COVID-19 tests are performed UCSC Molecular Diagnostic Lab.
COVID-19 tests are performed UCSC Molecular Diagnostic Lab, from which positive samples will be curated for genetic sequencing starting later this month.
(Carolyn Lagattuta / UCSC)
COVID 2022

UCSC gears up to to begin search for COVID-19 variants in Santa Cruz County

Genetic sequencing of virus samples sourced from the campus and partner clinics is set to begin by the end of February, providing a new surveillance tool that has the potential to detect variants and chart the pandemic’s progression here.

While new and potentially more contagious COVID-19 variants continue to crop up across California, not a single such case has been confirmed in Santa Cruz County. But that might only be true because — until now — no one has been looking.

In coming weeks, that’s set to change. The Genomics Institute at UC Santa Cruz is gearing up to begin routinely sequencing the genetics of virus samples for the first time, using positive tests from the campus and its partners across the county.

Routine sequencing is on track to begin by the end of February, according to researchers and campus officials — starting at a pace of about 100 samples per week, with the aim of quickly expanding.

The work has potential to impact the local response to the pandemic in several ways. Not only will UCSC be able to detect new variants of concern, but sequencing could also enable clinics to track the path of the virus with a level of precision that goes beyond traditional contact tracing.

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And once researchers have sequenced all recent positive samples, they will begin working their way backward in time through positive tests analyzed by UCSC’s diagnostic lab since last spring, according to Miten Jain, a UCSC research scientist closely involved in the effort.

“It will help in understanding how the pandemic progressed, it will help in understanding where it might be going — and certainly help in understanding what the implications immediately are, because you can start looking at what strains are moving and what are the hotspots,” said Jain.

“In the absence of that,” he added, “you’re flying blind.”

Genomic sequencing is akin to “reading” the DNA of an organism by revealing its complete sequence of genes. A typical COVID-19 test, by contrast, is more like a light switch — positive, or negative. That’s useful to know whether a person is sick, but sequencing allows scientists to examine the genetic signature of a particular person’s infection.

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Viruses like SARS-CoV-2 are mutating all the time, and most mutations don’t affect how the virus interacts with its hosts. The small genetic differences caused by those mutations can enable scientists to track different strains of the virus as they move through a population. In some college towns sequencing has demonstrated that COVID-19 was spreading from university students to community members off-campus.

Without sequencing, “We were just operating with the idea that we have X number of positives,” said Jain. “That’s not the whole picture — we need to understand what those positives represent. And the community needs to know so that people are aware of what’s happening.”

It’s information that doctors such as Amy McEntee, the chief medical officer at Salud Para La Gente — one of UCSC’s partner clinics — are eager to have.

In the fall, the Watsonville medical clinic encountered one particular cluster of cases at a workplace that left doctors baffled and wishing for a clearer genetic picture, according to McEntee. All proper mitigation measures were followed, she said — masking, social distancing, hand washing and isolating while sick. “And yet we still saw a number of employees contract an illness,” said McEntee. “We were confused by it because all mitigation strategies were used, so that’s what just made us wonder.”

Salud Para La Gente has an existing partnership with UCSC to run its COVID-19 tests, typically on a scale of a couple hundred tests each week.

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Discussion about expanding the partnership to include genetic sequencing kicked into a higher gear amid the emergence of virus variants, with the nonprofit health clinic formally requesting UCSC begin genomic sequencing late in December. “Right now, everybody wants to know about the variants,” McEntee said.

Because of patient privacy concerns, results from UCSC’s sequencing will have some limitations. Data reported back to the Santa Cruz County Public Health Agency will be anonymized and reported in aggregate based on a partial Zip Code, so health officials will likely only be able to see whether and when certain variants are present in the community.

Long a hotbed of genomics research, UC Santa Cruz has played a major role in compiling and analyzing the genetics of COVID-19 since the early days of the pandemic. It hosts a public database of genetic profiles collected from samples across the world via its Genome Browser, which includes a dedicated interface built specifically for the SARS-CoV-2 virus that causes COVID-19.

View of SARS-CoV-2 genomic datasets in the UCSC Genome Browser.
View of SARS-CoV-2 genomic datasets in the UCSC Genome Browser.
(UC Santa Cruz)

The campus has also played a significant role in running a high volume of COVID-19 tests for students and staff as well as several partner clinics in the surrounding community, including Salud Para La Gente, the county jail, and Santa Cruz Community Health Centers.

“Our overall view is that we know this pandemic is clearly a crisis, we all need to contribute,” said Isabel Bjork, executive director of the Genomics Institute. “And the more information that we can get out there for all the brilliant people who can analyze it and figure out solutions — that’s our duty. That’s what we need to do.”

Across the U.S., health officials are now rushing to improve genetic surveillance of the virus, but currently only a few thousand samples are sequenced per week in the entire country. In California, only 13,138 virus samples have been sequenced to date, according to the CDC.

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In Santa Cruz County, no significant genetic sequencing of COVID-19 samples has taken place to date, according to deputy health officer Dr. David Ghilarducci.

Underscoring the desire for more genetic surveillance, two cases of the potentially more transmissible variant that originated in South Africa were reported in nearby Santa Clara and Alameda counties on Wednesday — the first cases of that variant confirmed in California so far.

Ghilarducci said he was “not surprised at all,” by the finding, and thinks it’s plausible the variant is already circulating in Santa Cruz County as well.

“I don’t want people to get too worried,” he said. “I think the current vaccines are probably going to cover us well. But we should fully expect that this virus like many others will continue to mutate.”


12:53 PM, Feb. 11, 2021: On Thursday morning, Lookout heard from Dr. Ghilarducci that he had been misinformed and the county has not, in fact sent any samples to a state lab for sequencing, as was stated in the original story. Ghilarducci said that “we have had a handful of cases that we wanted to have sequenced but in most cases the sample was discarded before we had a chance to retrieve it.” The story has been updated to reflect this information.