Student-led project improves COVID-19 testing efficiency
Old protocol ‘required instruments that cost as much as my condo and required pretty specialized training to run,’ research coordinator says.
More than 15,000 University of Washington students, faculty, and staff have participated in the Husky Coronavirus Testing program since its start this past September.
But most of those participants likely are unaware of the backstory of how students working in UW Medicine’s Brotman Baty Institute helped develop a streamlined protocol to ensure rapid delivery of test results. Their efforts at bypassing cumbersome and costly procedures are explained in a scientific paper, “SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing,” published April 29 in the online preprint journal bioRXiv.
The work consumed hundreds of hours for Dr. Lea Starita, research assistant professor of genome sciences at the UW School of Medicine’s and co-director of the Brotman Baty Advanced Technology Lab, as well as for dozens of others, including numerous graduate and undergraduate students.
“When we started working in March of 2020, almost immediately the supply chain broke down. Everyone was trying to do the same test,” said Sanjay R. Srivatsan, the paper’s lead author, who later this month will defend his doctoral thesis on single cell genomics.
That supply chain included specialized long nasal swabs and specialized plastic tubes with a solution of salts, antibiotics, fungicides, and serum from bovine fetuses to preserve the nasal sample. Once the sample arrived at the lab, a technician needed to extract RNA, a nucleic acid inside the virus and human cells, from the swab. Next, the RNA would be transferred to a test tube and placed on a tray with other samples so the genetic material could undergo a molecular test on specially designed instruments and machines.
The new system, called “SwabExpress,” uses mass-produced nasal swabs and bypasses the requirement for transport media and nucleic acid extraction, according to the paper. Now a Husky Coronavirus Testing participant can simply stop by one of three kiosks, swab one inch deep in the nose with a less invasive 3-inch swab, then place it in a dry tube. No need to extract the RNA from the nasal sample. Rather, the swabs are rehydrated and incubated for 30 minutes. The remaining fluid is subjected to a molecular test called PCR (polymerase chain reaction).
“Our old pipeline required instruments that cost as much as my condo and required pretty specialized training to run,” said Peter D. Han, the research coordinator for Starita’s lab. “I could run most of SwabExpress with equipment available on eBay.”
Among the grad students working on the project was Sarah Sohlberg, who in June will complete her master’s degree in public health with an emphasis on health metrics and evaluation in the UW Medicine Department of Global Health. She is working in the lab of UW Medicine infectious disease specialist Dr. Helen Chu, who now leads the Husky Coronavirus Testing program and serves as a principal investigator of the Seattle Flu Study. Sohlberg’s responsibilities included writing how- to scripts for participants to help ensure the swabbing was done correctly.
“It was amazing to be a part of something cutting edge in COVID testing and research – and something that takes creative thinking and problem solving to get around those supply issues,” she said. “This team did an amazing job empowering and trusting students to do a lot of the important work.”
Several undergraduates participated in Starita’s Advanced Technologies Lab, including junior Maanasee Deshmukh, who is majoring in microbiology. Despite having worked in labs since high school, she admitted finding the work in Starita’s lab quite rewarding. She said it was “a little daunting at first – actually handling the virus real time,” but noted the long-term significance of the project.
“Downstream of what I do eventually permeates out.” she said. “And it’s a great thing to feel, knowing the work we do is ultimately saving lives.”
In addition, two roommates, Abi Elerding and Sadie Van den Bogaerde, contributed to the effort by helping keep the lab environment sterile. Their work included autoclaving glassware as well as processing incoming swabs for lab technicians to prepare for testing.
“What they do at BBI is really cool,” said Elerding, a graduating junior in microbiology who has been admitted for graduate studies in the UW School of Medicine’s Department of Pharmacology. “It was inspiring to see how they buckled down and refined this entire process to open up even more school districts for testing, and areas in Seattle for testing, and the on-campus testing sites to deliver fast COVID tests.”
The new protocol enables about 25 percent of the results to be delivered on the same day the samples are collected; the remainder in less than 48 hours.
Van den Bogaerde, a pre-med junior majoring in marine biology, was able to use her minor in Spanish for an interview on the project with Univision, the New York-based television network and the nation’s largest provider of Spanish-language broadcast content.
“I saw the importance of having communication with the public, not just the scientific community about science, and how hard that is to do well,” she said. “I realized there was really low enrollment [for COVID testing] in the Latino community, and how information we were trying to put permeated differently into different communities and trying to find ways to have equal access to that information for everyone.”
Srivatsan, the paper’s lead author, reflected on the bigger picture this endeavor has had regarding the imperative role science must play in society.
“Science and scientists can make a huge difference in the world with the work we do,” he said. “A lot of times it is not accessible to people, but there are moments in which we can be of great benefit to the world. People always associate research with impacts on the future we may not know, but this is definitely research that addressed the moment and met it.”
By the numbers: Husky Coronavirus Testing
(As of May 6, 2021)
- More than19,600 participants enrolled
- ~13,400 students
- ~4,500 staff
- ~1,500 faculty
- More than 86,300 samples tested from more than 15,600 individuals
- More than 550 positive samples detected
- More than 250 SARS-CoV-2 genomes sequenced
Written by Dean Owen, Brotman Baty Institute for Precision Medicine