Bay Area has dodged most contagious strain — why?

High vaccination rates could help suppress B.1.1.7 variant, experts say

B.1.1.7, the coronavirus variant first detected in the United Kingdom in December, is expanding its dangerously infectious empire across the U.S., especially in Los Angeles and some other areas of the state.

But it’s just a minor player, so far, in the Bay Area.

This mysterious power struggle offers a riveting lesson in viral behavior and evolution, as the Machiavellian new variant seeks to dominate a landscape long ruled by less aggressive strains.

Are we just lucky? Or are our efforts — masking, distancing and vaccination — protecting us? Scientists propose different theories about the distinctive geographic differences.

The variant’s expansion suggests the urgency of getting as many people protected as possible to suppress circulation, especially as mask rules are relaxed and more businesses offer indoor activities.

To be sure, the highly transmissible strain is an increasing presence in the state, representing about 38% of all new cases, up 21.5% just a month ago. In Los Angeles, overall cases are declining. But 60% of the new cases over the past two months are linked to that variant.

Still, California has been spared

the fate of COVID-stressed states like Michigan, Florida and Texas, where B.1.1.7 accounts for 67%, 63% and 60% of cases, respectively.

The variant is linked to only 19% of Santa Clara County cases, 26% of San Francisco cases and 33% of Alameda County cases — and is virtually undetected in Contra Costa, San Mateo and Santa Cruz counties, according to Scripps Research Institute in La Jolla, which tracks the prevalence of new variants.

“It never really took off in the Bay Area,” said Shannon Bennett, a microbiologist and chief of science for San Francisco’s California Academy of Sciences.

And now our high vaccination rates can help keep it at bay. All Bay Area counties now rank in the top 12 of the state’s most vaccinated counties. More than onethird to one-half of Bay Area residents are vaccinated, with rates ranging from 51.6% in Marin County to 37% in Santa Clara County.

The trend in California offers a “mini experiment” in viral evolution, reflecting patterns that are seen across the U.S. — with B.1.1.7 dominant in some states but not others, Bennett said.

First spotted in San Diego in late December, its emergence alarmed experts, because it is both more deadly and more contagious than the original version of the virus. One study estimated that the risk of death is 61% higher than with preexisting variants. Another study found its transmission rate was 43% to 90% higher.

It spreads so rapidly because it has a genetic mutation that helps it latch more tightly to the human cell, so it can readily infect the cell and multiply.

Meanwhile, the role of the two California variants is shrinking, with cases falling by nearly half from their February peak. While we have cases of the worrisome South African variant, they haven’t exploded. Two other variants of concern — from Brazil and New York — have doubled in prominence, but each contributes merely 6% of all cases, according to the California Department of Public Health.

B.1.1.7’s success is not a case of “survival of the fittest,” where this variant is outcompeting the original Wuhan strain or other more recent strains. With so many people still susceptible, there are plenty of opportunities for multiple strains to thrive, according to experts.

But hyper-infectious variants like B.1.1.7 are quicker to establish a toehold, so can claim a larger proportion of overall cases, said Bennett.

“It just takes a lot less to get them going,” she said. Over time, they become dominant.

The original variant will eventually vanish, say virologists.

“There are effectively two COVID-19 epidemics in the U.S. at the moment,” according to Trevor Bedford, an evolutionary biologist at the Fred Hutchinson Cancer Research Center in Seattle. Non-B.1.1.7 cases are declining, while B.1.1.7 cases are increasing, he said. He is also concerned about the growth of a Brazilian variant called P.1.

Southern California was at a disadvantage because that’s where B.1.1.7 landed first, and gained traction, said Stacia Wyman, a computational genomicist at the Innovative Genomics Institute at UC Berkeley, who is sequencing the viruses.

By the time it arrived in the Bay Area in late January, initial cases were identified — then people were successfully traced and quarantined, she said.

“We were fortunate in that it didn’t really make it up to Northern California as strong, and so our measures were more effective here,” she said. “There’s a certain point at which you can’t contain it, like in Southern California.”

That’s what likely happened in Michigan, a state where masking was more divisive, said UC San Francisco epidemiologist Dr. George Rutherford.

“Michigan had an introduction early, then once it took over, it was harder to bring under control,” he said. “It came on like gangbusters.”

In places where there are fewer precautions, “the new variants, which are more infectious, are sweeping in — and becoming more dominant,” said Bennett.

“These new infectious strains get ‘hotter’ wherever people are less vigilant, and the vaccine rollout hasn’t happened as quickly,” she said.

In contrast, our restrictions have helped us stay ahead of it, agreed experts.

“It’s given us a big cushion to get vaccination rates really high and provide a level of protection,” said Rutherford. In the war between variants and vaccines, vaccines are winning.

“It’s important to ‘stay the course,’ ” he said. “So far, we’ve been extremely successful.”