What is L452R? Here’s what we know about Covid-19 strain linked to several outbreaks in California
According to public health officials, it is too soon to know if this Covid-19 variant will spread more rapidly than others
Scientists have identified a new coronavirus variant in California, which has been linked to multiple outbreaks in Santa Clara County. Referred to as ‘L452R,’ this strain is not the same as the B.1.1.7 variant, which was recently discovered in the UK.
According to public health officials, 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. One of the outbreaks has led to many infections at the Kaiser Permanente medical center in San Jose, informed authorities.
“The California Department of Public Health (CDPH), in coordination with Santa Clara County and the UCSF, announced that an L452R variant of Covid-19 is increasingly being identified by viral genomic sequencing in multiple counties across the state,” reads a statement.
Scientists at the University of California San Francisco (UCSF) sequenced genomes of coronavirus gathered from around the state in mid-November 2020, and found that the variant was present in 3.8% of their samples. By January 2021, it had spiked to 25.2%.
Hi all, we & other labs in CA identified a L452R spike mutation SARS-CoV-2 variant 3.8%->25.2% cases mid-Nov-early Jan. Assoc with several high attack rate outbreaks in Santa Clara County. Epi/lab studies pending @SCCgov @UCSF @CAPublicHealth @CDCgov— Charles Chiu (@cychiu98) January 18, 2021
This 452R variant carries three mutations, including L452R, in the spike protein, which the virus uses to attach to and enter cells. The spike protein is the target of the Pfizer and Moderna coronavirus vaccines that are currently available in the US.
“It is common to identify variants of viruses like SARS-CoV-2 (the virus that causes Covid-19), and we are working with our federal, local, and university partners to better understand this variant and how it might impact Californians. 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,” suggests Dr Erica Pan, state epidemiologist for CDPH.
What does it mean?
Currently, it remains unclear whether the new variant is more contagious. 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 to control its spread. They want to understand whether the variant spreads more easily from person to person and if it causes milder or more severe disease in people.
Researchers are also trying to ascertain whether this variant responds to medicines currently being used to treat people for coronavirus and if it changes the effectiveness of Covid-19 vaccines.
“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,” says Dr Charles Chiu, a virologist, and professor of laboratory medicine at UCSF.
The rise in L452R coincided with a surge in coronavirus case numbers in California, making it possible that the mutation was “carried by the surge rather than causing it,” tweeted Trevor Bedford, associate member at the Fred Hutchinson Cancer Research Center, Seattle, in the Vaccine and Infectious Disease Division and the Computational Biology Program.
Nice work! It's of course possible that L452R combined with W152C is playing some role here, but I would note that this clade hung around at low frequency for Sep through Oct before taking off in Nov (https://t.co/EqJ0qyMFWg). 1/2 pic.twitter.com/XTqlUM62H3— Trevor Bedford (@trvrb) January 18, 2021
This would fit with this clade being carried by the surge rather than causing it. Additionally we have the common ancestor of this clade inferred to be in ~July. Not a recent emergence. 2/2— Trevor Bedford (@trvrb) January 18, 2021
Where else have experts found the 452R strain?
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 last year.
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.
The 452R variant has also 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 fact that this variant was identified in several large outbreaks in our county is a red flag and must be investigated further. 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,” emphasizes Dr Sara Cody, Santa Clara County health officer.