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)

February 10, 2021 | Nick Ibarra, Mallory Pickett | Lookout Santa Cruz

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.

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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