Early data suggests that a variant of coronavirus first discovered in California may be more transmissible, may cause more serious disease, and impact vaccine efficacy.
The study authors are awaiting approval from public health departments to publish a preprint, although Dr. Charles Chiu, co-study author and professor of laboratory medicine at the University of California San Francisco, shared the findings and elaborated on Fox News.
“I’m worried, I’m worried but don’t panic,” said Chiu. “This is something that needs to be explored further and I really don’t think we know enough at this point to recommend changes to the standard public health measures we use to prevent infection.”
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The team sequenced the viral genomes of 2,172 nasal samples from COVID-19 patients in 44 California counties from September 1, 2020 to January 29, although sequencing was concentrated in major metropolitan areas such as Los Angeles, Alameda, San Francisco, and Santa Clara. .
The team analyzed nasal swabs from more than 2,000 genomes to collect findings.
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The variant, called B.1.427 / B.1.429 or 20C / L452R, grew to more than 50% of the cases in multiple countries during the five-month sampling period. The study notes that the variant was detected in 459 of the 2,172 genomes sampled, or about 21%. The first reported case of the variant occurred in Los Angeles in July, although sequence analysis suggests it likely surfaced in May 2020. This variant contains an important unique mutation called L452R that does not exist in other affected variants as first identified in the UK, Brazil and South. Africa, among other mutations.
“We have been able to get some evidence that this is a more contagious variant,” said Chiu, who noted a two-fold increase in patients’ virus concentrations in the nasal swabs. “That doesn’t necessarily prove it, but it does suggest it could be more contagious.”
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Another piece of evidence behind increased transmissibility involved pseudoviruses that researchers genetically engineered to include the main L452R mutation.
“We found that those viruses were at least 40% more contagious than viruses that didn’t have that mutation,” continued Chiu. “At least in vitro, in the laboratory, the major mutation found in this variant appears to be more infectious to cells.”
Public health experts say the same mitigating measures, such as wearing a mask, keeping a good distance, hand hygiene, and prompt, widespread vaccination will help protect against a variety of virus strains.
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Three lines of evidence combine to form clinical, laboratory, and other data that support claims that the variant might be more tolerable.
What’s more, when researchers examined 13 blood samples from recovered patients and vaccine recipients and tested how well the antibodies neutralized the variant compared to other strains, the antibodies in the blood of two of the three recovered patients were four times less effective at neutralizing the variant, and antibodies from six of the eight vaccine recipients were two times less effective in neutralizing the variant.
Chiu said these vaccine recipients were given two doses of the Pfizer or Moderna vaccine.
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Studies have suggested that the South African variant reduced the neutralizing power of the Pfizer vaccine by about two-thirds, while Moderna saw a six-fold reduction in neutralizing antibodies. Chiu notes that the California strain had, by comparison, a “moderate” effect.
The coronavirus variant caused a “moderate” reduction in the neutralizing potential of the recently approved vaccines, the study authors said.
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The retrospective analysis of virulence, or severe disease associated with the strain, was a difficult analysis, but findings from 324 hospitalized COVID-19 patients in a tertiary hospital suggested an increased association with ICU stay and death. More specifically, the variant was detected in 69 patients. Chiu said 11% of hospitalized patients infected with the variant died, compared to 2% of hospitalized COVID-19 patients infected with a different strain. This difference is statistically significant, he said.
“Since the number and proportion of serious cases was low in our cohort, resulting in wide confidence intervals, further research is needed to confirm these findings,” the study said. In addition, as shown for B.1.1.7, it is difficult to distinguish whether the variant is inherently more virulent or whether the higher risk of serious disease is related to other factors, such as increased transmissibility [in] an influx of cases that could put pressure on available health care resources. “
“This is still very preliminary data, but it does suggest that there may be a possible link between more serious disease from infection of the variant,” said Chiu.
There are still unanswered questions, such as the exact mechanism behind the main L452R mutation. Although the mutation is in the same region (the receptor binding domain) as other mutations identified in global variants of concern, it does not come into direct contact with the ACE2 receptor, compared to the N501Y mutation on the B.1.1.7 . variant first discovered in the UK, for example. Instead, the mutation is close to the ACE2 receptor, and separate early data suggests that the mutation helps stabilize the interaction between the spike protein and the ACE2 receptor.
Chiu said it is unclear at this point whether the strain is responsible for a surge in the number of virus cases in California. State data shows that California experienced a severe rise in the number of cases from late December to mid-January, with more than 40,000 infections daily. Chiu said a so-called ‘genetic abnormality’ or a random emergence of the ‘right kind at the right time’ could also be behind the wave. Another puzzling piece is the timing behind the state wave, when the variant likely surfaced earlier last spring. Researchers are still working to answer this question.
The main L452R mutation has also been previously found in Denmark, but this was not the same variant, harboring its own set of unique mutations.
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The California variant has yet to rise to the level of a “VOC” or variant of concern, likely because of the unknown factors associated with it thus far, the study author said. This decision to give the tribe a “VOC” should ultimately be left to public health authorities and the Centers for Disease Control and Prevention, Chiu said.
Chiu said researchers “urgently” need to collect more data to further confirm the findings, especially the initial findings regarding infectivity, transmissibility and effect on neutralizing antibodies.