COVID-19 Variants Identified in Santa Barbara County

And They’re Not Yet the Scary Kind, Cottage and UCSB Scientists Say

Microbiologist Carolina Arias’s lab at UC Santa Barbara is using genome sequencing of COVID-19 samples from Santa Barbara County to find variants, an essential tool in planning against the coronavirus. Here, post-doctoral fellow Becca Best works with a virus sample. | Credit: UCSB

Carolina Arias has worked with disease-causing bacteria and viruses her entire career, some of them more dangerous than others. In the past week, packages with a neon-orange biohazard label have arrived at her lab at UC Santa Barbara containing samples of the SARS-CoV-2 coronavirus, a pathogen so contagious it caused a worldwide epidemic in mere months.

UCSB microbiologist Carolina Arias. | Credit: Courtesy

The virus that causes COVID-19 has been evolving, as viruses will do, and it is these genetic mutations that Arias’s lab is decoding. Some of the new variants are merely interesting to scientists, but others are highly concerning to both clinicians and public health officials.

For the dozens of Santa Barbara doctors, researchers, administrators, and public health officials who are forming plans against the arrival of dangerous variants, Arias and the expertise she lends is the core of the action. California’s variant lab has thousands of samples to deal with, and it took two months to return a handful of results to Santa Barbara. Within a week’s worth of work, Arias was able to announce on Thursday early results from 29 samples.

So far, the variants that have made it to Santa Barbara aren’t classified as the dangerous ones that are more contagious or cause reinfection, but that’s just a preliminary assessment, cautioned Dr. Lynn Fitzgibbons, a member of the Local Variant Task Team. The examined samples — from Cottage Health and UCSB — contained no variants labeled “concerning” by the Centers for Disease Control, such as the English variant called the B.1.1.7, the South African one labeled the B.1.351, or the Brazilian mutation, the P.1.

Dr. Lynn Fitzgibbons, Infectious Disease specialist at Cottage Health. | Credit: Daniel Dreifuss (file)

“Interestingly, 16 of the 29 are identified to be the West Coast variant,” Fitzgibbons said during a conference call on Thursday. That’s the preferred moniker for a variant also known as CAL.20c and B.1.427/B.1.429. The newly identified New York variant, or B.1.526, had not shown up yet.

In California as a whole, the West Coast variant is the most prevalent at the moment, outstripping the quickly spreading U.K. variant. It’s moved into 19 states and six countries, according to a February study by Cedars Sinai, and it seems to be an easy spreader but is not yet confirmed to be more deadly or resistant to vaccines by the CDC. However, a new study from UC San Francisco indicated it had caused severe or terminal illness in a small but statistically significant number of patients, and that a higher viral load in nasal passages indicated its transmissibility. The paper is not yet peer-reviewed but was widely anticipated. Some have noted the study period coincided with the height of the holiday surge when hospitals were beyond peak capacity, which could account, in part, for the severe outcomes.

The mutation became prevalent around last October, shortly before the case rate shot upward in both the state and Santa Barbara County. Fitzgibbons, who is an infectious disease specialist at Cottage, observed that many things could have caused the increase, among them a variant, but it could also have been the holidays, the winter weather, or the premature opening of shops and businesses. At the time, after a long summer of closures, the political pressure was fierce to reopen.

Although case rates dropped as steeply as they’d risen, Fitzgibbons expressed worry they have leveled off at a high level. “It’s as high as during the summer surge,” she pointed out, “and nationally we saw a lot of suffering and a lot of death at that time.”

Significantly, Arias’s lab is sequencing the entire genetic code, more than 30,000 nucleotides, or the molecules that make up the DNA and RNA found in all living matter.

“The spike-protein sequencing that you hear about looks at 10 percent of the genome,” said Stuart Feinstein, a biologist who is instrumental in the COVID work at UCSB, who was also on the call.

Think of it like a song, Fitzgibbons continued: “Carolina’s incredibly sophisticated virology lab is giving us not just one section of the song, like the chorus, for example; it’s giving us every word in the lyrics.” But next week, next month, “undoubtedly a new variant of interest or concern will appear.”

Arias picked up the explanation: “Being able to see the entire sequence allows us to differentiate between them completely. We see all the mutations peppered throughout the genome,” which becomes important when new variants appear.

In fact, Cottage has banked past COVID tests, which could allow them to see when the variants became prevalent in the community, Fitzgibbons observed, as well as contain information about the ones we don’t know about yet.

A genome sequencer lists a sample’s DNA, which the lab compares against a database of hundreds of thousands of sequences to spot mutations. | Credit: UCSB

To get the minuscule virus to release its secrets, Arias and her lab partners — post-doc fellow Becca Best and graduate student Zach Aralis — neutralize the infectious samples, crack open the virus, extract its genome, and sequence the genetic data. The information comes out as a “long word composed of a combination of A, T, C, and Gs,” said Arias, the shorthand for the building blocks of DNA. “Typos” in the word could result in mutations that change the virus significantly. They compare their results against the hundreds of thousands of genome sequences for this virus that are in public databases, she said.

Asked about the odd variant names containing dots, Arias laughed and said virologists were terrible at coming up with names. The numbers indicate how the strains are related to each other, she explained: “Most of the variants circulating are the B.1 variants, which originated in the outbreak in Italy.” That includes the Brazilian variant, which was first called the B.1.1.28.1 — it contained so many new changes (and more dots in its name) it was renamed P.1 and considered a new lineage, Arias said.

The samples come from UCSB Health Services and Cottage Health, and they’ve invited Marian Regional Medical Center in Santa Maria to participate. But for the university, which has no medical teaching college, testing students has been a matter of surmounting obstacles. In December, by piggybacking on a small laboratory permit at Student Health, the school received approval for a full-scale COVID-19 testing lab, normally a two-year process they got done in four months. It took the combined effort of a group of more than a dozen departments and individuals, from the chancellor to the physics machine shop, to build the lab and be able to test people on campus regularly; a small number are resident students, and a staggered group of researchers continue to work in their labs.

Housed at UCSB’s Biological Nanostructures Laboratory, the work Arias’s lab is carrying out adds invaluable insight to the state of the pandemic in Santa Barbara County. She was optimistic about the return of normalcy in the future, mainly due to the vaccines available: “We had one vaccine and now there are three, all of which work amazingly well,” Arias said.

“Perhaps we can attribute the decreased cases to more people seeing the vaccine come closer and thinking, ‘It’d be such a shame to catch COVID now. The end is so near.’” People were being observant and careful as a result, she thought, saying, “This is the best moment not to let our guard down.”

Update: This story was updated to add recent information on the UCSF study of the West Coast variant and to amend the name of UCSB’s Biological Nanostructures Laboratory.

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