View of SARS-CoV-2 genomic datasets in the UCSC Genome Browser.
View of SARS-CoV-2 genomic datasets in the UCSC Genome Browser.

(Courtesy UC Santa Cruz)

No ‘variants of concern’ in first Santa Cruz County tests, though bulk of samples show California strain

UCSC has just completed its first sequencing of 84 COVID-19 samples from Santa Cruz County. Similar to the rest of the state, 65% of them show the worrisome — but not alarm-worthy — California strain.

UC Santa Cruz scientists said Monday that they had completed genomic sequencing of 84 COVID-19 samples from Santa Cruz County, with none of the CDC’s three official “variants of concern” turning up.

But approximately 65% of the samples contained the so-called California variant, known as B.1.427/B.1.429, that is creating worries — though not quite sounding alarms — in the medical community.

County health officer Dr. Gail Newel cautioned that scientists really don’t know much about this variant yet. “Preliminarily, we think that it may be more transmissible and maybe more lethal,” she said, “but not enough is known.”

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Dr. Russ Corbett-Detig, whose lab led the analysis of the sequencing data, said the UCSC findings are “reasonably consistent with findings from other counties in California.” He echoed Newel’s statement that the “the jury’s out,” on whether the variant is more transmissible, or more lethal.

He also advised the public not to “freak out” about the California variant, but also noted that it’s reason for the public to continue following physical distancing, masking and other virus control guidelines.

Scientists at UC San Francisco have said the California strain spreads more easily than its predecessors and is now dominant statewide. In laboratory tests, it was shown to be less vulnerable to antibodies generated by COVID-19 vaccines or by prior infections.

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But Corbett-Detig said he is hopeful that the vaccines will be reasonably effective against the California variant, based on their performance against the official variants of concern.

Regardess, the California strain has not made the CDC’s list of “variants of concern.” Those variants are B.1.1.7, the variant first detected in the UK, B.1351, the variant first detected in South Africa, and P.1, the variant first identified in Brazil.

Newel said she was “really surprised,” B.1.1.7 wasn’t detected because at one point, “it was expected that by the end of March, that would be the predominant variant in in the Bay Area and all of California.”

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The UCSC Genomics Institute is ramping up its sequencing, and is now able to sequence 90 tests per week, with plans to ramp that up 200 soon. The samples will be taken from the COVID-19 tests that the university processes for a number of clinics around the county.

Newel added that a state lab is also doing sequencing, and that officials there are expected to develop and publish a map soon that will show where the different variants are.