Two worrying new variants of the coronavirus – first identified in Brazil and the UK – have been detected in the San Francisco Bay area by Stanford Medicine amid growing concerns that the continuing evolution of the virus will help it spread, kill and prevent vaccines developed to combat the deadly disease.
The discovery of these strains, along with the growing number of home-grown versions of California itself, comes as no surprise to experts – as viruses spread through the population, they inevitably mutate. And they ignore international borders.
But this discovery underscores the need for accelerated vaccinations to prevent its spread, as well as the continued use of masks, social distance and the isolation of patients. The spread of these variants means that vaccine manufacturers may have to develop booster doses to protect themselves against them.
“The general strategy for preventing these things is just to vaccinate everyone,” said UC San Francisco epidemiologist George Rutherford. As long as we have groups of non-immunized people, the virus will mutate, he said.
“The more people we can immunize,” he said, “the lower the risk of developing increasingly new strains that are more resistant to vaccines than those that currently exist.”
The strains from Brazil and the United Kingdom were found at the Stanford Clinical Virology Laboratory, which developed tests to detect the presence of viruses that are already spreading around the world. The Stanford team is examining hundreds of viral samples collected from people across the bay area, with expansion plans. They are also sequencing entire viral genomes to identify new mutations as they arise.
Finding viral variants and quickly identifying new mutations is critical to detecting sudden changes in the pandemic.
“I expected to see these variants sooner or later,” said Dr. Ben Pinsky, medical director of the laboratory. The lab 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 are likely to increase in prevalence,” he said.
In the Darwinian struggle of life, the most successful viruses are those that spread quickly and can escape our defenses. Over time, they become dominant.
But there are not an infinite number of mutations, said Dr. Barry Bloom, professor of public health and former dean of the Harvard School of Public Health TH Chan. If the COVID-19 virus makes many changes, it will no longer be able to infect our cells efficiently.
The news comes when two vaccine manufacturers report new data about their clinical trials, which raise concerns about viral mutations. On Thursday, Novavax said its vaccine was 90% effective in the UK, but only 49% effective in South Africa, where a new variant of the highly worrying coronavirus has become commonplace. Johnson & Johnson said on Friday that its single-dose vaccine COVID-19 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 peak proteins in the UK and South Africa variants, according to a recent laboratory study. A laboratory study of the Moderna vaccine indicated that it was effective against peak proteins in the UK variant, but it worked less well against proteins in the South African variant. As a precaution, the company is now developing a booster injection.
So far, the United States has distributed 48 million doses of vaccines; of these, 26 million were administered.
Faced with the pace of viral change, Rutherford suggested prioritizing vaccination in areas where these variants are occurring – a version of what is known as “ring vaccination”.
“I think there may be some strategic focus in these areas – trying to get more vaccine to more people,” he said.
The new Stanford test uses a technology called reverse transcription polymerase chain reaction, or RT-PCR, to find the genetic material of the virus in samples taken from people’s noses. Then, using DNA probes, they identify whether the samples are infected with the original coronavirus strain – or one of the new variants.
“Our hope is that Stanford’s enhanced surveillance, combining RT-PCR and complete genome sequencing, will provide critical information to help public health efforts over the coming months,” said Pinsky.
Until now, the UK’s highly contagious variant – known as B.1.1.7 – had been found only in San Diego and San Bernardino counties in California, as well as in 28 other states. It is known to be more transmissible and there is emerging evidence that it can also be more deadly. Stanford’s laboratory found a confirmed case of 837 selected specimens. This variant is projected to become the country’s dominant lineage in early April.
The Brazilian variant discovered in the Bay Area – called P.2 – is not well understood. So far, he is less feared than his cousin P.1, who is now devastating the Brazilian city of Manaus. P.2, spreading over the state of Rio de Janeiro, shares only one of P.1’s three mutations. But this shared mutation, called an “escape mutation”, is worrying because it helps the virus escape our antibodies. Therefore, it can reduce the effectiveness of the vaccine. Of the 837 specimens selected, the Stanford laboratory found no evidence of P.1 – but a case of P.2.
“There is a small difference” between the two Brazilian strains, Pinsky said. “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 this variant in non-travelers from different parts of the state, suggesting spread across the community. Vaccines and some antibody treatments may be less effective against this strain. One study found that half of the patients had a complete loss of immune recognition; the others showed a modest decline, with immunity probably still sufficient to protect.
But our California variant – first reported just 12 days ago – is increasingly abundant, accounting for about 20 percent of the Stanford strings analyzed. This strain is not of great concern, as it is vulnerable to vaccines and treatments.
“This is a warning to all of us that we will continue to see the evolution of mutants,” said Dr. Anthony Fauci, director of the National Institutes of Allergy and Infectious Diseases, at a White House press conference on Friday. “The virus has a playing field to mutate. If we stop its replication, it cannot mutate ”.
“It is an incentive to vaccinate as many people as we can,” he said, “as soon as possible.”