Researchers identify five new cases of variant in California

A healthcare worker wearing personal protective equipment (PPE) inserts a Covid-19 test tube into a box at a drive-through test location at the Alemany Farmers Market in San Francisco, California on November 19, 2020.

David Paul Morris | Bloomberg | Getty Images

Stanford University researchers have identified five new cases of a “double mutant” strain of Covid-19 recently discovered in the San Francisco Bay Area. Doctors suggest it may be more contagious than previous strains and may be resistant to existing vaccines.

The new variant is originally from India, where after months of declining cases in Maharashtra state, home of Mumbai, cases have increased by 55%.

It contains two key mutations that scientists call E484Q and L452R that have been found in other variants separately but not together in a single strain, according to Dr. Benjamin Pinsky, Medical Director of the Stanford Clinical Virology Laboratory, who discovered the new variant in the United States

“There’s a decent amount of information on how these mutations behave in viruses themselves, but not in combination,” Pinsky said in an interview.

In other variants, the L452R mutation has been shown to make the virus more transmissible. There is also evidence that antibodies fail to recognize this mutation, which has been found in other strains to reduce vaccine effectiveness.

The E484Q mutation has also been shown to be less susceptible to neutralizing antibodies that help fight the coronavirus. It’s too early to tell if the mutation makes the virus more contagious.

“But you would expect that when combined with L452R, it would increase transmission and decrease neutralization of antibodies,” Pinsky said.

If the mutation makes the virus more resistant to antibodies, Pinsky said it could reduce the effectiveness of both vaccines and antibody treatments, which have become a crucial tool for doctors in fighting Covid-19.

“I suspect that existing vaccines are a little less effective at preventing infection with this new variant,” he said, “but all vaccines are extremely effective at preventing hospitalizations and death.”

Treatment with Eli Lilly’s Bamlanivimab antibodies has been shown to be less effective in the treatment of strains containing the E484Q or L452R mutations. US health officials stopped distributing this antibody treatment last month, saying it was not as effective against the new variants.

The double mutant variant “has known mutations in the scariest spot where a mutation is – the receptor binding domain where the virus attaches to cells in our bodies to enter,” said Peter Chin-Hong, an infectious disease expert at the University of California San Francisco. “The mutations are either identical or eerily similar to mutations in variants that we already know are scientifically proven to be more transmissible and / or evade vaccines. So many believe this Indian variant will have these superpowers too.”

Dr. Tom Kenyon, chief health officer at Project HOPE and former director of global health at the Centers for Disease Control and Prevention, said scientists are finding more mutations, at least in part, because the new CDC director Dr. Rochelle Walensky has instructed the agency to increase surveillance. “The more we look for these, the more we will find them,” he said.

“There’s something about the world that scares people and makes it sound like it’s doubly bad,” Kenyon said in an interview. “Any mutation that affects transmissibility or virus replication would be dangerous.”

There is a chance the new variant will stay in the Bay Area, unlike variant B.1.1.7 from the UK, which has become the predominant variety almost everywhere, Chin-Hong said.

“If the British variant goes into a boxing ring with the Indian variant, the British variant will likely emerge victorious. But only time will tell,” said Chin-Hong.

The longer it takes to vaccinate the world, the more chance the virus has of mutating into even worse strains, scientists say. Walensky has warned of “impending doom” in the US as states lift Covid-19 restrictions. She has urged people to get vaccinated and continue to follow public health precautions, including wearing masks and practicing social distancing.

“The variants that scare me the most are the ones that haven’t been invented yet. The more the virus replicates, the more we will see these escape mutants,” said Chin-Hong. “We need global vaccination justice and continued battles against pandemic fatigue.”

California will lift most of its Covid restrictions by June 15, but still plans to maintain a mask mandate.

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