South Africa coronavirus variant that reduces vaccine efficacy found in two Bay Area counties

A worker is seen at a coronavirus testing site in San Francisco in November. The city has had no known cases of the South Africa variant, but elsewhere in the Bay Area two cases have been recorded.
A worker is seen at a coronavirus testing site in San Francisco in November. The city has had no known cases of the South Africa variant, but elsewhere in the Bay Area two cases have been recorded. Lea Suzuki / The Chronicle 2020
San Francisco Chronicle, by Erin Allday, Feb. 10, 2021

Two cases of a coronavirus variant first found in South Africa that reduces the effectiveness of some vaccines have been identified in the Bay Area, in Alameda and Santa Clara counties, Gov. Gavin Newsom said Wednesday.

They are the first two cases of this variant, called B.1.351, to be found in California. They were identified by scientists at the Stanford Clinical Virology Laboratory Tuesday night and reported to the state Wednesday morning.

Variants that are more infectious or reduce vaccine effectiveness pose a threat to the state’s ability to control and quickly end the pandemic, public health officials have said. More than 150 cases of a variant first identified in the United Kingdom that is known to be more infectious have been found in California, including Alameda and San Mateo counties.

Another pair of closely related variants identified in California have been spreading quickly in the Bay Area and Southern California. Scientists believe those variants respond to vaccines but they are running tests now to determine if they reduce effectiveness. They’re also studying whether the variants are more infectious.

The variant from South Africa is considered particularly concerning because studies have found that it is able to partially evade the body’s immune response, whether it’s generated from a vaccine or previous infection with the coronavirus. So far the vaccines appear to prevent severe disease and death from the variant.

“The British variant, it’s still susceptible to vaccines and it’s going to spread anyway. But let’s get this one back in the box,” said Dr. George Rutherford, an infectious disease expert at UCSF.

As of Tuesday, nine cases of the variant from South African had been identified in three states, according to the Centers for Disease Control and Prevention. That number did not include the new California cases.

“These variants are here,” Dr. Nicholas Moss, the Alameda County health officer, said at a press event on Wednesday. “We should prepare and plan accordingly.” Because relatively few coronavirus cases are genomically sequenced, he said, “we only have a very limited picture of their spread locally.”

Dr. Benjamin Pinsky, who heads the Stanford lab that found the variants, said they are identified through a process that first screens positive coronavirus samples for specific mutations. Samples that have those mutations then go through genomic sequencing to confirm the variant.

The two cases announced on Wednesday were from samples sent to the lab about a week to ten days ago, Pinsky said. His lab also identified the first cases of the variant from the United Kingdom found in the Bay Area.

The two vaccines currently available in the United States, made by Pfizer and Moderna, provide some protection against B.1.351, but perhaps less than the initial virus from China for which they were designed.

The Moderna vaccine induced an immune response six times lower against the variant from South African compared to earlier variants, the company said in late January after conducting a small study. But even this lower level of immune response, or neutralizing antibodies, is likely enough to protect against COVID-19, the company said.

Still, Moderna is testing a booster vaccine to see if it can provide more immunity.

Similarly, the Pfizer vaccine also induced a slightly lower level of neutralizing antibodies against the variant but it should still be enough to protect against COVID-19, according to studies by Pfizer and the University of Texas Medical Branch. The difference is “unlikely to lead to a significant reduction in the effectiveness of the vaccine,” Pfizer said.

Pfizer and Moderna are both made using messenger RNA, a type of technology that allows vaccine manufacturers to tweak vaccines quickly to account for variants. So the companies could essentially “plug in” a slightly adjusted genetic sequence into the vaccine. This could still be concerning, though, because even though the vaccine itself could be tweaked fast, it would take time to produce and distribute.

Also concerning is whether other vaccines in the pipeline, particularly one made by AstraZeneca and Oxford University, will work against emerging variants. South Africa recently stopped using the AstraZeneca vaccine because of reduced effectiveness. That vaccine is not yet approved for use in the United States. South Africa switched to the Johnson & Johnson vaccine, which has yet to be authorized in any country but in clinical studies was shown to be 57% effective at preventing moderate to severe disease caused by B.1.351.

Scientists in South Africa also have said that people who were previously infected with other coronavirus variants appear to be susceptible to reinfection with the new one.

Moss of Alameda County expressed optimism about vaccines. But meanwhile, he said, “We have to stick with the things we know work for the time being. That means, face coverings, distancing, and limiting gatherings.”

“The most important thing with variants is to just limit the amount of COVID that is out there,” he added.

San Francisco Chronicle staff writers Aidin Vaziri and Catherine Ho contributed to this report.  Erin Allday is a San Francisco Chronicle staff writer.