This coming Monday, Jan. 31, marks the resumption of in-person instruction at UC Santa Barbara after nearly a month of remote learning for the beginning of winter quarter. The two weeks of remote instruction were intended to mitigate a spike in COVID-19 cases that campus medical experts predicted was imminent upon students’ return from winter break. Indeed, cases in Santa Barbara County peaked at 1,493 on Jan. 13. From Jan. 18-31, it has been up to instructors to decide whether remote or in-person instruction is more adequate for their respective courses.

The prevalence of the omicron variant especially — which accounted for 37% of positive results in Santa Barbara in January — has fostered collaboration between the UCSB COVID-19 Response Team, local health care providers, the Santa Barbara County Public Health Department (SBCPHD) and UCSB’s own graduate students, with the goal of facilitating students’ return to campus. 

One of the most important collaborations was an assay that could detect whether a positive COVID-19 test result was of the omicron variant or not, developed by graduate student researcher Zach Aralis — from the biomolecular science and engineering program in the molecular, cellular, and developmental biology department — who was overseen by MCDB-affiliated researcher Carolina Arias.

Aralis had been working on SARS-CoV-2 research since the beginning of the pandemic, specifically working with the team that helped develop an assay for the general detection of COVID-19 and applied it for early outbreak detection in Santa Barbara. Then, he helped establish the COVID-19 clinical testing laboratory on UCSB’s campus — which he still manages and runs samples for to this day. In addition, he established Santa Barbara’s protocol that is used to help provide sequencing results for monitoring local COVID-19 variants. 

The omicron variant of COVID-19 is significantly more contagious than other previously prevalent variants (such as the delta variant), leading to a heightened necessity to distinguish the variant. Arias and Dr. Lynn Fitzgibbons, an infectious disease specialist at Cottage Health, contacted Aralis to see how quickly he could put together an assay to do just that. 

One of the most important collaborations was an assay that could detect whether a positive COVID-19 test result was of the Omicron variant. Courtesy of Pennsylvania Department of Health.

“[Because the campus was closed,] the main issue was acquiring the reagents needed for testing of the assay,” Aralis said. “I had to have the custom primers I designed delivered to my apartment. For everything else, I just had to make do with what was lying around in the lab.” 

Aralis said that this limited his options and dictated some aspects of the assay designs. Still, just a few days before Christmas, Aralis got to work. 

“The design was fairly simple in theory,” Aralis said. “I chose to develop a qPCR assay that would target a region of the SARS-CoV-2 genome that was heavily mutated in only the omicron variant.” 

After he found a suitable region, Aralis’ next step was to design two sets of primers that would bind to and amplify that region only when RNA from omicron was or wasn’t present in a sample. 

“Once I had these primers, the only thing left to do was optimize the reaction conditions to maximize our specificity and sensitivity,” Aralis said. 

After a day or two of refining and optimizing, Aralis said that he had his first set of results. 

“While many of us suspected that the dramatic increase in positives in Santa Barbara were due to omicron, we really didn’t know for certain,” Aralis said. “Unsurprisingly, most of the samples provided by County Public Health and Pacific Diagnostic Laboratories were omicron.” 

The development of this assay has helped inform physicians in the county on the approximate prevalence of the omicron variant in Santa Barbara. Distinguishing between variants of COVID-19 could be key to preventing the overrun of health care workers as cases – and unavoidably hospitalization rates — rise. 

“From a clinical perspective, it’s important to note that this assay is a research tool and should not be used to directly impact patient treatment,” Aralis said. “This in turn has helped give them confidence in what treatments the county should use for treating COVID-19 patients.”