December 4, 2022

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Omicron: The molecular mechanism of enhanced infectivity and immune escape

Omicron: The molecular mechanism of enhanced infectivity and immune escape

Omicron: The molecular mechanism of enhanced infectivity and immune escape. 

Cell Blockbuster: Structural biology studies reveal the molecular mechanism of enhanced infectivity and immune escape of Omicron mutant strains

On November 26, 2021, the WHO classified the new coronavirus variant strain B.1.1.529 found in South Africa as the fifth “variant of concern” (VOC) and named it after Omicron.

An astonishing 35 mutations appeared in the Spike protein of this mutant strain, especially 15 mutations in the RBD region, which plays an important role in the process of virus recognition of host cells, arousing the attention of scientists around the world.

Subsequently, Omicron quickly replaced Delta as the mainstream strain in many countries in just 2 months , showing a strong ability to spread .

In addition, studies have shown that people who are naturally infected or vaccinated will still be infected with Omicron, and the titers of neutralizing antibodies to Omicron in serum samples of the above-mentioned populations have decreased significantly, indicating that the mutant strain has a strong immune evasion ability .

Many questions about Omicron

  • What is the molecular mechanism by which the infectivity and immune evasion of Omicron are significantly improved compared with WT and other VOCs?
  • How do the 35 mutations in the Omicron Spike protein affect the virus?
  • How should safe and effective vaccines and therapeutic drugs be designed for Omicron?

On January 25, the team of Professor Wang Xiangxi from the Institute of Biophysics of the Chinese Academy of Sciences published a blockbuster article entitled ” Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant ” in Cell magazine.

The Omicron Spike Trimer antigen and the complex mechanism of Spike Trimer and ACE2 receptors were used to answer the above questions through structural analysis and biochemical experiments.

In this study, ACROBiosystems provided important research reagents and made important contributions in antigen and antibody expression and biochemical analysis of antibodies.

In the Omicron Spike protein structure analysis experiment, the project developed and used the Spike trimer protein (Cat.No. SPN-C52Hz ) produced by ACROBiosystems .

ACROBiosystems continues to pay attention to the development of the COVID-19 epidemic.

You are welcome to follow the official account for more cutting-edge reports and progress in the development of vaccines and therapeutic antibodies.

Omicron Spike trimer enhanced stability

The researchers firstly expressed the Omicron Spike Trimer in the Prefusion state by recombinant in vitro, and analyzed the structure of Spike Trimer using cryo-electron microscopy at normal physiological pH 7.5 and endosome pH 5.5 (Figure 1).

The structure shows that the spatial conformation of Omicron Spike protein in the two pH environments is almost the same, with one RBD in the “up” conformation and two RBDs in the “down” conformation, while the Spike Trimer of WT and other VOC strains is in addition to the above In this spatial state, there are also three RBDs in the “down” conformation.

Omicron: The molecular mechanism of enhanced infectivity and immune escape

Figure 1. Spatial 3D structure of Omicron Spike Trimer at pH 7.5 and pH 5.5

By comparing the structures of the two mutant Spike proteins, Omicron and Delta, it was found that because the newly emerged mutation site on the Omicron Spike protein increased the hydrophilic and hydrophobic interactions between the “up” conformation RBD and the “down” conformation RBD, these two The RBDs of this conformation are closer in space and have a larger interaction area, which provides an explanation for the existence of only one spatial structure state of Omicron Spike protein.

In addition, the interaction area of ​​S1 and S2 subunits of different monomers in Omicron Spike Trimer is larger, which makes the overall structure of Spike Trimer appear more “compact”, and the stability of the protein is improved.

Not only that, the results of biochemical experiments also showed that the thermal stability of Omicron Spike protein was higher than that of WT and Delta Spike protein (Figure 2).

Omicron: The molecular mechanism of enhanced infectivity and immune escape

Figure 2. Spike Trimer stability of Omicron is higher than WT and Delta

Increased stability of the Spike protein increases the efficiency of recognizing the receptor ACE2, but it also reduces the efficiency of subsequent fusion of the viral envelope with the host cell membrane.

The Spike proteins of different strains were treated by adding Trypsin and ACE2 in vitro, and the proportion of Omicron Spike proteins converted from the Prefusion conformation that recognizes the receptor ACE2 to the Postfusion conformation that mediates membrane fusion was observed by counterstaining electron microscopy, which was lower than that of WT and Delta Spike proteins. (image 3).

Omicron: The molecular mechanism of enhanced infectivity and immune escape

Figure 3. In vitro addition of Trypsin and ACE2 to the Spike protein in the Prefusion conformation

Omicron neutralization activity decreased by class 5 antibodies

According to previous literature reports, a number of FDA-approved commercialized COVID-19 neutralizing antibodies almost lost their neutralizing activity against Omicron mutants, such as Regeneron’s REGN10933 and REGN10987; Eli Lilly’s LY-CoV555 and LY-CoV016; Aspen Likang’s AZD1061 and AZD8895.

Through structural analysis, it was found that the new amino acid deletion or mutation in the NTD and RBD regions of Omicron Spike protein resulted in great changes in the antigenic epitope, resulting in the loss of neutralizing activity of many neutralizing antibodies against Omicron, such as S477N and T478K on RBD. , E484K, Q493R, G496S, Q498R, N501Y, Y505H, etc.

Previous studies have classified neutralizing antibodies into I-VI classes according to different antigen-binding epitopes on RBD by analyzing the structure of the complexes of SARS-CoV-2 neutralizing antibodies and RBD antigens that have been resolved in the PDB database .

In this study, a total of 18 antibodies of these 6 classes were tested for their ability to neutralize WT and Omicron pseudoviruses.

The results showed that although the neutralizing activity of class V antibodies was weak, it was not greatly affected by the Omicron mutation, while the remaining 5 classes of antibodies had little effect on Omicron.

The neutralizing ability of Omicron was significantly lower than that of WT, which also explained why the neutralizing activity of commercial neutralizing antibodies against Omicron was greatly reduced (Fig. 4).

Omicron: The molecular mechanism of enhanced infectivity and immune escape

Figure 4. Detection results of neutralizing activity of class I-VI antibodies against Omicron mutant strains

Conserved regions can be used as the development direction of new generation antibodies

The researchers used the SPR method to detect the affinity of Omicron RBD protein to ACE2 and found that the result was 2.8 times higher than that of WT RBD.

By analyzing the three-dimensional structure of Omicron Spike Trimer and ACE2, it is found that there are two RBDs in the “up” conformation on the Omicron Spike protein that bind to two ACE2s.

The amino acids of Omicron form an interaction, which can increase the affinity of Spike to ACE2, but the presence of K417N and E484 mutations reduces the binding of Spike to ACE2, so overall, like other mutant strains, Omicron’s Spike protein has an increased affinity for ACE2 (Figure 5).

Figure 5. Structural analysis of the complex between Omicron Spike protein and ACE2

The researchers also analyzed the Spike protein sequence of β-coronaviruses that use ACE2 to recognize and infect host cells, and found that 11 conserved amino acids are involved in binding to ACE2, and these amino acids can be divided into groups I-IV.

Group I includes 6 highly conserved amino acids G447, Y453, N487, Y489, T500, G502; group II includes 5 amino acids with similar properties Y449/F/H, F456/L, Y473/F, F486/L and Y505H, group III includes 5 less conserved amino acids G446/S/T, L455/S/Y, A475/P/S, G476/D and G496/S, group IV includes 5 highly variable amino acids K417/V/N/R/ T, E484/K/P/Q/V/A, Q493/N/E/R/Y, Q498/Y/H/R and N501/Y/T/D/S (Figure 6).

Among them, there are few amino acids in group I-II, and it is speculated that these two groups of amino acids may play an important role in recognizing ACE2 and maintaining the conformational stability of Spike protein, while amino acids in group III-IV have mutations in VOC. Some neutralizing antibodies reported so far, such as XGv47, A23-58.1 and S2K146, recognize the amino acid epitopes of group I-II, so these neutralizing antibodies can compete with ACE2 for binding to Spike protein, and the antigen-binding epitopes are highly conserved , is expected to become a new generation of antibodies for the treatment and prevention of Omicron and potential new coronavirus mutant strains.

Figure 6. Classification of amino acids involved in binding to ACE2 on Spike protein of betacoronavirus


In this study, cryo-electron microscopy was used to analyze the mechanism of Omicron Spike Trimer and the complex between Spike Trimer and ACE2, and the molecular mechanism of Omicron’s enhanced infectivity and immune escape was explained through structural analysis and biochemical experiments.

The above two groups of highly conserved antigen-binding epitopes provide a theoretical basis for the design of broad-spectrum vaccines and neutralizing drugs.

(source:internet, reference only)

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