A coronavirus variant first identified in Denmark is now rising through California, representing more than half of samples in 44 provinces, according to the new UC San Francisco data.
The variant, called L452R, is more contagious than the original strain of the virus, although it does not appear to spread faster than the British variant, scientists have found.
Also revealing is new evidence linking the variant to increased risk of serious illness and death. In addition, people who are vaccinated seem to produce less protective antibodies in response to the variant, suggesting that it may evade our immune resistance.
This raises concerns that it could provoke the pandemic, cause more deaths or make vaccines less effective.
The tension ‘should probably be a variant of concern that justifies urgent follow-up investigation’, concludes Dr Charles Chiu of UC San Francisco, whose laboratory is working with the Department of Public Health to investigate the cases of the new variant. The findings were announced Monday morning.
The variant, which according to Chiu’s laboratory originated in California in May 2020, increased in incidence from 0% to more than 50% of cases during the sampling period. It is accused of outbreaks in nursing homes, prisons and the emergency department in Kaiser Permanente San Jose, where a staff member wearing an inflatable Christmas tree costume may have infected at least 90 people.
New insights from tests in the Mission District in San Francisco provide a closer look at the behavior of the virus. The variant is not limited to this area – although the test site at the 24th St. Mission BART Station, a predominantly Latinx community, attracted people from all over San Francisco and seven other provinces in the Bay Area.
The variant represents 53% of the positive test samples collected between January 10 and January 27 – a significant increase from November, when it accounted for only 16% of the positive tests, according to dr. Diane Havlir of UCSF Infectious Disease.
With the help of the Mission District community, the team was able to investigate key questions about household transmission, symptoms, and infections in children.
They found that the L452R variant has an increased ‘secondary attack rate’ – that is, transmission within a household – indicating that it is more transmissible than other strains.
Evidence for increased portability was also found by Chiu’s laboratory. It detected faster reproduction rates and increased viral shedding, which occurs when a virus repeats itself within the body and is released into the environment. When the variant was introduced into laboratory cultured cells and tissues, it showed greater infectivity.
To test whether antibodies can repel this new strain, Chiu’s team tested the cultured virus in the laboratory against antibodies from people who have been vaccinated or previously infected with the virus, although not this strain.
The finding found a two- to four-fold reduction in the ability of antibodies to ward off the variant virus. This could possibly contribute to a reduced protection of the vaccine – or widespread reinfection to so-called ‘herd immunity’.
To determine if the variant caused serious illness, they studied the medical records of patients admitted to UCSF. After checking age, gender, and ethnicity, the team found that people infected with the variant were significantly more likely to be admitted to the ICU and to die.
The L452R variant was first detected in Denmark last March and in May in Los Angeles. It has four mutations in the genetic code for its vein-shaped protein, which is used by the virus to enter cells. Therefore, the virus is more transmissible, infects and spreads more easily.
Several other variants originated in different regions of the world. It is created when the virus makes small copying changes, called mutations.
The B.1.1.7 variant, first described in the UK, contains 17 mutations, including one that increases infection and can also cause serious illness. The variant was not found on the San Francisco Mission District test site. That does not mean it is not here – but at least at the time of the study it is very unusual.
The emergence of variants B.1.351 in South Africa and P.1 in Brazil is also of concern, as both have a mutation that makes the pathogen more resistant to antibody attack.
At the moment, the new variant of California looks less ominous than these three other tribes. It is less portable than the British version, and less durable than the South African and Brazilian versions.
The efforts of the Chiu Laboratory efforts are part of a larger effort to detect variants of the virus across the country in California. The California COVID Tracker, a joint effort between Chan Zuckerberg Initiative, CZ Biohub, and the State of California, has since provided free sequencing and analysis of the SARS-CoV-2 virus to all public health and local health law departments in California. July 2020, which enables officials to better map the virus. To date, this partnership has done about 45% of all sequencing in California and 5% of the country’s sequencing efforts.
The Mission District study was conducted by Unidos and Salud, a voluntary collaboration between UC San Francisco, the nonprofit Chan Zuckerberg Biohub (CZ Biohub), the Chan Zuckerberg Initiative, and the Latino Task Force for COVID-19.