A group of researchers from the Medical School of the University of São Paulo (FMUSP) believe they have found the mechanism that allows the South African variant of Sars-CoV-2 (also known as B.1.351) to escape the antibodies it generates previous infections by the strain of the virus.
The discovery, which has yet to be confirmed by new experiments, could pave the way for the development of effective vaccines against the variant that has already appeared in South Africa and that already exists in Brazil and against the one from Manaus (P.1). as well as their predecessors.
The study, which was published as a form on the medRxiv platform, is in the peer review process.
Using computer simulations, the group studied the key protein of Sars-CoV-2, known as spike. It is responsible for binding to the receptor of human cells (the ECA2 protein) and enabling infection.
The results suggest that one of the mutations at the top of the tip of the South African variant – characterized by the replacement of the amino acid lysine for asparagine – may lead to the appearance of a biochemical phenomenon known as glycosylation, which changes the trait of the viral protein and prevents the binding of antibodies. In the P.1 variant, lysine is replaced by a threonine that does not undergo glycosylation.
“Today, when developing a vaccine, one has to choose what is most effective against the virus, including the variants. In the case of Sars-CoV-2, two of the three mutations that occur in P.1 and B.1.351 are exactly the same. It is therefore possible that a vaccine that focuses on the South African variant will also be effective against P.1 and against the ancestral virus. However, vaccines against the latter two are likely to be less effective against the South African variant, ”explains Keity Souza Santos, professor at FMUSP and author of the article.
The work is the result of a project supported by Fapesp and coordinated by Jorge Kalil, professor at FMUSP and coordinator of the Immunology Laboratory at Instituto do Coração (InCor), which also signs the article.
The group led by Kalil is working on the development of a vaccine against Covid-19. The project is supported by the foundation and the Financier of Studies and Projects (Finep).
“Previous work by other groups has failed to find the specific region where human antibodies bind to RBD [domínio de ligação ao receptor, na sigla em inglês]is known as the tip of the spike protein that fits human cells. By then, conclusions had been drawn. We used a technique that allowed us to pinpoint a predominantly recognized region that we call immunodominant. It’s the same thing that one of the mutations occurs in the Manaus and South Africa variants, ”says Santos.
After identifying the region in the first strain of the virus, the group of researchers from the USP, Universidade Estadual Paulista (Unesp), the Federal University of São Paulo (Unifesp), and the University of Salzburg (Austria) submitted the amino acid sequence to which the blood serum of 71 patients was initially recovered from Covid-19 during the pandemic in Brazil in the hospital das Clínicas by FMUSP. In 68% of the samples, the antibodies present in the serum were able to bind to the peptide P44, which is present in the RBD of the protein tip.
Computer simulations were carried out to understand how antibodies bind in this region found by the researchers. The RBD information from the two variants and the ancestral virus has been crossed with that of the monoclonal antibody REGN10933, which is known to bind to the immunodominant region and is currently in clinical trials for the treatment of Covid-19. The computer carries out what is known as a neutralization prediction, ie it estimates the ability of antibodies to neutralize the virus.
In the simulations, the prediction of neutralization against the ancestral virus was complete and somewhat lower for the P.1 variant. In the South African variant, however, there was a drastic decrease in the prediction of neutralization, which confirms what an article published by scientists dismissed by Americans just before the Brazilian submission of the article.
For the group headed by USP, the link in B.1.351 does not occur, since one of their mutations is precisely the exchange of the amino acid lysine for asparagine, which goes through the process of glycosylation. This change would likely account for the low estimate of the neutralization of the South African variant by antibodies generated by infection with the original strain of Sars-CoV-2. The phenomenon of glycosylation has already been observed in the influenza virus of the flu, but has not yet been demonstrated in the case of Sars-CoV-2.
“In the variants P.1 and B.1.351 the RBD mutation consists of only three different amino acids compared to the RBD of the ancestral virus. However, the change seems sufficient to make the Manaus and South Africa variants more transferable. A vaccine that creates antibodies that target the two mutations that both variants have in common, as well as the glycosylated amino acid from B.1.351, will likely be more effective, ”says Santos.
To confirm the hypothesis, the group is now planning in vitro experiments with samples of the P44 peptide with glycosylation in asparagine. The goal is to confirm that antibodies do not actually bind to this amino acid once it is glycosylated. In addition, the researchers received serum from patients who had recovered from P.1 and intend to confirm that these patients’ antibodies even bind to the peptide P44.