Increase In L452R In California Since November
#15,722
From a Sunday evening Zoom press conference (see below) and a press release from the California Department of Health, we get details on yet another covid variant - dubbed L452R - which appears to be rapidly gaining ground in California.
This variant has been linked to last month's outbreak at a Kaiser Permanente emergency room in San Jose, where more than 90 staff and patients were infected.
In the graphic above, this variant showed up in 3.8% of sequenced COVID viruses between Nov 22nd and Dec 13th (23 days), but in roughly 25% of those sequenced between Dec 14th and Jan 3rd (21 days). More recent data is pending.
Admittedly, the number of viruses sequenced in California over this time period was small (n=332), and there was undoubtedly some bias (driven by investigating clusters, not random samples) in selecting which viruses to sequence, but this rapid increase is viewed as significant.
This is not the same as the B.1.1.7 variant we've been watching intently since mid December.
At this time it is not known whether this variant is more transmissible than others, although its rapid increase in market share is suggestive of that. It also isn't known if this variant produces more (or less) severe illness, or would evade the current vaccines.
Dr. Charles Chiu, who took part in the Zoom Press Conference, does note that this variant contains mutations that have been linked to reduced antibody recognition, which could prove problematic for reinfection risks and vaccine protection.Work is underway to culture several samples of this variant, so that work can begin on answering these questions.
The 35 minute press conference is well worth listening to in its entirety.
The full statement from California's Department of Public Health follows. I'll return with a brief postscript.
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
Date: January 17, 2021
Number: NR21-020
Contact: CDPHpress@cdph.ca.gov
SACRAMENTO – 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 Dr. Erica Pan, 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 Dr. Sara Cody. “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 452 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 Dr. Charles Chiu, a virologist and professor of laboratory medicine at UCSF. Dr. 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 Dr. 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: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.
- 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 6 feet apart
- Washing hand for 20 seconds
- Getting the COVID-19 vaccine if you are eligible and vaccine is available in your area
With millions of people walking around this planet carrying the SARS-CoV-2 virus, and each host producing millions of copies of the virus each day, there are plenty of opportunities for new, more `biological fit', variants to emerge.
Undoubtedly, the more we look, the more we are going to find.
There are already thousands of COVID variants identified. Fortunately most will fall by the wayside, unable to compete with more `fit' variants. Some with potential may mutate themselves out of contention, while a relative few may thrive.
The only constant with viruses is that they change over time. While there is hope that SARS-COV-2 will eventually evolve into a milder virus, hope is not a plan.
Like it or not, the only influence we can have on this pandemic's outcome right now is to deny the virus as many opportunities to evolve that we can, by reducing transmission through social distancing, NPIs, and by rolling out vaccines.
