'Double mutant' coronavirus variant surfaces in SF Bay Area

 The Bay Area has yet another coronavirus variant to contend with.

Through genomic sequencing, the Stanford Clinical Virology Lab has identified and confirmed one case of an emerging variant that originated in India, according to lab director Dr. Benjamin Pinsky. The lab is screening seven other presumptive cases and should have the results early this week, he said.

According to Pinsky and news reports, the confirmed case is a patient from a Stanford Health Care clinic and likely occurred in Santa Clara County. County health officials said they are not yet monitoring the new variant because it is not yet on the Centers for Disease Control and Prevention’s list of concern.

The variant is being dubbed the “double mutant” because it carries two mutations in the virus that helps it latch itself onto cells. It could possibly be responsible for the troubling new surge in cases in India. It is not yet known if the variant is more infectious or resistant to vaccine antibodies.

Peter Chin-Hong, an infectious disease expert at UCSF, said it appears the variant could be more infectious because it accounts for 20% of cases in the heavily hit state of Maharashtra. Chin-Hong said cases have increased more than 50% there in the past week.

“It also makes sense that it will be more transmissible from a biological perspective as the two mutations act at the receptor binding domain of the virus, but there have been no official transmission studies to date,” he wrote in an email.

One of the mutations, E484Q, is similar to the E484K mutation found on both of the variants first detected in Brazil and South Africa. The other mutation, L452R, is also found in a variant first detected in California. Pinsky said both mutations could possibly reduce neutralization by antibodies, therefore making vaccinations less effective against the strain.

“This Indian variant contains two mutations in the same virus for the first time, previously seen on separate variants,” Chin-Hong said. “Since we know that the domain affected is the part that the virus uses to enter the body, and that the California variant is already potentially more resistant to some vaccine antibodies, it seems to reason that there is a chance that the Indian variant may do that too.”

He said so far no studies have confirmed any of this. Still, Chin-Hong said it appears this variant may be more regional, as the B.1.1.7 variant that originated in the U.K. is the more dominant strain in India. And while it’s not certain if the variant is resistant to vaccines, he is “optimistic” that vaccinations will work given what is known about their efficacy against the variants originating from South Africa and California.

The latest discovery adds to the list of worrisome variants that have made their way to the U.S., including the widely spreading B.1.1.7. variant, which is 50% more infectious. The P.1 strain that originated in Brazil and a variant from South Africa have both been found in the Bay Area, and both are believed to be somewhat resistant to vaccines.

There are many cases statewide of the variants originating in California that are more infectious and could possibly be resistant to vaccines, and ones from New York identified in Santa Clara County that could also be potentially vaccine-resistant.

Pinsky said there is still much to be learned about the variant from India, but nobody should panic, especially because case numbers are down in California and large numbers of people are getting vaccinated.

“It’s important for us to continue to monitor the emergence of these variants,” he said. “The point is to keep getting vaccinated and to keep monitoring for the emergence of variants. I don’t think it is of significant concern yet. We just have to be vigilant.”

https://www.sfchronicle.com/local/article/Double-mutant-coronavirus-variant-surfaces-16076361.php