Each weekday at 8 a.m., the process for tracking COVID-19 variants in Missouri begins with vials of sewage samples.
The boxes from across the state are unpacked at the Sewershed Surveillance Project lab at the University of Missouri.
The vials get spun around in a centrifuge, separating the solids to the bottom. Next, anything bigger than a virus, like bacteria and wastewater solids, are filtered out. The samples are mixed with a chemical called polyethylene glycol, which acts as a sponge, soaking up the water. The rest of the particles, now chemically dehydrated, stick together.
The samples go back in another centrifuge, leaving microscopic particles at the bottom of the tube. Marc Johnson, associate professor of molecular microbiology and immunology at Mizzou, compares the particles to the residue at the bottom of a cup of coffee, except these are invisible. Finally, a robot pulls out RNA, the messenger material created by DNA that is used to make proteins, from the sample.
From this RNA, scientists are able to monitor the prevalence of COVID-19 and its genetic variants.
All viruses, including the coronavirus, mutate over time. The Centers for Disease Control and Prevention compare how viruses change to a tree growing and branching out.
So far, some variants appear to spread more easily, some are more resistant to antibodies from vaccinations or are less likely to be affected by antibody treatment. State governments are monitoring variants and using them to inform public health decisions.
“The recommendations are all still the same, so we’re not really doing something different because a variant is there,” said Jeff Wenzel, the bureau chief of environmental epidemiology for the Missouri Department of Health and Senior Services. “But it’s informative to know what viruses are out there, what variants are out there, and how that might be moving throughout the state or changing over time.”
DHSS is updating a map showing sewershed data results each Friday. Wenzel said the department would send out a press release if it sees something different or unusual that would be a trigger for wanting people to do something differently.
Kansas monitors variants through sequencing normal PCR (polymerase chain reaction) tests. Samples that are sequenced to look for variants are random positives that come through the state lab or are flagged down by another health official, said Kristi Zears, a spokesperson for the Kansas Department of Health and Environment.
Samples are chosen because of screening data, unusual symptoms, someone potentially being infected by COVID-19 despite being vaccinated, or a case investigation in a certain geographic area, Zears said.
Kansas regularly updates data on a public dashboard showing where COVID-19 variants are located on a map with a breakdown by county. It also shows the proportion of which COVID-19 variants are found.
In the week of May 30, Alpha, also known as B.1.1.7 or the variant first identified in the United Kingdom, made up 24.64% of the specimens that were sequenced. Three months earlier, the lineage was just 1.68% of the specimens sequenced.
KDHE published news releases when variants of concern initially showed up in Kansas, Zears said. Some counties have sent out additional updates.
How a collaboration helped launch the program
Sewershed surveillance is a more cost effective and faster way of monitoring COVID-19 genetic variants than lab tests, said Wenzel.
“Right now, we’re not able to sequence every human sample, and there’s a lot of those samples to look at, so with one sewershed sample we’re able to look at a community and get a general idea of what’s going on in that community,” said Wenzel with DHSS.
A main advantage of sewershed monitoring is that it includes people who are asymptomatic and people not getting tested, according to the Centers for Disease Control and Prevention. Around 80% of U.S. households are served by municipal sewer systems.
The sewershed monitoring program started when the Department of Natural Resources had a meeting with wastewater operators across the nation. At the time, some countries, like the Netherlands, had shown the program’s promise for monitoring COVID-19 trends.
DHSS reached out to the University of Missouri-Columbia and found a lab that could conduct the testing., In May, the department started with examining nine locations. Now, the lab has over 50 participating locations. About 24 different wastewater samples are tested for variants each week.
Missouri was one of the earliest adopters of the program. Although other states and cities, like Ohio, Wisconsin, and Truckee Meadows, Nevada, have similar programs, each program has developed different approaches.
Wenzel said Missouri’s sewershed testing program has been successful because of collaboration between the DNR, wastewater operators, DHSS and Mizzou.
“Many of those (Missouri) wastewater operators have been interested in this project to the point where they are collecting wastewater samples on their own and submitting them,” he said.
Also, the state public health department had a carrier system set up to deliver samples to a central location, which saved money on postage and shipping.
“We received a grant from the NIH at the beginning of the year which allowed us to do a bit more research and really get a good jump on this,” Wenzel said.
In Missouri, sewershed testing reveals good news about Covid
A device called an autosampler takes a sample from sewage at each participating facility. The autosampler takes a small sample every 15 to 30 minutes, eventually adding up to a liter of sewage water in the course of a day.
A wastewater operator splits the wastewater sample into vials and sends it to the lab in Mizzou to be processed.
Once RNA is extracted, researchers analyze the samples through different tests.
The first type of test is like a human PCR test, Wenzel said. But where a human PCR just looks for a positive or negative result, this test tries to measure the total amount of viral particles in the wastewater sample. A targeted version could also be used to look at the amount of one specific variant if there is a sample that is suspicious, said Johnson.
For this type of test, results come back quickly, within two to three days. When there is a spike in the amount of COVID-19 viral material in wastewater, there is usually a spike in cases in humans about four to six days later, Wenzel said.
The lab uses a different test called high throughput sequencing to look for COVID variants. The test looks at specific sections of the virus’ RNA.
“We’re not looking at the whole RNA, but we’re looking at those positions where mutations are occurring and making assumptions that if we’re seeing those key mutations in known locations that it’s likely or probable that’s the variant,” Wenzel said.
Getting variant testing results takes about 2 weeks, which is longer than getting viral load analysis results.
There are also some unknowns with the high throughput sequencing.
“We’re looking at segments, we’re not looking at RNA strands, so we’re never going to be 100% positive that the variant we’re saying is probable or possible actually is that variant,” Wenzel said. “And with high throughput sequencing, we’re not able to get a real measure of how much.”
Also, high throughput sequencing isn’t able to measure how much of a variant is present, just whether or not it is detected.
Currently, the presence of COVID-19 variants isn’t changing public health actions, said Wenzel.
That’s because although variants are present, the sewershed monitoring shows positive changes. The total viral load, or amount of COVID-19 present in the sewage, is declining, Wenzel said.
“Our actions that we’re doing are working,” he said. “Continue to go out there and become fully vaccinated if you’re not already, continue to be tested if you’re not feeling well. And then any local recs or ordinances there might be, please follow those.”