Having Natural Immunity to the Original Coronavirus May Not Protect Against the South African and Brazilian Variants

Scientists from Seattle have demonstrated the influence of various mutations in the S protein on the effectiveness of neutralizing antibodies. One of them, which occurs in new variants of the coronavirus, drastically reduces it.

Coronavirus Vaccine

The emergence of new variants of SARS-Cov-2 is of concern to health authorities in affected countries because they have many changes in the S protein that affects their infectiousness. But that’s not the only cause for concern. If the S protein is different in the variants, will vaccines developed before their arrival be effective against the COVID-19 they cause? The Moderna and Pfizer vaccines stimulate the production of antibodies against the S protein. The sequence that served as the basis for the two pharmaceutical companies is the one published by Chinese scientists in early January 2020 when SARS-Cov-2 was discovered. It, therefore, does not contain the mutations described in the English, South African, and Brazilian variants. The S protein is essential for the replication of the virus; without it, it is impossible for it to infect cells. It is also an important target of antibodies, but if the S protein is mutated, the antibodies may not be able to recognize it, preventing viral replication.

Seattle scientists have studied the neutralizing capacity of polyclonal antibodies in patients with Covid-19 in various mutated forms of the S protein. Their results show that certain mutations dramatically reduce the neutralizing power of the antibodies, including one present in the South African and Brazilian variants described in December. The work is currently available as a prepublication in BioRxiv, subject to change after peer review.

E484K, the mutation that fools the immune system

Table of Contents

1 E484K, the mutation that fools the immune system

The starting point for this research is a library of more than 3,800 mutants of the SARS-Cov-2 S protein. Each mutant carries a unique modification in the receptor-binding domain, the region of the S protein that physically binds to ACE2. Neutralizing antibodies preferentially bind to this region to inhibit viral entry from its host cell. The antibodies were derived from the serum of 17 patients collected approximately one month after the onset of their symptoms. Eleven of these samples were tested for the presence of neutralizing antibodies.

The scientists then exposed the S-proteins from the mutated viruses to the neutralizing antibodies from the convalescent patients. The goal was to observe which mutations allow SARS-CoV-2 to escape neutralization. The results showed large differences between samples: In general, the neutralization capacity ranges from 63 to 99%, depending on the samples considered.

Nevertheless, one particular mutation seems to affect the neutralization capacity of the antibodies in most cases (9 out of 11 samples), namely a mutation in position E484. This residue is located on a “ridge” of the S-protein receptor binding domain. When glutamic acid (E) is replaced by lysine (K) or glutamine (Q), the neutralizing power of the antibodies decreases by a factor of ten. The E484K mutation is one of the specific mutations of the South African and Brazilian variants. Other mutations had the same effect, but only in a minority of the sera tested. Finally, a mutation in phenylalanine at position 456 (F456) also restricts the binding of antibodies to this epitope but does not hinder their ability to neutralize the virus.

Is there an impact on the efficacy of the vaccine?

The E484K mutation is the most significant, but it is quite rare. In fact, by December 23, 2020, scientists calculated the frequency of occurrence of certain mutations among all sequences listed by GISAID (Global initiative on sharing all influenza data). The E484K mutation occurs in only 0.11% of the sequences, while the four most common mutations, S477N, N439K, N501Y, and Y453F, affect 5.69%, 1.49%, 1.39%, and 0.36% of the analyzed sequences, respectively. These sequences do not affect the neutralizing capacity of the antibodies but confer additional advantages to coronavirus. The N501Y mutation, present in the English, South African, and Brazilian variants is associated with the higher transmissibility of the virus, on the order of 50%.

Thus, a variant carrying the E484K and N501Y mutations have two advantages over other coronaviruses: the ability to escape from neutralizing antibodies and better transmissibility. This is the case with the South African and Brazilian variants, which are infecting increasing numbers of people worldwide. Does this mean that the immunity induced by the vaccine is not able to stop its replication? It is difficult to draw conclusions by looking only at these results. Although they show how a simple mutation can outsmart neutralizing antibodies, the immune response is not limited to that; the effectors on the cell are just as important as other antibodies targeting epitopes other than the receptor-binding domain. Therefore, the efficacy of vaccination does not seem to be affected by the appearance of these new variants so far.