Covid: South African, Brazilian strains raise new fears on vaccines, immunity

Mutations of the Sars-Cov-2 virus found in South Africa and Brazil have begun worrying authorities and scientists who say that these – they are distinct from the new variant first found in the UK – could trigger more re-infections, even reduce vaccine efficacy, though more tests are underway.

The first major mutation of the Sars-Cov-2 virus was reported from the UK in the so-called B.1.1.7 variant (also called VOC202012/01) ; authorities said in December that it was more infectious, and it was later seen as a factor in leading to the country’s worst wave yet.

Scientists also discovered a handful of other significantly mutated strains. Two of these, B.1.351, found in South Africa, and P.1 found in Brazil, now seem like they can escape, at least partly, the immune response in people who have been vaccinated or were infected earlier, preliminary studies and government reports published this week say.

“It is possible that these mutations and others that emerge in individuals with suboptimal or waning immunity will erode the effectiveness of natural- and vaccine-elicited immunity. The data suggests that Sars-CoV-2 vaccines may need to be updated,” said a team led by researchers from Rockefeller University in a study submitted to Biorxiv on January 19.

Mutations in a virus are a natural phenomenon and the Sars-Cov-2 was seen to be gaining two significant mutations every month. But in December, researchers began discovering some strains with unusually high number of mutations – the UK-associated strain has 23 changes, the South Africa-linked one has eight and the Brazil-linked one has 20.

Among these changes are N501Y and E484K. These letters refer to descriptions of how a particular portion of the virus has changed – these in particular are all changes in the Spike protein, the component that the virus uses to infect cells. Of these, N501Y has been linked to the virus becoming more infective, while E484K is the mutation that possibly makes the virus more resistant.

The variant in UK carries N501Y, the one seen in Brazil carries E484K and the one seen in South Africa has both.

The researchers took these mutations for laboratory tests to check how immune cells triggered by vaccines reacted to them. With plasma from 14 people who received the Moderna vaccine and from six who got the Pfizer-BioNTech dose, they saw a “modest” but significant drop in how the immune cells neutralised the mutated strains as compared to how they neutralised the older one.

Similar findings were shared by South African authorities on January 18. The variant B.1.351 (which contains E484K) did not react with antibodies in 21 out of 44 serum samples collected from people infected in the first wave, South African scientist Salim Abdool Karim said at a discussion streamed online on January 18.

There is also at least one confirmed case of re-infection caused by the P1 variant (which too has E484K). This was detailed by Brazilian researchers in a study published on January 18, detailing the case of a 29-year-old woman in Manaus, Brazil, who developed a symptomatic infection in March. In late December, she was infected again with symptoms such as fever. Genetic sequencing showed the second infection was with the P1 variant.

The Covid-19 Genomics UK (COG-UK) consortium said the emergence of such variants raises the concern that there might be an evolutionary convergence that could make the virus capable of spreading faster and harder to fight. “However, the effect of this mutation in relation to natural immune or immunity from vaccination has yet to be determined,” they added in a report released on January 19.

Researchers also say that the evolution of Sars-Cov-2 at present does not pose a major risk since the changes seen even till now do not make existing immunity (from older infections) or vaccines completely obsolete.

It ties into projections that Covid-19 could become endemic, where it will be able to keep circulating by evolving but not lead to as debilitating effect. “What the long-term effect of accumulation of mutations on the Sars-CoV-2 on the pandemic will be is not known, but the common cold coronavirus HCoV-229E evolves antigenic variants that are comparatively resistant to the older sera but remain sensitive to contemporaneous sera,” the researchers in the first study said.

In a study published in Science on January 12, a team led by researchers from Emory University used transmission modelling and estimates of immunity prevalence to suggest that once Sars-Cov-2 becomes endemic, it will resemble a common cold since childhood infections will confer protection against severe disease later.