A coronavirus variant first identified in Denmark is now surging through California and represents more than half of samples in 44 counties, according to new UC San Francisco data.

The variant, called L452R, is more infectious than the original strain of the virus, although it does not appear to spread more quickly than the U.K. variant, scientists found.

Also troubling is new evidence that links the variant to increased risk of severe illness and death. Additionally, people who are vaccinated seem to produce fewer protective antibodies in response to the variant, suggesting it might evade our immune defenses.

This raises worries that it may draw out the pandemic, cause more deaths or make vaccines less effective.

The strain “should likely be designated a variant of concern, warranting urgent follow-up investigation,” concludes Dr. Charles Chiu of UC San Francisco, whose lab is collaborating with the state’s Department of Public Health to seek cases of the new variant. The findings, which have not been peer reviewed, were released Monday morning.

The variant, which Chiu’s lab estimates to have emerged in California in May 2020, increased in prevalence from 0% to more than 50% of cases during the sampling period. It has been blamed for outbreaks at nursing homes, jails and the emergency department at Kaiser Permanente San Jose, where a staff member wearing an inflatable Christmas tree costume might have infected at least 90 people.

New insights from testing in San Francisco’s Mission District offer a closer look at the virus’s behavior.  The variant isn’t confined to this neighborhood — while the test site at the 24th St. Mission BART Station, a predominantly Latinx community, it drew people from all over San Francisco and seven other Bay Area counties.

The variant represented 53% of the positive test samples collected between Jan. 10 and Jan. 27 – a significant increase from November, when it comprised only 16% of the positive tests, according  to UCSF infectious disease expert Dr. Diane Havlir.

With the assistance of the Mission District community, the team was able to investigate key questions about household transmission, symptoms, and infections in children.

They found that that the L452R variant has an elevated “secondary attack rate” – that is, transmission within a household – that suggests it is more transmissible than other strains.

Evidence for increased transmissibility was also found by Chiu’s lab. It detected faster rates of reproduction and increased viral shedding, which occurs when a virus replicates inside the body and is released into the environment. When the variant was introduced to lab-grown cells and tissues, it showed greater infectivity.

To test whether antibodies could fend off this new strain, Chiu’s team tested the cultured virus in the lab against antibodies from people who were either vaccinated or had previously been infected with the virus, although not this strain.

The found a two to four-fold reduction in the ability of antibodies to fend off the variant virus. This could potentially contribute to lowered vaccine protection — or widespread reinfection after so-called “herd immunity.”

To learn whether the variant caused more severe disease, they studied the medical records of patients admitted at UCSF. After controlling for age, gender, and ethnicity, the team found that people infected with the variant had significantly higher odds of being admitted to the ICU and dying.

The L452R variant was first detected in Denmark in March 2020. It  has three three mutations in the genetic code for its spike-shaped protein, which the virus uses to enter cells. That’s why the virus is more transmissible — it infects and spread more readily.

Multiple other variants have emerged in different regions of the world. They are created when the virus makes tiny copying changes called mutations.

The B.1.1.7 variant, first described in the United Kingdom, contains 17 mutations, including one that boosts contagion and may also cause more severe disease.  That variant has not been found at San Francisco’s Mission District test site.  That doesn’t mean it isn’t here — but that, at least at the time of the study, is very uncommon.

The emergence of the variants B.1.351 in South Africa and P.1 in Brazil is also concerning, because both share a mutation that makes the pathogen more resistant to antibody attack.

Right now, California’s new variant seems less ominous than these three other strains.  It’s less transmissible than the U.K. version, and less resistant than the South African and Brazilian versions.

The efforts of the Chiu lab efforts are part of a larger effort to track variants of the virus statewide in California. The California COVID Tracker, a joint effort between Chan Zuckerberg Initiative, CZ Biohub, and the State of California has provided free whole-genome sequencing and analysis of the SARS-CoV-2 virus to all California Departments of Public Health and local health jurisdictions since July 2020, enabling officials to better map the virus. To date this partnership has done roughly 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 Latino Task Force for COVID-19.