID-19) virus in communities, to contain and defeat it.”

The press release explains: “Using this wastewater-based epidemiology (WBE) approach, the public health community is banding together to identify and treat health threats in a non-invasive way.”

So … what does all this jargon mean? It means scientists are tracking SARS-CoV-2—and, perhaps, other viruses and nasty things—in poop.

So far, here in the Coachella Valley, only the city of Palm Springs has employed this testing, at the city’s wastewater-treatment plant—and it helped city officials sound early alarms about the huge COVID-19 spike the state endured in December and January.

“Our assistant city manager, Marcus Fuller, had actually seen a report on a television show about another city testing their wastewater for COVID,” said Palm Springs City Councilman Geoff Kors. “So he investigated it, and working with the staff, they decided that it made sense to test our wastewater for COVID, to get a better sense of what the real numbers were in cases, and so we could see trends in increases or decreases.

“That tracking has always shown more active cases than the county showed, because the county only has the data from the people who are tested. Right after Thanksgiving 2020, we saw a huge increase—first of 600 percent, and then I think it was a 1,000 percent increase in active COVID. So when the state did the shutdown, because of the data I’d seen, it wasn’t that surprising.”

Fuller said it’s normal for wastewater management to sample and test for various things, including pathogens.

“So it was easy to sample and test for the virus,” Fuller said. “But the question was if you have ‘x’ amount of virus per liter, then how many cases of the disease does that represent, and how many copies of the virus does somebody shed in their urine or their feces?”

To answer these questions, the city connected with GT Molecular. The Fort Collins, Colo., company, according to its website, “was created to develop new molecular detection technology for cancer research and harmful pathogen detection,” and has “recently focused these powerful tools on the detection of SARS-CoV-2 in wastewater to support communities around the country with their monitoring programs.”

Ramon Lopez collects samples at the city of Palm Springs’ wastewater-treatment plant and gets ready to package it with dry ice and send it for testing at GT Molecular in Fort Collins, Colo. Photo courtesy of the city of Palm Springs.

“They’re working in collaboration with labs and universities across the country that are trying to come up with the best guess on their models for how to interpret this data,” Fuller said. “That’s why when they give us the results, it’s kind of in a range.

“We do our tests on Mondays and Tuesdays every week. Samples are taken over 24 hours to make a composite sample, and then it’s sent to Colorado. Obviously, people who just became positive don’t know they’re positive, and some are asymptomatic, so they can’t be reflected in the county’s data yet—so (the wastewater-testing program) is almost like a preview of what’s to come.”

Rose Nash is the director of research and development at GT Molecular.

“The testing process entails filtering the sample to remove solids, and then concentrating the virus that’s present in the wastewater,” Nash said. “This is required because, even though we’re using the most state-of-the-art technologies for counting viral particles—the type of technologies that are often reserved for forensic laboratories or cancer research—the amount of virus in wastewater is just so low that it requires we concentrate it further.

“After concentrating it, we extract the viral RNA. This is done because the molecule that we quantify as RNA is on the inside of viral particles. So we open the virus up, grab the RNA, clean it and concentrate it, and then we put this RNA into what’s called ‘droplet digital PCR,’ which is an advanced molecular technology for counting nucleic acid molecules. We can design our droplet digital PCR tests to target SARS-CoV-2, as well as variants of SARS-CoV-2, such as the UK variant or the South African variant, which has gotten a lot of news coverage lately as being hyper-transmissible and starting to circulate around the world.”

Back here in Coachella Valley, data on the community spread of SARS-CoV-2 and its various variants would be undeniably helpful. So why is only Palm Springs currently collecting that data?

Primarily, one word: Money.

Beverli Marshall is the general manager of the Valley Sanitary District, which manages the wastewater system for the city of Indio, and parts of Coachella and La Quinta.

“I believe that any data you can gather is important,” Marshall said. “Obviously, there are several agencies nationwide, as well as in California, that are participating in this (practice) and helping to develop the metrics so that it can be used for future outbreaks from a wide variety of sources. But it really comes down to a cost factor, because this would be additional testing that we don’t normally do.

“Certainly, I think that if there were grants available—and I think there should be, so that ratepayers aren’t bearing the burden of the costs—that would be most helpful. The data that’s being collected is being handed over to the CDC and to public-health (organizations) who are benefitting from it, but they’re not really paying for it, so to speak. So I really think that the important issue is who should bear the cost of it.”

GT Molecular’s Nash said there is indeed a cost associated with doing such testing.

“When wastewater-based epidemiology really started, it was a national pilot program that got a lot of people involved and helped people realize that it was possible,” Nash said. “But when the fee-for-service models (were rolled out and the country) transitioned away from the free pilot program, the cost per sample tested was over $1,000 a sample, and so a lot of communities were priced out of participating. So when we (at GT Molecular) got involved, we absolutely wanted this to be affordable. We wanted as many communities—especially low-income communities that might not have as much tax revenue—to participate. We started with our price at $295 per sample, and we’ve held it there throughout this entire pandemic. That includes the kit that we ship with the tubes that the wastewater gets transferred to, and the shipping labels to get it back to us. … We’re about one-fourth of the price of anyone else in the market.

“The way our system is built, at this point, it wouldn’t really be very useful. Even if we went out and sampled manholes, we have tens of thousands of them. So to get useful data, it would cost who-knows-how-much money to go out and test samples at a lot of manholes—and that really wouldn’t give us any information that we don’t have now.” Katie Evans, conservation and communications director, cVWD

“We’re all affected by viruses. As I like to say, viruses don’t know borders, and they don’t know different communities or different income levels.”

The Coachella Valley Water District is responsible for managing the wastewater systems throughout the valley, with the exceptions of Palm Springs, Indio and various areas within other valley cities. Katie Evans, the district’s conservation and communications director, said the sprawling size of the CVWD presents a challenge.

“When you’re looking at a system as large as ours, which covers 100,000 different accounts, (spot testing for SARS-CoV-2) is just not really a useful piece of data,” Evans said. “I definitely would not say that the CVWD is not interested in following or engaging (with this technology at some point). But the way our system is built, at this point, it wouldn’t really be very useful. Even if we went out and sampled manholes, we have tens of thousands of them. So to get useful data, it would cost who-knows-how-much money to go out and test samples at a lot of manholes—and that really wouldn’t give us any information that we don’t have now. We know, because of community testing, just how widespread COVID-19 is. So if we were to start testing our wastewater, it would basically tell us the same thing: how widespread COVID-19 is.”

I asked Evans about the point made by Marcus Fuller about wastewater testing offering “almost like a preview of what’s to come,” because it detects early and asymptomatic COVID-19 cases.

“Whatever public-health actions would result from the data would have to be weighed against the time and expense it required to accomplish,” Evans said. “Again, (the wastewater test results) will not give us pinpointed data, or specific information. Because we can’t get that granular on information without literally testing tens of thousands of manholes, it doesn’t really provide us data that would make a decision possible.”

Nash said her company is working on this very issue.

“GT Molecular collaborates with this wonderful company called GoAigua,” she said. “They have a team of epidemiologists, but they’re also great at hydraulic monitoring and understanding the sewer pipes’ configuration and operations. … We’re working with GoAigua, for instance, in the city of Burlington, Vt., to understand where the different trunks are, and what are all the different communities, and where you could collect in the sub-sewer shed to identify a given population, or a given neighborhood, or a given community. Then, a sampler can be installed there, rather than at the wastewater-treatment plant. So there’s some really fantastic modeling that can be done to actually get at that (source identification).”

Given that the application of this technology is so new—we’ve only known about the existence of SARS-CoV-2 for a little more than a year, after all—some are concerned about the accuracy of the models that extrapolate the projected number of COVID-19 cases.

“That is a very common topic in the field,” Nash said. “Early on in the pandemic, a couple of groups published a mathematical model that can be used to estimate exactly how many COVID-19 cases are in an area. I find that there are some benefits to this (model), because it helps to contextualize the data.

“That said, the first concern from scientists, myself included, is that the data we are using in these models to understand how much virus one person sheds when they’re infected is based on a study where only 20 patients were monitored for shedding in the stool—and any scientist will tell you that 20 people is not enough. However, we are in the middle of a pandemic. This is all evolving very rapidly, and we don’t have bigger datasets that are more representative. So it’s an estimate that’s based on the best science there is right now.”

However, the more that testing is done, the better the data gets, at least as far as detecting trends goes.

“We’ve done this for 30 different communities, and we’ve overlaid our data with their case numbers from diagnostic testing, and our average correlation coefficient is 0.8, and that’s (on a scale) where ‘1’ is perfect, and ‘0’ is very poor. So the testing of wastewater has a beautiful (trending) correlation with the amount of cases in a given area. … There are so many variables. For instance, there’s a large variation in the size of an average stool across the population, and that’s an important metric when coming up with a case estimate. Also, the amount of viral matter that’s being shed is important to the estimate, and the models don’t take into account any form of viral or RNA degradation as the virus travels through the wastewater. So that’s another issue. … Our actual number that we report for the viral concentration only has an error measurement of about 5 percent. The concentrations that we report do not have a large range. It’s only when we feed it into that (case-number) model, which has to take into account a lot of variables, that we get the large range.”

Nash suggested that as we learn more about the virus that causes COVID-19, the applications for wastewater-testing data will also evolve and improve.

“There’s data that suggests that a patient sheds virus from their intestine for up to a full week before they get symptomatic and would usually be tested,” Nash said. “I like to think of this as the Achilles’ heel of COVID-19, in the sense that it throws up a red flag that it’s coming—but (you see it) only if you’re looking in the sewer. Right now, though, I think the most impactful use of this (testing program) is looking for the hyper-transmissible variants. … We can certainly use our testing as an early warning system against these hyper-transmissible variants.”

Palm Springs initiated testing for the variants early this year.

“There’s still great use for it when the levels are high,” Nash said. “Palm Springs did a really great analysis where they took the data we provided them, and they overlaid the different policies that had been put in place, like when they shut down bars, or when they shut down restaurants, or when they went to ‘purple’ status versus ‘red.’ You could see (the viral load levels in) the wastewater respond to those actions. So it can be used to drive policy decisions … but I think the best use of it is looking for new viruses, whether it’s new forms of COVID-19, or hepatitis, which is something else we’re working on right now.”

While the scientists continue their work, Beverli Marshall, of the Valley Sanitary District, said wastewater-management officials need to be kept in the loop.

“I applaud this,” Marshall said. “Somebody actually thought about where we could find a source of data that’s less invasive, without compromising personal privacy, or HIPPA-type stuff. We’re not going household to household asking if you’re sick. This way, we can test at a more macro level by using wastewater. So there is room for that discussion even beyond COVID-19—but we (wastewater service providers) have to be at the table.”

Because of wastewater testing, officials with the city of Palm Springs knew COVID-19 cases were on the rise before the recent stay-at-home order—and knew cases were falling before the order was lifted.
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Kevin Fitzgerald

Kevin Fitzgerald is the staff writer for the Coachella Valley Independent. He started as a freelance writer for the Independent in June 2013, after he and his wife Linda moved from Los Angeles to Palm...