COVID-19 Variant First Found in Other Countries and States Now Seen More Frequently in California

L452R Variant is Linked to Multiple Outbreaks in Santa Clara County and Being Studied by California Genomic Sequencing Experts

By Laura Kurtzman

samples pipetted in preparation for a PCR test

The California Department of Public Health (CDPH), in coordination with Santa Clara County and the University of California San Francisco (UCSF), today announced that an L452R variant of COVID-19 is increasingly being identified by viral genomic sequencing in multiple counties across the state. The 452R variant has previously been detected in other countries and states, including California, and is now increasingly being found in multiple counties throughout California. The state is working with the Centers for Disease Control and Prevention (CDC), local public health departments and laboratory sequencing partners to learn more about the variant, including how it spreads.

“It is common to identify variants of viruses like SARS-CoV-2, and we are working with our federal, local and university partners to better understand this variant and how it might impact Californians,” said Erica Pan, MD, MPH, State Epidemiologist for CDPH. “It’s too soon to know if this variant will spread more rapidly than others, but it certainly reinforces the need for all Californians to wear masks and reduce mixing with people outside their immediate households to help slow the spread of the virus. We also urge anyone who has been exposed to the virus to isolate from others to protect themselves and their loved ones.”

The 452R variant was first identified last year in other countries and states, including California. This variant is different than the B.1.1.7 variant first detected in the United Kingdom. As the number of specimens tested to monitor for variant strains has increased at California labs, including UCSF, the 452R variant has been identified more frequently since November. The 452R variant been identified in several large outbreaks in Santa Clara County.

“The fact that this variant was identified in several large outbreaks in our county is a red flag and must be investigated further,” said Santa Clara County Health Officer Sara Cody, MD. “This virus continues to mutate and adapt, and we cannot let down our guard.  This news underscores the need for everyone to follow all prevention measures and get vaccinated as soon as they are offered the vaccine.”

Santa Clara County has sequenced a large number of positive specimens collected from community testing sites and outbreaks in the county. The 452R variant was present in specimens from the community and from several large outbreaks, including outbreaks where very high numbers of people exposed contracted the virus. Analysis regarding the role of this and other variants in outbreaks and community spread in Santa Clara County is ongoing.

In addition to Santa Clara County, the 452R variant has been detected in Humboldt, Lake, Los Angeles, Mono, Monterey, Orange, Riverside, San Francisco, San Bernardino, San Diego and San Luis Obispo counties. Because genomic sequencing is not done equally across the state or country, it is too soon to know how prevalent the 452R variant is statewide, nationally or globally.

The 452R variant was most recently noted to contribute to an increasing proportion of COVID-19 cases in specimens sequenced by Charles Chiu, MD, PhD, a virologist and professor of laboratory medicine at UCSF. Chiu has been sequencing cases from multiple counties across the state over the past several months as part of the state’s SARS-CoV-2 Whole Genome Sequencing Initiative known as COVIDNet.

“This variant carries three mutations, including L452R, in the spike protein, which the virus uses to attach to and enter cells, and is the target of the two vaccines that are currently available in the United States,” said Chiu. "Now that we know this variant is on the rise in our local communities, we are prioritizing it for study. Researchers at UCSF and elsewhere will now be able to perform the critical laboratory experiments to determine whether or not this virus is more infectious or affects vaccine performance.”

Due to the ongoing surge of COVID-19 cases and hospitalizations, regardless of circulating variants, CDPH asks Californians to keep taking steps that will limit transmission of the virus and reduce strain on our health care systems. This includes:

  • Staying home except for essential activities
  • Wearing a mask when leaving home
  • Limiting interactions with people outside your immediate household
  • Keeping physical distance of at least six feet apart
  • Washing hand for 20 seconds
  • Getting the COVID-19 vaccine if you are eligible and vaccine is available in your area

CDPH has partnered with local public health labs, diagnostic labs, Chan Zuckerberg Biohub, Invitae Corporation, UCSF, and Scripps Research Institute to form COVIDNet, a network of labs working to conduct genome sequencing of SARS-CoV-2 in the state to understand transmission and evolution of the virus. To date, several thousand specimens have been sequenced in California. CDPH is notified when specific strains are identified, and network labs coordinate to assess the different strains circulating in California. In addition, network laboratories coordinate with local health departments to conduct sequencing to inform outbreak investigations.