Over the past few weeks, California’s Covid-19 numbers have dropped dramatically, easing fears of a continued surge in cases. But state health officials have also begun to warn about the spread of new variants of the virus that may be more adaptable and/or more vaccine resistant.
The first of these is B.1.1.7, also known as the UK variant. B.1.1.7 is thought to be about 50% more transmissible. Los Angeles County health officials identified the first case of B.1.1.7 in the region in mid-January but, according to CA Health and Human Services Director Dr. Mark Ghaly on Tuesday, the strain is “not rapidly increasing” in the state. Ghaly said that 133 cases have been recorded to date, “largely in the southern part of the state.” But there is another strain of the virus that’s lesser-known and more widespread in the state.
Dubbed variously B.1.429 and B.1.427 or the West Coast Variants, or sometimes called CAL.20C, the new strains are still mostly a mystery.
Dr. Charles Chiu, a virologist and professor of laboratory medicine at UCSF who, in concert with state authorities, has been genetically sequencing test samples to identify new variants said early indications are the CAL.20C might be less susceptible to the currently approved vaccines, but more investigation is needed.
“This variant carries three mutations, including L452R, in the spike protein, which the virus uses to attach to and enter cells, and is the target of the two vaccines that are currently available in the United States,” said Dr. Chiu. A spike protein mutation could, then, interfere with the vaccine’s efficacy. Given that spike protein’s importance, L452R is another name sometimes used for the West Coast Variants.
Asked about vaccine resistance, Ghaly was more circumspect saying he was, “Unclear about its exact role in either making people sicker or its impact on things like vaccine.”
Ghaly did reveal, however, that the state had over 1,000 cases of the West Coast Variants. That’s far more than the much-talked-about UK variant. More specifically, Ghaly revealed on Tuesday that the state had identified 767 instances of B.1.429 and 290 cases of B.1.427.
“This variant was identified in several large outbreaks in our county,” said Santa Clara County Health Officer Dr. Sara Cody in January. She called that correlation “a red flag and must be investigated further.”
The West Coast Variants also have been detected in Los Angeles, Mono, Monterey, Orange, Riverside, San Francisco, San Bernardino, San Diego, San Luis Obispo, Humboldt and Lake counties. Because genomic sequencing is sparse, it is currently unknown exactly how prevalent L452 is statewide, nationally or globally.
Dr. Chiu said L452R grew from about 3.8% of the samples he tested in late November 2020 through early December to more than 25.2% in late December through early January 2021.
Eric Vail, the director of molecular pathology at Cedars-Sinai, told The New York Times that CAL.20C may have played a part in the surge in cases that overwhelmed Southern California’s hospitals earlier this month. “I’m decently confident that this is a more infectious strain of the virus,” said Dr. Vail.
Scientists are concerned about L452R because it might help coronaviruses stick to human cells and infect them more readily.
Dr. Vail and other researchers in the state say that the L452 mutations they have found were always alongside four other specific mutations. That unvarying arrangement was a strong sign of a single lineage “native” to California.
Cedars researchers discovered CAL.20C in July. As far as limited genetic testing could detect, the variant didn’t appear in Southern California again until October. At the time, it didn’t seem to be widespread.
By December, however, 36% of virus samples from Cedars-Sinai patients were identified as CAL2.0C. The variant also represented nearly one-quarter of all samples from Southern California. But again, the number of samples tested is minuscule next to the overall number of daily Covid tests.
At the beginning of January, the state had administered over 30 million Covid-19 tests. Of those tens of millions, only about 7,000 had been analyzed genomically, according to the San Jose Mercury News. It should be said that the nation as a whole is woefully behind in such analyses. But California — and specifically Los Angeles — is the worldwide epicenter of the pandemic. The need here is more acute. But such tests are expensive.
Los Angeles County is only genomically analyzing a few dozen test specimens each day, so it’s hard to know. That’s out of an average 81,000 tests a day. (Health officials DO say that they’re flagging the most suspicious samples for genomic examination.)
Asked by Deadline about that disparity on Friday, L.A. County’s Chief Science Officer Dr. Paul Simon admitted, “We don’t really have a sense of the prevalence [of new strains], but we don’t think it’s high. As we expand, we hope to have a better idea. I think we’re doing everything to test as many as we can, but there’s no new infusion of resources.”
Speaking of testing, the state recorded 12,064 new cases on Tuesday, with 422 pandemic-related deaths. The number of available hospital and ICU beds continue to rise.
As far as reopening further, state officials announced that Los Angeles County had an adjusted case rate of 48.2 per 100,000 last week. This week, that number has fallen to 38.7 per 100,000. When it reaches 25 cases per 100,000, elementary schools can apply for waivers to reopen. That number would have to fall to 7 per 100,000 for more widespread openings to occur.