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.
Both people who tested positive for the new variant were diagnosed with COVID-19 in January. The Santa Clara County individual had recently traveled and was in quarantine with one other person, who also became sick but was never tested. That individual is presumed to also have been infected with the new variant, public health officials said.
The Santa Clara County individuals were “extraordinarily careful” about quarantine and do not pose a risk of further spread of the variant, said Dr. Sara Cody, the Santa Clara County health officer.
The Alameda County case is still under investigation and the person’s travel history and potential interactions with others is not yet known, said Dr. Nicholas Moss, the county health officer.
“We don’t want any of these variants if they are here to spread any further. That’s really, really, really important,” Cody said at a news conference Wednesday. She said finding this variant in the region should signal people to “double down” on behaviors that slow down spread of disease such as wearing masks and maintaining social distance.
Though the winter surge is waning in the state and Bay Area, daily case counts are still worryingly high and the death toll is grim, Cody said. News of the variant’s arrival came the same day that California surpassed New York as the state with the most coronavirus deaths.
California reported 45,351 total coronavirus deaths as of Wednesday evening, just over New York’s 45,312 deaths, according to data compiled by Johns Hopkins University. California remains far behind New York in deaths per capita, with about 115 deaths per 100,000 residents compared to 231 per 100,000 in New York, according to data analyzed by The Chronicle.
Public health officials have worried that new variants could pose a threat to the United States’ ability to quickly end the pandemic, either by evading vaccines or spreading too fast to contain. New variants could lead to more illness and death if they cause more severe symptoms or are more infectious and trigger fresh surges in cases.
The variant from the United Kingdom is thought to be about 50% more infectious than the original virus, and experts have warned it could become dominant in parts of the United States, including Southern California, by early March. More than 150 cases of that variant 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 they respond to vaccines but are running tests now to determine if the variants 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 from a vaccine or previous infection by 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 Africa 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,” Moss said at a press event 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 were identified through a process that screened positive coronavirus samples for specific mutations. Samples with those mutations then went through genomic sequencing to confirm the variant.
The two cases announced Wednesday were from samples sent to the lab about a week to 10 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, the South African variant, 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. However, 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, Catherine Ho and Meghan Bobrowsky contributed to this report.
Erin Allday is a San Francisco Chronicle staff writer. Email: eallday@sfchronicle.com Twitter: @erinallday