Two worrisome new coronavirus variants — first identified in Brazil and the U.K. — have been detected in the San Francisco Bay Area by Stanford Medicine amid growing concerns that the virus’s continuing evolution will help it spread, kill and evade vaccines developed to combat the deadly disease.
The discovery of these strains, along with growing numbers of California’s own homegrown version, comes as no surprise to experts — as viruses course through a population, they inevitably mutate. And they ignore international borders.
But this finding underscores the need for accelerated vaccinations to prevent their spread, as well as continued mask-wearing, social distancing and isolation of sick people. The spread of these variants means that vaccine makers may have to develop booster shots to protect against them.
“The overall strategy for preventing these things is just to get everybody vaccinated,” said UC San Francisco epidemiologist George Rutherford. “The more people that we can immunize, the lower the risk of developing newer and newer strains that are more vaccine resistant than the ones that exist right now.”
The Brazil and UK strains were found at Stanford’s Clinical Virology Laboratory, which has developed tests to detect the presence of viruses already spreading around the world. The Stanford team is screening hundreds of viral samples collected from people across the Bay Area, with plans to expand. They also are sequencing whole viral genomes to identify any new mutations as they emerge.
Finding viral variants and quickly identifying new mutations is critical to detecting sudden changes in the pandemic.
“I was expecting that we would see these variants sooner rather than later,” said Dr. Ben Pinsky, medical director of the laboratory. The lab has uploaded the genomes of the Bay Area variants to GISAID, an international database that is shared with global researchers.
“We need to continue to monitor the prevalence of these mutations — and determine how common they become in our population, with the expectation that they will likely increase in prevalence,” he said.
In life’s Darwinian struggle, the most successful viruses are those that spread quickly and can dodge our defenses. Over time, they become dominant.
But there aren’t an infinite number of mutations, said Dr. Barry Bloom, Professor of Public Health and former dean of Harvard T.H. Chan School of Public Health. If the COVID-19 virus makes too many changes, it can no longer efficiently infect our cells.
The news comes as two vaccine manufacturers reported new data about their clinical trials that heightened concerns about viral mutations. On Thursday, Novavax said that its vaccine was 90% effective in the U.K. but just 49% effective in South Africa, where a new, highly worrisome coronavirus variant has become common. Johnson & Johnson said Friday that its single-dose COVID-19 vaccine was 72% effective among clinical trial volunteers in the U.S, but only 66% among those in Latin America, and 57% among those in South Africa.
The Pfizer vaccine appears to work against the spike proteins of the U.K. and South African variants, according to a recent lab study. A lab study of the Moderna vaccine indicated it was effective against the U.K. variant’s spike proteins but worked less well against the South African variant’s proteins. As a precaution, the company is now developing a booster shot.
So far, the U.S. has distributed 48 million doses of vaccines; of these, 26 million have been administered.
Faced with the pace of viral change, Rutherford suggested prioritizing vaccinations in areas where these variants are occurring — a version of what’s known as “ring vaccination.”
“I think that there might be some strategic focus on those areas — to try and get more vaccine into more people,” he said.
Stanford’s new test uses a technology called reverse transcription polymerase chain reaction, or RT-PCR, to find the virus’s genetic material in samples collected from people’s noses. Then, using DNA probes, they identify whether the samples are infected by the original strain of the coronavirus — or one of the new variants.
“Our hope is that Stanford’s increased surveillance, combining RT-PCR and whole-genome sequencing, will provide critical information to help public health efforts during the coming months,” Pinsky said.
Until now, the highly contagious U.K. variant – known as B.1.1.7 — had been found only in California’s San Diego and San Bernardino counties, as well as 28 other states. It is known to be more transmissible, and there’s emerging evidence that it could also be more deadly. The Stanford lab found one confirmed case of 837 specimens screened. This variant is projected to become the nation’s dominant strain by the beginning of April.
The Brazilian variant discovered in the Bay Area – called P.2 – is not well understood. So far, it is less feared than its cousin P.1, which is now devastating the Brazilian city of Manaus. P.2, spreading in the state of Rio de Janeiro, only shares one of P.1’s three mutations. But that shared mutation, dubbed an “escape mutation,” is concerning because it helps the virus evade our antibodies. So it could reduce vaccine effectiveness. Of the 837 screened specimens, the Stanford lab found no evidence of P.1 — but one case of P.2.
“There is a slight difference” between the two Brazilian strains, said Pinsky. “But I think it’s reasonable to say that there are some of the same concerns.”
The South African variant has not yet been detected by Stanford. On Thursday, South Carolina reported two cases of that variant in non-travelers from different parts of the state, suggesting community spread. Vaccines and some antibody treatments may be less effective against this strain. One study found that half of patients had a complete loss of immune recognition; the others showed a modest decline, with likely still enough immunity to be protective.
But our California variant — first reported only 12 days ago — is increasingly abundant, representing about 20 percent of the Stanford’s sequences screened. This strain is not currently cause for heightened concern, because it is vulnerable to both vaccines and treatments.
“This is a wakeup call to all of us that we will continue to see the evolution of mutants,” Dr. Anthony Fauci, director of the National Institutes of Allergy and Infectious Disease, said at a White House press briefing on Friday. “The virus has a playing field to mutate. If we stop its replication, it can’t mutate.”
“It is an incentive to vaccinate as many people as we can,” he said, “as quickly as we can.”
Contributed by local news sources