California variant of the coronavirus identified in Marin, Lake counties

As health officials struggle to contain the coronavirus and immunize Americans as a line of defense against its ravages, all have kept a close eye on the “variants” — self-perpetuating mutations that could potentially make the virus more transmissible, more deadly to humans or more impervious to vaccines.

At least one of those mutated viruses is already at our doorstep: the so-called “California variant,” which has been detected in both Marin and Lake counties, according to data compiled by GISAID Initiative.

The full meaning of the California variant’s presence in areas that neighbor Sonoma County isn’t clear. Dr. Kismet Baldwin, the county’s deputy health officer, said she had no information on this strain of the virus or its level of risk.

There simply hasn’t been enough research on this variant to know how it compares to the globally dominant strain of the virus that was first detected in Wuhan Province, China, in January 2020.

“The early data indicates this is maybe more transmissible,” said Dr. Patrick Ayscue, a senior biosecurity fellow at the Chan Zuckerberg Biohub. “But we’re not seeing a clear signal yet.”

There is obvious reason to take this seriously.

Early studies have indicated that another coronavirus variant, the B117 strain first identified in the United Kingdom, is significantly more contagious, a factor that could have disturbing implications for the 6-foot social distance rule that has shaped our interactions in the past year. The rise of the California variant, known to scientists as B1429, has coincided with the “second wave” of the virus, a deadly winter season that has seen transmission rates skyrocket across the state. Cases are only now beginning to ebb in Sonoma County, which withstood its highest daily case rates of the pandemic during December and January.

Ayscue cautions against assuming causality in the winter surge.

“The question is,” Ayscue said, “was (the California variant) contributing to the surge, or was it just riding the wave? Maybe it was already in circulation, then everyone went on holidays and rates exploded.”

Lake County Health Officer Dr. Gary Pace noted in a statement that two other coronavirus strains have been labeled “variants of concern,” while B1429 is merely a “variant of interest.”

How can a variant be detected?

Genetic researchers at UCSF’s Chiu Laboratory first identified the California variant in Los Angeles County in mid-July. Data suggests it spread at a minimal rate until the beginning of November, when it began to claim an increasingly larger share of coronavirus infections in California while fanning out to locations as distant as New York City, South Carolina and Seattle.

Between Dec. 14 and Jan. 3, about 25% of the coronavirus samples (37 of 147) analyzed by the Chiu Lab revealed the California strain, according to the San Francisco Chronicle. Gov. Gavin Newsom said Wednesday that 1,203 samples of “West Coast variants” have been identified in California thus far. That includes a closely related strain called B1427, but would mostly be made up of B1429.

An interactive map on the website Outbreak.info based on GISAID data shows that four cases of the California variant have been found in Lake County, at least one of them during the week of Dec. 7, and one case in Marin, discovered the week of Dec. 14.

“The state is doing surveillance testing on specimens from different areas around the state,” Pace said. “Meaning that they randomly pick some specimens that are sent to Quest or another lab, and do the genomic sequencing. In early January, (the state) sampled 40 specimens, and nine of them had the California variant.”

There may have been additional cases in those counties, though, or even some in Sonoma County, according to Alaa Abdel Latif, a research programmer at Scripps Research, which manages Outbreak.info. Latif noted that a large portion of coronavirus data submissions in the United States are missing county information.

Genetic information doesn’t show up in a typical coronavirus swab test. To isolate a particular strain, the sample must be sent to a research lab for genome sequencing, a layer of time and cost that most local health offices can’t manage. Yet there is tremendous interest in identifying variants, for a couple of reasons.

One is using the information in contact tracing.

“If I see what appears to be an outbreak at a meat packing plant, or a school, or a jail, there’s a common question,” Ayscue said. “Am I looking at spread within a facility, or am I seeing multiple individuals bringing in the virus from the community. It acts as breadcrumbs, essentially.”

If the virus samples have the same or very similar genomes, it was probably transmitted at the site. If the genomes are varied, they are more likely to have come from different sources.

How will the variants affect vaccination efforts?

The other primary factor driving research into coronavirus variants is vaccinations.

The major mutations detected thus far have affected the spike proteins that give the coronavirus its name. It is these spikes that allow the virus to bond to human cells. There are alarming implications for the vaccination effort, since mRNA vaccines like the ones currently being produced by Pfizer-BioNTech and Moderna work by creating dummy spike proteins to stimulate the body’s natural antibodies.

Recent clinical trials demonstrate that the Novovax vaccine is less effective against the B1351 strain first found in South Africa, while the Pfizer vaccine is slightly less effective against it and Oxford-AstraZeneca offers only minimal protection. (Novovax and AstraZeneca have not yet been approved by the Food and Drug Administration for use in the United States.) The results were so bad that South Africa delayed its vaccination program this week, stranding a million doses of AstraZeneca.

The first two incidences of the South African variant in California were reported Wednesday, Newsom said, in samples from Alameda and Santa Clara counties.

It’s no surprise the virus would be undergoing these changes, because viral mutations are common. It’s the way they evolve and survive.

“As a virus spreads through communities and more people become infected, individuals and their immune systems are constantly putting the virus under pressure to mutate, escape and become infectious despite the immune response,” explained Dr. Phil Febbo, senior VP and chief medical officer at the genetics company Illumina. “You will start to see more and more over time.”

The Pfizer and Moderna vaccines are described as adaptable. They can be altered to combat new threats. But in a game of biological Whack-a-Mole, the question is whether coronavirus variants can be discovered and sequenced quickly enough to allow the vaccines to stay a step ahead. It has become a race between mutations and vaccinations, with lives in the balance.

Febbo said Moderna is already working on a booster shot that includes strains closely related to the South African variant. If we are doing proper sleuthing, he said, we have all the tools we need to contain this virus.

Sonoma County has begun participating in the CDC’s NS3 genotyping program, Baldwin said, but has not yet received any results from the submitted samples. She said she hopes the county lab soon will also be linked to a state-level genotyping program called COVIDNet.

The genetic researchers say the United States is making big strides toward tracking these variants, but has been hampered by the lack of a centralized research system and robust channels for data to be shared among labs and medical providers.

“We’re not doing enough surveillance of viral genomes to be able to detect when a new strain emerges,” Febbo said.

You can reach Staff Writer Phil Barber at 707-521-5263 or phil.barber@pressdemocrat.com. On Twitter @Skinny_Post.