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A variant of the coronavirus first identified in Denmark now crosses California and accounts for more than half of the samples in 44 counties, according to new data from UC San Francisco released on Monday.
The variant, called L452R, is more infectious than the original strain of the virus, although it does not appear to spread any faster than the UK variant, scientists have found.
The new evidence that links the variant to an increased risk of serious illness and death is also disturbing. Additionally, vaccinated people appear to produce fewer protective antibodies in response to the variant, suggesting that it may escape our immune system.
This raises concerns that it could lead to the pandemic, cause more deaths or make vaccines less effective.
The strain “should probably be named as a variant of concern, warranting urgent follow-up investigation,” concludes Dr Charles Chiu of UC San Francisco, whose lab is working with the state’s Department of Public Health to look for case of the new variant.
Even as cases of COVID-19 in the state decline, “it highlights the need for us to keep our eyes on him … to understand why this is going to be important and how he is responding to the vaccine,” said the Dr Joe DeRisi, co-chair of the nonprofit Chan Zuckerberg Biohub in San Francisco, which is leading a massive effort to accelerate the genetic sequencing of the COVID-19 virus throughout California.
“Now is not the time to let our guard down,” he said.
The variant, which Chiu’s lab estimates emerged in California last May, increased its prevalence from 0% of cases sampled in early September 2020 to over 50% at the end of January 2021. It has been blamed for epidemics in nursing. homes, prisons and the emergency department at Kaiser Permanente San Jose, where a staff member wearing an inflatable Christmas tree costume may have infected at least 90 people.
New information from research in the Mission District of San Francisco, also released on Monday, offers a more in-depth look at the behavior of the virus.
The team found that this variant accounted for 53% of all positive test samples collected at the 24th Street Mission BART station in the predominantly Latinx community of San Francisco between January 10 and 27 – a significant increase from November when it only represented 16% of the positives. tests, according to UCSF infectious disease expert Dr. Diane Havlir.
The Mission District study was conducted by Unidos en Salud, a volunteer-led collaboration between UC San Francisco, Chan Zuckerberg Biohub (CZ Biohub), the Chan Zuckerberg Initiative, and the Latino Task Force for COVID-19. With the help of the community, scientists were able to investigate key questions about domestic transmission. Compared to the original virus, the L452R variant is a bit more aggressive, with a high “secondary attack rate” of 35%, compared to 25% – spreading faster in a home.
Chiu’s research also found evidence of increased transmissibility. His lab has detected faster reproduction rates and increased viral “shedding” when the virus is released into the environment. He also found that the variant was more infectious when introduced into cells and tissues grown in the lab.
The proportional increase in cases statewide due to the variant was rapid, doubling every 18 days. Cases linked to the variant were doubling every 14 days in Santa Clara County and 33 days in Alameda County.
To test whether the antibodies could repel this new strain, Chiu’s team tested the lab-grown virus against antibodies from people who were either vaccinated or had previously been infected with the virus, but not this strain. They found a two to four times reduction in the ability of antibodies to repel variant virus. This means that vaccines may need to be retooled to remain effective.
Will we need updated “booster” vaccines? Although no one knows it yet, Havlir called it a “definitive possibility.”
To find out if the variant was causing more serious illness, Chiu’s team studied the medical records of patients admitted for care at UCSF. After controlling for age, sex, and ethnicity, he found that people infected with the variant had a significantly higher chance of being admitted to the intensive care unit and of dying.
The L452R variant was first detected in a few isolated cases in Denmark last March and appeared in California as early as May, although we only started to find it in the summer and fall. It has four mutations in the genetic code for its spike-shaped protein, which the virus uses to enter cells. This is why it is more transmissible, infecting and spreading more easily.
Many other variants have appeared in different parts of the world. Variants are created when the virus makes tiny copy changes, called mutations.
The B.1.1.7 variant, first described in the UK, contains 17 mutations, one of which stimulates contagion and can also cause more serious disease. This variant was not found on the San Francisco Mission District test site. That’s not to say it’s not here – but that, at least at the time of the study, it was rare.
Two other variants – B.1.351 in South Africa and P.1 in Brazil – are also of concern because both share a mutation that makes the virus less vulnerable to antibody attack. The South African strain has been detected in the bay area. The Brazilian strain P.1 has not been detected in the state, but another variant first detected in Brazil – P.2 – has been found in the bay area.
Right now, the new California variant looks less of a concern than these other three varieties. It is less transmissible than the British version and less resistant than the South African and Brazilian versions.
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