Covid-19 cases and hospitalizations fell 77% and 44% last month, respectively, LA county health officials said on Monday. This is great news for the most affected region of the country. The question remains, however, whether new variants of the virus will create another outbreak.
LA County Public Health Director Barbara Ferrer said on Monday that, “We will report later today that we now have 5 cases associated with the UK variant.” Not many, but the amount of genomic tests in the county to identify new variants is exceedingly small compared to the number of Covid tests being delivered.
“There is no way we cannot have a fair amount of [that] variant circulating here, ”said Ferrer. The UK mutant strain is believed to be 30-50% more transmissible. According to a new report, the UK variant is doubling its prevalence among the cases identified every 9 to 10 days.
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As for the South African variant, which is also more transmissible and possibly resistant to vaccines, “suppose you are here,” said Ferrer. Then she dropped the real bomb.
“At least 50% of our samples showed the West Coast variant,” said Ferrer, before guaranteeing that “more research needs to be done”.
Last week, California’s chief health officer revealed that more than 1,000 cases of the West Coast variant were discovered in the state. California Governor Gavin Newsom said on Monday that that number had risen to 1,200. This is a 20% increase in less than a week.
These increases could make the effort to vaccinate Los Angeles residents even more critical. The region has considerably increased its vaccination infrastructure in recent weeks, but a bottleneck in vaccine supply is hampering the effort.
Newsom revealed on Monday that 1.2 million doses of the vaccine are expected to arrive in the state this week. But only 540,000 of these will be the first doses. “We need to see more doses coming into the state to keep these sites up and running,” said Newsom.
Ferrer said the situation in LA is even more desperate. For the rest of this week at the county’s vaccination sites, she said, “All we can offer is consultations for the second dose.” In a 10 million county with new variants circulating, this is a problem.
Dubbed in various ways B.1.429 and B.1.427, the West Coast Variant or sometimes called CAL.20C, the new strains are still a mystery.
Dr. Charles Chiu, a virologist and professor of laboratory medicine at UCSF who, in conjunction with state authorities, has been sequencing test samples genetically to identify new variants, said the first indications are CAL.20C may be less susceptible to vaccines today approved, but more research is needed.
“This variant carries three mutations, including L452R, in the protein spike, which the virus uses to bind 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 effectiveness. Given the importance of this peak protein, L452R is another name sometimes used for West Coast variants.
Asked about vaccine resistance, Ghaly was more circumspect saying that he was, “It is not clear about its exact role in making people sick or its impact on things like the vaccine.”
West coast variants have also been detected in Los Angeles, Mono, Monterey, Orange, Riverside, San Francisco, San Bernardino, San Diego, San Luis Obispo, Humboldt and Lake counties. As genomic sequencing is sparse, it is currently not known exactly what the prevalence of L452 is across the state, nationally or globally.
Dr. Chiu said that the L452R grew from about 3.8% of the samples tested in late November 2020 until early December to more than 25.2% in late December by early January 2021.
Eric Vail, the director of molecular pathology at Cedars-Sinai, said The New York Times that CAL.20C may have played a role in the increase in cases that overwhelmed Southern California hospitals earlier this month. “I am quite confident that this is a more infectious strain of the virus,” said Dr. Vail.
Scientists are concerned about L452R because it can help coronaviruses to attach to human cells and infect them more easily.
Dr. Vail and other researchers in the state say the L452 mutations they found were always next to four other specific mutations. This invariable arrangement was a strong sign of a single “native” California lineage.
Cedars researchers discovered CAL.20C in July. As far as limited genetic testing could detect, the variant did not appear in Southern California again until October. At the time, it did not seem to be widespread.
In December, however, 36% of virus samples from Cedars-Sinai patients were identified as CAL2.0C. The variant also accounted for almost a quarter of all Southern California samples. But again, the number of samples tested is minuscule close to the general number of daily Covid tests.
In early January, the state administered more than 30 million Covid-19 tests. Of those tens of millions, only about 7,000 have been analyzed genomically, according to San Jose Mercury News. It must be said that the nation as a whole is terribly behind in such analyzes. But California – and specifically Los Angeles – is the global epicenter of the pandemic. The need here is more acute. But these tests are expensive.
Los Angeles County is genomically analyzing only a few dozen test specimens each day, so it’s hard to know. This averages 81,000 tests per day. (Health officials say they are signaling the most suspicious samples for genomic testing, so it appears to increase the likelihood of discovering mutations.)