Molecular properties of SARS-CoV-2 mutants that allow antibody escape

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread rapidly around the world and has evolved into multiple variants with antigenic escape and higher infectivity than ancestral variants.New review paper published in PLoS pathogen Describes the new variants and the structural mechanisms underlying antibody-mediated neutralization and escape of mutant antibodies.

study: Structural and antigenic variation of the new SARS-CoV-2 mutant spike protein.. Image credit: ktsdesign / Shutterstock

Preface

The virus uses multiple mechanisms to escape the host’s immune response. These include the addition of complex glycans to shield viral antigens, antibody-mediated blocking of neutralization and complement activation, mutation of epitope residues, and shortened viral glycoproteins with common viral spike epitopes. Includes the production of.

Activated B cells in the germinal center undergo a class switch to become memory B cells, further indicating choices for cell population expansion, somatic hypermutation, and enhanced antigen binding.

For SARS-CoV-2 Spike protein An antigen that binds to the angiotensin converting enzyme 2 (ACE2) receptor in the host cell via the S1 subunit and achieves membrane fusion via the S2 subunit. Being an RNA virus, it exhibits high mutation rates, high yields, and short replication times. These allow them to adapt to different environments under selective pressure, evade host immunity, and demonstrate drug resistance. Despite its calibration system, over 25,000 mutations have been identified in the viral genome.

Some of these mutations facilitate antibody escape, and mutant antigen profiling helps identify hotspots for such mutations in spikes or enveloped proteins. By defining a functional binding epitope, antibody escape mapping Convalescent plasma Or a monoclonal antibody (mAbs). This can be important in developing treatments.

The SARS-CoV-2 spike protein exhibits greater conformational variation in later mutants compared to its ancestors or D614G mutants. This may be due to the fact that the mutant plays an important role in the binding and localization of angiotensin converting enzyme 2 (ACE2) to the host cell surface.

Various SARS-CoV-2 variants

So far, the World Health Organization (WHO) has four classes of SARS-CoV-2 variants: monitored variants (VBMs), interested variants (VOIs), and concerned variants (VOCs). And identify variants with significant consequences. (VOHC). There are 10 VBMs and 2 VOCs: Delta and Omicron.

Alpha VBM has Δ69 / 70 and Δ144 for NTD and N501Y mutations in the receptor binding domain (RBD), with higher infectivity, faster syncytium formation, and higher binding affinity. The structure of RBD and NTD has not changed significantly, but is associated with higher mortality and virus spread than ancestral variants. Both the Pfizer and AstraZeneca (AZ) vaccines provide long-term protection against this variant, comparable to that against the D614G.

Beta variants have multiple mutations, including K417N, E484K, and N501Y in the spike, with an NTD deletion in 241-243, which reduces antibody binding and alters the structure of the NTD neutralizing epitope. The E484K mutation enhances the electrostatic interaction at the interface, increasing RBD binding to ACE2 and contributing to improved infectivity.

There are suggestions that beta variants weaken viral interactions with T and B cells, leading to the avoidance of immune surveillance. Both vaccines are less effective against this variant than D614G or Alpha.

Gamma has the same or very similar mutations as the beta variants of RBD (K417T / N, E484K, and N501Y), but is more susceptible to antibodies due to allosteric interactions with distant mutations. increase. Vaccine efficacy against this variant is high.

In the delta variant, there are 11 distinct mutations in the spikes, and P681R is highly conserved, promoting efficient furin cleavage, enhancing membrane fusion and pathogenicity. The alpha variant has another non-synonymous mutation in P681, but the delta has a 60% higher transmission rate.

The presence of several RBD mutations, such as L452R, near the edge of the ACE2 binding surface may indicate that this variant accumulated multiple antigenic and antibody avoidance mutations while retaining high ACE2 binding. there is. The T478K mutation replaces the E484K mutation in the previous variant, resulting in reduced loss or binding by class 1 and class 1. Neutralizing antibody..

Both Omicron and Delta variants, unlike other variants known to date, contain multiple mutations and deletions in NTD at the supersite. They alter the antigen surface and glycan shield around this supersite, allowing these variants to escape NTD-specific neutralizing antibodies in convalescent sera induced by infection or vaccination of ancestral variants. Make it possible.

Omicron contains more than 34 spike mutations, many of which are known to be more contagious and, in fact, more contagious than the highly contagious delta mutants. In addition, it contains mutations that promote spike fusion and mutations that enhance receptor binding affinity.

Vaccine-inducing and therapeutic antibodies

With the Pfizer vaccine, neutralizing antibodies were low or undetectable against the D614G, alpha, beta, and delta variants, but increased after the second dose. Nevertheless, the neutralizing titers were 3-fold or 16-fold lower in the beta and delta variants compared to the alpha variant. The AZ vaccine yielded similar results, indicating that the neutralization response to these mutants was significant only after the second dose of the vaccine.

Most monoclonal antibodies that are considered potential or practically valuable against SARS-CoV-2 infection have lost their activity against Omicron. Only 3/9 mAb retained some activity such as ADG-20 and sotrovimab. Five months after the second dose of both vaccines, some reports showed that recipient sera showed little or no antiviral activity against the Omicron mutant. Nevertheless, booster vaccinations with nucleic acid vaccines, such as the Pfizer vaccine, increased the effectiveness of the vaccine to 75%.

Neutralizing antibodies are directed against RBD, and in 90% of cases the rest target the S2 subunit and NTD. However, the S2 subunit appears to be more conserved and may therefore be a better target for the development of broadly neutralizing antibodies. The immune predominance of RBD may be due to low glycosylation, easy access, and exposed potential sites due to multiple conformations.

Antibodies-mediated neutralization and escape

Analysis between structural contact sites and escape maps suggested that these maps complement each other. Therefore, a comprehensive knowledge of the immunodominant epitopes of peplomer proteins and escape mutations will help in our efforts to understand the evolution of viruses and the rational design of antibody therapeutics, vaccines, and other countermeasures... “

Antibodies bind to epitopes that overlap with the ACE2 receptor and are classified according to their ability to recognize RBD in the open, closed, or both states. Class 1 nAb directly competes with ACE2 by binding to RBD in the “upper” conformation, and class 2 nAb directly competes with the receptor by binding to both “upper” and “lower” RBD. And class 3 nAb binds to the spikes on the outside of the RBD-ACE2 bond. Interfaces for both “up” and “down” RBDs.

Class 4nAb binds to the mysterious epitope of “up” RBD. Finally, there is anti-NTDnAb. However, because NTD supersite mutations occur in many variants such as alpha, beta, and gamma, therapeutic nAbs continue to target RBD. These mutations block neutralization by anti-NTD antibodies.

However, the paper also points out that antibodies are being produced against these mutants, which can be effectively neutralized, but at a slower pace than the evolution of the mutants themselves. increase.

So far, no viral variants have emerged with mutations that circumvent all three antibody classes. Therefore, close monitoring of the SARS-CoV-2 sequence is required. This is due to the heavy burden of developing strains that can avoid all four antibody classes... “

Future: Widely neutralize nAb

Several anti-RBD antibodies have been identified, including A23-58.1, B1-182.1, and mAb 222. These are widely neutralizing nAbs that bind to highly conserved regions at the tip of the RBD away from mutant hotspots containing K417. , E484, and N501. Such antibodies have great potential for development and use as cocktails in the effective treatment of SARS-CoV-2 infections.

Manipulated molecules such as Nanobodies that bind to conservative regions on RBDs that are inaccessible to human antibodies and are broadly neutralized outside the ACE2-binding surface have also been conceptualized and developed. Biospecific antibodies, including paired antibodies with non-overlapping epitopes on the spikes. And multivalued Nanobodies. All have been reported to be highly effective in neutralizing and effectively blocking the escape of mutations.

In addition, a vaccine-induced cross-reactive adaptive cell-mediated immune response is also important in long-term immunity to the virus, minimizing the risk of mutation-induced escape. But as the virus continues to evolve

Global genome surveillance, better vaccination promotion, bnAbs development, and new drugs are essential to combat COVID-19... “