A variant of the coronavirus first identified in Denmark is now emerging in California and represents more than half of the samples in 44 counties, according to new data from UC San Francisco.
The variant, called L452R, is more infectious than the original strain of the virus, although it does not appear to spread faster than the UK variant, the scientists found.
Also worrying is the new evidence linking the variant to the increased risk of serious illness and death. In addition, vaccinated people appear to produce less protective antibodies in response to the variant, suggesting that it may escape our immune defenses.
This raises concerns that it could prolong the pandemic, cause more deaths or make vaccines less effective.
The strain “should probably be designated a variant of concern, ensuring urgent follow-up investigation,” concludes Dr. Charles Chiu, of the University of California at San Francisco, whose laboratory is collaborating with the state’s Department of Public Health to look for cases of new variant. The findings, which were not reviewed by peers, were released Monday morning.
The variant, which Chiu’s laboratory estimates appeared in California in May 2020, increased its prevalence from 0% to more than 50% of cases during the sampling period. He was held responsible for outbreaks in nursing homes, prisons and the emergency department of Kaiser Permanente San Jose, where a team member wearing an inflatable Christmas tree costume may have infected at least 90 people.
New testing insights in the San Francisco Mission District offer a more detailed look at the virus’s behavior. The variant is not confined to this neighborhood – while the test site at the 24th Mission BART Station, a predominantly Latinx community, has attracted people from all over San Francisco and seven other counties in the bay area.
The variant represented 53% of positive test samples collected between 10 and 27 January – a significant increase from November, when it comprised only 16% of positive tests, according to UCSF infectious disease specialist, Dr. Diane Havlir .
With the help of the Mission District community, the team was able to investigate important issues about home transmission, symptoms and infections in children.
They found that the L452R variant has a high “secondary attack rate” – that is, transmission within a home – which suggests that it is more transmissible than other strains.
Evidence of greater transmissibility has also been found by Chiu’s laboratory. He detected faster rates of reproduction and increased viral elimination, which occurs when a virus replicates within the body and is released into the environment. When the variant was introduced into cells and tissues grown in the laboratory, it showed greater infectivity.
To test whether antibodies could defend against this new strain, Chiu’s team tested the virus in culture in the laboratory against antibodies from people who had been vaccinated or had already been infected with the virus, although not with this strain.
They found a two to four-fold reduction in the ability of antibodies to ward off the variant virus. This can potentially contribute to reduced protection of the vaccine – or widespread reinfection after so-called “herd immunity”.
To find out if the variant caused more serious illness, they studied the medical records of patients admitted to UCSF. After controlling for age, sex and ethnicity, the team found that people infected with the variant were significantly more likely to be admitted to the ICU and die.
The L452R variant was first detected in Denmark in March 2020. It has three notable mutations – including one in its spike protein, which allows the virus to attach itself and enter cells. This mutation is what makes the virus more transmissible, because it can infect and spread more quickly.
Several other variants have appeared in different regions of the world. They are created when the virus makes small copy changes called mutations.
Variant B.1.1.7, first described in the UK, contains 17 mutations, including one that increases contagion and can also cause more serious illnesses. This variant was not found at the San Francisco Mission District test site. This does not mean that you are not here – but this, at least at the time of the study, is very unusual.
The appearance of variants B.1.351 in South Africa and P.1 in Brazil is also worrying, as both share a mutation that makes the pathogen more resistant to attack by antibodies.
At the moment, the new California variant looks less threatening than these three other varieties. It is less transmissible than the British version and less resistant than the South African and Brazilian versions.
The efforts of Chiu’s lab are part of a larger effort to track variants of the virus across the state of California. The California COVID Tracker, a joint effort between Chan Zuckerberg Initiative, CZ Biohub and the state of California, provided complete genome sequencing and free analysis of the SARS-CoV-2 virus for all California Departments of Public Health and local health jurisdictions since July 2020, allowing authorities to better map the virus. To date, this partnership has done about 45% of all sequencing in California and 5% of the nation’s sequencing efforts.
The Mission District study was conducted by Unidos en Salud, a volunteer-led collaboration between UC San Francisco, the nonprofit Chan Zuckerberg Biohub (CZ Biohub), the Chan Zuckerberg Initiative and the Latin Task Force for COVID-19.