Missouri tracks spread of delta variant using wastewater

The COVID-19 delta variant is spreading rapidly through Missouri and state officials are turning to wastewater for answers.

The delta variant, which first emerged in India last fall, now accounts for about 10% of new virus cases in the U.S., according to estimates from the Centers for Disease and Prevention, and is hitting small, rural Missouri towns particularly hard.

Officials in Missouri have tracked COVID-19 and its variants since February by testing samples of wastewater from more than 50 communities across the state through the Sewershed Surveillance Project.

The initiative is a collaborative effort between the Missouri Department of Health and Senior Services, the Missouri Department of Natural Resources and the University of Missouri.

The delta variant first appeared in wastewater samples in the town of Branson on May 10. By the next week it appeared in a wastewater treatment plant across town and in the communities of Brookfield, located about 230 miles away, and Licking.

Linn County, which includes Brookfield, was not prepared for the spike and COVID-19 cases in the city "skyrocketed," according to Marc Johnson, a University of Missouri professor of molecular microbiology and immunology working on the project.

“At the end of April, [Linn County] stopped giving COVID updates because the cases were so low. They were getting like two or three cases a week, so they just quit reporting it. Since we detected this, they've had about 400 confirmed infections,” Johnson told ABC News, based on data from the Linn County Health Department.

"This is a county of 12,000. So that's about 5% of the population within the last six weeks," he added.

Wastewater testing showed the alpha COVID variant had a hold in big cities in the early spring. By May, the delta variant had taken over.

"It was faster than alpha. It really took delta only three weeks. We saw it and two samplings later it was present in the majority of the samples we collected," Johnson said.

And the presence of COVID-19 in wastewater is spreading. Viral load increased by 40% or more from last week, according to Sewershed Surveillance Project data.

Missouri had the highest percentage of the delta variant nationally as of June 5, with 21.9% of reported cases, according to the CDC.

Many of the cities seeing increased viral load include rural areas like Brookfield, St. Joseph, Warrensburg and Joplin -- regions already grappling from low vaccination rates.

In Missouri, 43.7% of the population has gotten at least one shot and 38% has completed the series, state department data show.

So, just how does this wastewater testing process work?

Chung-Ho Lin, a research associate professor at the Center for Agroforestry, Bioremediation Program at University of Missouri, told ABC News that his lab, which monitors human pathogens in wastewater, worked with Johnson's lab to analyze wastewater samples and quantify the viral load of COVID-19. Scientists distinguish variants using a process called quantitative reverse transcription polymerase chain reaction.

Lin said that viral load appears in wastewater "like seven days before any outbreaks."

“Since May last year, we have processed almost 9,000 samples across the state," Lin said. "We cover almost 125 facilities, including municipal wastewater treatment plants, also, wastewater treatment for mental health facilities, the university, nursing homes, training camps, you name it. So we basically cover almost 70% of Missourian population."

Researchers alert state health professionals so they can direct resources and curb outbreaks.

"I think we have successfully prevented several major outbreaks in correction facilities," Lin said. "From the data we generate, I’m confident somebody can benefit from that number the next day."

ABC News contributor John Brownstein, an epidemiologist and professor at Harvard Medical School, said wastewater surveillance has many benefits, including offering early warning signs of COVID-19 without violating privacy concerns. It's growing in popularity among state health departments.

"With wastewater surveillance you could target it at a very high resolution. And you can actually have more refined targeting and public health efforts. Prisons, nursing home, schools are great examples," he said.

The delta variant is a growing concern in the U.S. and was upgraded by the CDC last week from a "variant of interest" to a "variant of concern."

Officials in the state are now urging the public to get vaccinated.

"You're always better having the vaccine than not. The vaccine has at least some efficacy against all of the variants. If anything, that should be a reason to go get the vaccine," Johnson said.