Home Trade school Tracking COVID-19 with dust at Ohio State University

Tracking COVID-19 with dust at Ohio State University

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NORTHAMPTON, MA/ACCESSWIRE/October 18, 2022/ When COVID-19 hit, most of Ohio State University, home to the Buckeyes in the state capital of Columbus, closed. But the Applied Microbiology Services Laboratory (ASML) within its Infectious Diseases Institute (IDI) remained open.

“The Buckeyes are amazing students,” says Seth Faith, who is executive director of the Center of Microbiome Science and strategic alliance manager for the IDI, but who also oversees the lab. “Many of them are hungry and passionate. At least one person working in the lab had family in Wuhan, China, and they hadn’t seen their family in two years. They wanted to be part of solving the problem. this pandemic.”

Over the next two years or so, AMSL employed 88 lab workers at various times, who administered over 850,000 PCR diagnostic tests for COVID-19, with an average turnaround time of 8.75 hours.

Meanwhile, an OSU professor named Karen Dannemiller had been visiting homes and businesses looking for toxic chemicals in the built environment. It was also looking at microorganisms that could cause allergies or otherwise affect human health.

In the fall of 2020, Dannemiller and his team traveled to campus isolation rooms, where students who had tested positive for COVID-19 stayed for seven to 10 days. They entered into a search protocol to see if they could find coronavirus in the built environment. Indeed, through PCR testing, Dannemiller and his team discovered that the highest loads of coronavirus were present in the vacuum bags collected during carpet cleaning in these rooms.

“We can literally walk into any room, any building, any floor and know what it’s all about.” – Seth Faith, Institute of Infectious Diseases

Dust collection

Faith explains that with a respiratory virus, a person exhales particles that will land in the space around them, without necessarily entering the HVAC system: “Biological materials have a charge associated with them and they accumulate. That’s what dust is. The virus gets entangled in it, and we can detect it with lab technology.” He contacted Dannemiller and suggested making his experiment operational. “We optimized his protocol. We made it more responsive. We made it more efficient, more streamlined, and then found a way to help bring the data back.”

Each week, they performed PCR tests to measure the relative rise and fall in virus levels from dust collected from different floors of strategically chosen buildings on campus. But Faith wanted to push the tests a little further. He proposed that they produce the virus sequence information to understand not only the level of viral load, but also the variants present on campus. His genomics team therefore modified his existing COVIDSeq protocol on his NextSeq2000 for environmental samples and produced complete SARS-CoV-2 genomes completely resolved from the dust. And sure enough, when levels of the omicron variant rose in their student population, they found the same pattern emerging in the dust.

“Take a building like a fourteen-story library,” Faith explains. “Where would you expect the virus to be spread? Most people guess at the lobby. That’s not what our data shows. The lobby actually has one of the lowest levels of viral load, and the highest levels are where people spend an extended period of time, and probably unmasked.” They now have a lot of data taken at a time when the university needed masks, and it shows that students who made themselves comfortable and even ate in study areas were more likely to put the virus on. in the environment where the laboratory would detect it.

OSU has given the go-ahead to fund weekly sample collection at strategic sites and lab processing through summer 2023. “This will help us immensely, as all testing of people is voluntary at this stadium. We have this huge data loss. people per day to test 10, so we don’t know the breakdown on campus. This health surveillance fills that gap.

Faith is delighted that the sequence information can be obtained through a targeted but non-invasive method. And since they’re using what’s in the waste stream, it draws a parallel with wastewater monitoring. “Vacuum bags just go in the trash. And now we’ve found a way to take that trash and give people public health data.”

Faith also plans to add flu testing to the scope of her project. In 2021, Dannemiller won an NIH grant to implement coronavirus and flu testing in Columbus elementary schools.

Among their other projects, AMSL recently received a $700,000 grant to continue to sequence wastewater samples from more than 60 wastewater treatment plants and 10 universities in Ohio and submit the data to the national system. wastewater monitoring.

Pictured: OSU student Austin Shamblin with full-time technician and OSU alumnus Noah Kayafas; both co-lead the dust project.

Data for public health and the common good

“With every epidemic, we will need some sort of genomic technology to manage it,” says Faith. “The whole future of pathogen diagnosis is based on sequencing.” He envisions a future where airports or restaurants use dust monitoring to ensure public health safety.

In the meantime, Faith is excited to prepare her students for the future and the opportunities that AMSL provides. “I don’t know of any students with experience operating half-million-dollar instruments or dealing with terabyte-sized datasets.” He plans to focus on helping students learn skills in bioinformatics. “Illumina has made sequencing accessible to everyone. The first step was on the lab side: anyone can create data from a NextSeq. But now we want students to be able to analyze and report large datasets .

“Since OSU was established as an engineering and business school, they’ve had 150 years to figure out how to train people in what used to be the Ohio industry. Both Ford and Honda have a big presence, and our engineering school is doing a really good job of finding opportunities for these students to interact with the automotive industry and solve problems. But now biotechnology is exploding. I feel like that biology is having its engineering moment.

That’s one thing an engineer can’t tell you: if there’s a virus hovering in the Hoover, or the delta variant in the Dyson.

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Illumina, Tuesday, October 18, 2022, Image from press release

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