Covid variant found in South Africa worries scientists

On January 15, US public health officials warned that a more contagious variant of the coronavirus, which causes Covid-19, could dominate infections in the United States by March. This harsh warning referred to B.1.1.7, a variant that was first identified in the United Kingdom.

But now, a week later, scientists are increasingly concerned about another variant that has emerged in South Africa.

There is evidence from several small studies, not yet peer-reviewed, that mutations in the South African variant – known as 501Y.V2 and already present in at least 23 countries – may be at increased risk for Covid- 19 in people who have been ill and should still have some immunity to the disease.

Scientists have not confirmed that this variant is more contagious, although the evidence points in that direction. They are also concerned that 501Y.V2 may have implications for treatments for Covid-19. Regeneron, a company that developed a cocktail of two monoclonal antibodies as therapy for patients with the disease, reported that 501Y.V2 may be able to avoid one of the antibodies in its mix. The drug is still effective, but subsequent mutations may make it less effective.

But perhaps the most alarming is the prospect that mutations in the variant could limit the effectiveness of existing vaccines, one of the best tools we have to control the pandemic.

The results of these recent studies are “a serious indication that we have to look closely at how vaccines can work,” Penny Moore, a virologist at South Africa’s National Institute of Communicable Diseases, told Vox. Together, they highlight the dangers of letting Covid-19 spread unchecked and also foreshadow the challenges that will come as the virus continues to evolve.

What the 501Y.V2 coronavirus variant could mean for Covid-19 vaccines

Moore is the lead author of a recent study on 501Y.V2, published on Tuesday as a prepress on BioRxiv. She and her team in South Africa collected blood plasma samples from 44 people who were infected with the coronavirus during the country’s first wave of infections last summer and then checked how their existing antibodies responded to 501Y.V2, as well as with the older variants.

The researchers classified the plasma samples into categories – high and low concentrations of antibodies. Although antibodies may decrease after infection, this does not necessarily mean that the protection will disappear completely. Another recent study showed that immunity from infection lasts at least five months in most people, so the antibodies of people who have had the virus should still protect against previous versions of the virus if someone gets infected again.

In 21 cases – almost half – the existing antibodies were powerless against the new variant when exposed in test tubes. This was especially true for the plasma of people who had a mild previous infection and lower levels of antibodies to begin with.

The findings suggest that a previous Covid-19 infection may not help individuals defend themselves against the new variant if they are exposed, especially if the previous case is mild or symptom-free.

For Trevor Bedford, a scientist at Fred Hutch Cancer Research Center, who was not involved in the research, the study also came as a possible warning sign about vaccines. In the fall of this year, manufacturers may need to start reformulating their vaccines to respond to changes in the virus’s genetic code, he wrote on Twitter:

Specific mutation scientists are more concerned with

The 501Y.V2 variant carries a mutation of particular interest, known as E484K. This change appears in the part of the virus, the protein spike, which fits into the receptor of human cells. Spike protein is also the main target of the currently available mRNA vaccines, from Pfizer / BioNTech and Moderna.

“This mutation is right in the middle of a peak access point,” said Moore. And it became notorious among virologists for its ability to avoid antibodies against the coronavirus.

Scientists have demonstrated how this can happen in other cell culture experiments. In another recently published BioRxiv preprint, researchers in Washington state tracked how the mutations altered the effectiveness of the antibody response in the convalescent plasma of 11 people – and also found that the E484K had particularly potent antibody evasion capabilities.

Other worrying variants also carry the E484K mutation, including one first identified in Manaus, Brazil, known as P.1. And a case study suggests that reinfection in some people may be possible when they are exposed to the new variant.

In a pre-press, researchers in Brazil documented the case of a Covid-19 patient, 45 years old, without comorbidities, who months after her first attack with the disease, was reinfected with the new variant. The patient had a more serious illness the second time. Although it is limited evidence, “it may have important implications for public health policies, surveillance and immunization strategies,” wrote the authors.

The broader context of the study is also worrying: after it was estimated that more than three quarters of the population of Manaus was infected with the virus during a spring outbreak, cases are piling up again and hospitals are filling up. The researchers suspect that reinfections with the new variant may be the reason.

“The news is not all gloomy”

But “the news isn’t all bleak,” said evolutionary virologist at the University of Utah, Stephen Goldstein. A preprint, led by scientists at Rockefeller University, suggested that the vaccine’s antibodies may be more potent than antibodies from a previous infection. The researchers tested blood samples from 14 people who received the Modern vaccine and six who were immunized with the Pfizer / BioNTech vaccine. The E484K mutation, and two others found in the South Africa variant, were associated with a “small but significant” drop in antibody activity, the researchers found.

Still, said Goldstein, the antibodies induced by the vaccine “are so high that the serum was still extremely potent against the mutant.”

To fully understand the threat that mutations pose to vaccines, we will need clinical trials involving vaccinated people, said Moore. “These studies signal a problem,” she added, “but we don’t know how it translates into real life.”

There is also a wide variation in immune responses between people, Goldstein said. In the Washington article, the researchers found “wide variation from person to person” in how the mutations affected an individual’s antibody response.

“At the end of the day, there is some reason for concern about reducing effectiveness, but effectiveness will not fall off a cliff,” said Goldstein. “Vaccines are incredibly potent. … What if [they go] 95% [efficacy] to 85% or even a little less, we are still in great shape. That is why researchers and public health officials are strongly advocating that everyone be vaccinated as soon as possible.

Even so, Moore warned: “From the point of view of immune escape, the variants detected for the first time in Brazil and South Africa are more worrying, but this is only the beginning. It is our first indication that this virus can and does change. “

It is possible that, as we learn more, even the E484K mutation will not harm vaccines. But there may be other changes in the virus lurking or evolving that will escape even the antibodies induced by the vaccine. “So many people are now infected that this is an armed race – the virus now has every opportunity to mutate,” said Moore, “so that it can take steps on the path to immune escape more easily.”