How Cal Poly created its own COVID testing program from nothing to full use in 1 year
It has been nearly a year since Cal Poly transitioned to fully virtual learning for its spring term and the San Luis Obispo university reported its first COVID-19 case.
Now, the university has reported more than 1,500 coronavirus cases among students and employees, and is still conducting the majority of its classes online.
But in that year, a team of scientists at Cal Poly saw the coronavirus pandemic as a chance to apply their skills and those of their students — in the ultimate learn-by-doing assignment.
“I feel like you don’t always get the chance to be heroes,” Jean Davidson, an assistant biology professor at Cal Poly, told The Tribune in an August interview. “We have the equipment, we have the protocols — can we get a large-scale, COVID-19 testing program running in our labs?”
Since then, Davidson and the five other scientists at the forefront of Cal Poly’s COVID-19 testing response — Chris Kitts, director of the university’s Center for Applications in Biotechnology; Pat Fidopiastis, a microbiology professor; Javin Oza, an assistant biological engineering professor; Nathaniel Martinez, an assistant biology professor; and Jen VanderKelen, a staff scientist — have been hard at work.
“It was such a Wild West in the beginning,” Davidson said during a tour of Cal Poly’s COVID-19 testing labs on March 2. “Everyone was building their own protocols. So we spent a lot of time reading and calling other universities and seeing what they’re doing. And then we looked inside, instead of just mimicking another university and buying all the things they bought.”
The team has created exactly what Davidson envisioned: a large-scale COVID-19 testing program that will serve the entire university’s student and employee population that comes to campus or needs a test.
What began as a concept in the early days of the pandemic has now been in full operation since Feb. 25. Asymptomatic students are now tested solely through Cal Poly’s in-house COVID-19 saliva testing method.
On-campus labs can test thousands for COVID-19 per day
The university professors work hand-in-hand with students to deliver quick, accurate COVID-19 test results to the roughly 9,000 students who are estimated to need tests twice every week in order to be on campus.
Right now, the lab is receiving about 600 to 1,000 tubes of saliva per day but has the capacity to ramp up to about 4,000 per day. Those samples come from students and employees who spit into small vials that are then carted over to the lab.
Once in the lab, those samples are pooled together in groups of five, meaning that five samples are mixed into one small vial using a robot.
If one group comes back positive, university scientists will retest individually to see which sample caused the positive result.
This is to save money, Martinez said during the lab tour.
“We do this so that we can capitalize on the real estate — it’s a small real estate — as well as on reagents,” Martinez said. “The cost is per reaction, and therefore we can get five into one.”
Reagents are chemicals used to determine whether COVID-19 exists in a substance — such as saliva. Since the start of the coronavirus pandemic, the reagent needed for COVID-19 tests has been in short supply as demand skyrocketed.
That’s the case with most materials needed to conduct large-scale surveillance testing for the virus. Cal Poly found that in April and May, when university scientists first approached the administration with their ideas for creating the testing program, getting its hands on the necessary vials and machines was difficult.
So, Cal Poly contracted Avellino Lab USA Inc. to get its initial nasal swab-based surveillance testing method up and running, allowing university scientists time to teach summer classes, build up supplies and hone down the specifics of their own testing program.
Cal Poly’s saliva testing program is far more efficient than Avellino Lab’s because it is done in-house. Previously, COVID-19 test results were often returned to students and employees up to 48 hours after they had taken the test.
Now, with the saliva testing program, it can take less than 24 hours for results to come back.
“Because of the nice infrastructure that we’ve built on campus to integrate with Campus Health and Wellbeing, that (test result) information immediately does something,” Davidson said.
Students can be notified within that 24-hour window whether they need to take another test due to an abnormal result, or whether they need to go into isolation or quarantine much quicker than they were able to before the saliva-based testing program was implemented, Davidson said.
That rapid turnaround prevents sick students from potentially spreading the virus to others while waiting for their test results to come in.
Additionally, Cal Poly’s saliva testing method is extremely sensitive as each test can detect three virus particles per microliter, Martinez said.
“Clinical significance usually doesn’t start until around 1,000 to 3,000 virus particles per microliter,” he said.
Cal Poly tests wastewater from on-campus housing for signs of coronavirus
To supplement the saliva-based testing program, Cal Poly has also begun testing the sewage at five locations around campus. The wastewater is drawn up from pipes below the ground.
Fidopiastis, who oversees the wastewater testing program, said that the wastewater from about 500 to 1,500 people is collected per location. So, every time a student flushes the toilet in one of the on-campus dorms, Fidopiastis may see a bit of what they ate in that sample.
The wastewater testing program is designed to catch potential COVID-19 outbreaks before they happen, and it’s extremely sensitive.
“In some results we get, the value is negligible,” he said during the March 2 tour of the labs. “So you can see the machine will tell you it’s positive, but we know intuitively that it’s negative — that it’s somebody who was infected three months ago or four months ago, that’s long since recovered and may be pooping out little bits of dead virus.”
So Fidopiastis found a threshold of the amount of detected virus per sample that determines whether “alarm bells should go off,” he said.
If that threshold — about 1 million virus particles per liter — is surpassed, he tells the saliva lab, which can then go and quickly test all of the students living in the dorm where the sewage sample was collected.
Cal Poly already had most of the material needed for the COVID-19 testing labs, though some materials did have to be purchased, according to the university.
Cal Poly’s test is designated as a Laboratory Developed Test by the U.S. Food and Drug Administration, according to university spokesperson Matt Lazier, meaning it was developed following procedures outlined by the FDA, created, tested and validated against existing tests.
Davidson said creating the in-house testing method has been a difficult but fulfilling task for the team of Cal Poly scientists.
“One of my favorite parts about this whole thing is everyone sort of brought their skill sets towards the solution. And when we needed a new machine shop, a new data resource, new robotics — there was someone on campus who could come in and support that,” Davidson said. “So it was really like everything existed. ... And there were these incredible microbiologists and virologists, and we just kind of put them all together to build this out.”
This story was originally published March 8, 2021 at 5:00 AM.
