What wastewater says about disease — including measles — in Utah

Forget the canary in the mine, at least when it comes to figuring out early that infectious diseases are in a community. Wastewater — a sanitized name for human fecal matter and urine — tells the story, providing evidence even before the symptoms of an illness may appear.

Wastewater surveillance is one key way Utah public health officials know that measles, one of the most contagious illnesses with potential for serious complications, is active in much of Utah, especially along the Wasatch Front. If you don’t believe it, just look at the state’s wastewater surveillance map.

The Centers for Disease Control and Prevention launched a National Wastewater Surveillance System in September 2020, with COVID-19 raging, to detect SARS-CoV-2, the virus responsible for the pandemic. Utah was one of the first eight states to join what is now a nearly universal national program, with most states participating.

Even before symptoms develop, people with the infections that can be found in wastewater shed virus or bacteria when they go to the bathroom or bathe, wash their hands or even wash their clothes. The water from toilets, sinks, tubs and other drains go into the sewer system, where the water will eventually end up in treatment plants to be sanitized and made safe for human use.

The Utah Public Health Laboratory is among the nation’s most capable and sophisticated when it comes to illness detection using wastewater collected before it’s treated.

For wastewater surveillance, samples are taken of the not-so-clean sewage, where viruses and bacteria can be found.

Deseret News recently visited the Utah lab in Taylorsville to see how detection is done and learn why it is so vital.

That latter question is easily answered, according to Kelly Oakeson, chief scientist for Next Generation Sequencing and Bioinformatics at the state lab. If public health knows what’s circulating early, health officials can warn the public, ramp up education and let health care providers know what to look for.

“We know where measles is and how it’s spreading across the state and where to focus our public health efforts,” he said.

Knowing where measles cases are allows local health departments to emphasize the need to take such precautions as getting vaccinated if one isn’t already protected, especially since measles can spread days before one has symptoms and is known to linger in the air for several hours. Someone can wander through a place where another individual who doesn’t yet know he or she has the disease has been and contract it.

Oakeson, who oversees all of the sequencing of infectious disease pathogens at the lab, said providers can be told early that “if somebody comes in with flu-like symptoms and a rash like this you might want to test for measles. Also, you may not want to have them sitting around in a waiting room for a long period of time.”

While measles is now fairly well spotted, health officials pointed out recently that it was declared eliminated — referring to the absence of continuous endemic spread — in the U.S. in 2000, so some doctors and other health care providers, especially young ones, had until quite recently probably only seen measles in a textbook or on a classroom slide.

What the state lab can do

According to the Utah Department of Health and Human Services, Utah has had 443 confirmed cases of measles in this outbreak, which began in 2025 and is ongoing. Of those cases, 98 were reported in just the past three weeks.

Utah has one of the most well-equipped public health labs in the country, with several million dollars invested in its technology at the height of the pandemic. The wastewater surveillance program launched during COVID, which has been continuously monitored since. But the entire operation was designed so the lab could pivot to testing for other emerging risks. Right now, that’s primarily measles.

Utah’s lab can test for COVID-19, measles, Influenza A and B, and respiratory syncytial virus (RSV) A and B. The lab can ramp up as needed.

Positive measles surveillance means there’s at least someone with measles in the area of the treatment plant from which a sample came. A negative, however, doesn’t mean the area is clear of the virus. The sample, typically collected in small amounts over six to 24 hours, may have missed some shed virus.

The water coming into the treatment plants is sampled twice a week to see if measles is detected. The lab runs two tests, starting with a polymerase chain reaction or PCR test to find the DNA and RNA inside the sewage samples. PCR can amplify small traces of the infection that’s being looked for, so it can be found early. It’s a quantitative test. The other test is genome sequencing to determine the measles variation or strain.

“That allows us to say, OK, yep, measles is present in this sewer shed; it’s there at this amount and we can tell that it’s this strain, which gives us kind of that complete picture of what’s happening in that sewer shed,” Oakeson said.

The lab can detect how many copies of the virus per milliliter.

What wastewater surveillance cannot do is drill down to individual or even neighborhood cases or see what’s happening in facilities that treat their own wastewater, a group that includes some hospitals, universities and prisons. Nor can wastewater surveillance always detect very low levels of infection.

Finding a virus in wastewater

The wastewater treatment plants collect the water in three- to five-liter bottles and a courier brings them to the lab. Oakeson notes that he’s over all of the sequencing aspects, but Jenni Wagner, Next Generation Sequencing Wet Lab manager, has a more hands-on role.

Besides measles, they currently also look for influenza. With flu, testing for the specific strain has the added benefit of letting health officials and the public know if the circulating variety is a mismatch to what’s included in the flu vaccine, which is constructed each year on a best guess of what strain will be circulating during flu season.

With both measles and flu, “we’re doing all of these really high-end, cutting-edge, very modern techniques to really put the state of Utah in the best place possible to help prevent these outbreaks and to help do the work to contain these outbreaks,” Oakeson said. “We are really focusing on making sure people in Utah have the best health they possibly can.”

German Pinas, who oversees PCR testing, told Deseret News that part of the process takes about five hours. In the lab, Bailee Troutman and Chris Fajardo donned the personal protective gear that is a necessary part of their jobs and simulated the process, showing how the liquid is removed from the samples using a special vacuum system. The genetic material — the shed RNA and DNA — sticks to a silicone membrane and is released into a very small tube.

The process takes the wastewater down to a concentrated sample of DNA and nucleic acid that can be tested for measles, reducing the wastewater sample material from 20 milliliters down to little tubes that can fit 96 into a holder about the size of an iPhone 16.

But the shrinking isn’t finished. For the genome sequencing, four of those plates of 96 are converted into another holder of the same size with even tinier wells that hold 384 extremely small samples. A robot does that, transferring the samples and converting the RNA to DNA. Little hooks, Oakeson said, find the measles RNA in the sample.

As the samples move through the entire process, their origin is tracked with a molecular bar code.

Utah’s public health lab is a leader of bioinformatics nationally and one of four capable of sequencing the genome of material in wastewater. It is, said Oakeson, “fancy science with real-world implications.”