Study suggests SARS-CoV-2 Omicron variant RBM binding may be weaker than in wild-type

The Omicron variant has recently risen to prominence, sparking several countries’ return to more severe social distancing measures and restrictions designed to reduce transmission. The Omicron strain carries several mutations in the spike protein. The spike protein is key to the pathogenicity of the disease; the S1 subunit carries a receptor-binding domain (RBD) that binds to the angiotensin-converting enzyme in order to allow cell entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), while the S2 subunit is responsible for membrane fusion.

Researchers from the University of Rostock have been examining the effects of some of these mutations.

Study: Compared with SARS-CoV2 wild type’s spike protein, the SARS-CoV2 omicron’s receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure. Image Credit: Fit Ztudio/ShutterstockStudy: Compared with SARS-CoV2 wild type’s spike protein, the SARS-CoV2 omicron’s receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure. Image Credit: Fit Ztudio/Shutterstock

A preprint version of the group’s study is available on the bioRxiv* server, while the article undergoes peer review.

The study

The RBD of the wild-type SARS-CoV-2 spike protein shows the amino acid sequence aa437 to aa508 stretch enough to encompass the receptor-binding motif (RBM). It has been reported that in VOCs, amino acid residue exchanges can be seen at distinct positions with the RBM. For example, the omicron variant shows ten exchanged amino acids, five of which can also be found in severe acute respiratory syndrome (SARS-CoV-1/SARS).Through these changes, the RBM of the Omicron variant can be distinguished from the wild-type. 3D structures from both SARS-CoV-1 and SARS-CoV-2 are revealed using X-ray data, while the RBM structure is modeled using alphafold. The five RBM amino acid exchanges that are not also found in SARS-CoV-1 or the wild-type are unique to Omicron. One of the mutations Omicron carries is Y501, which strengthens the binding to ACE2, and can be found in the Alpha, Beta, and Gamma variants.

Residue K4768 has been designated as the decisive amino acid exchange for the Delta variant. This exchange remains in Omicron, and alongside residues K440, S446 and N447, these changes lend Omicron characteristics not seen in other variants – for example, K478 matching with K465, which is more characteristic of SARS-CoV-1 than SARS-CoV-2. In the Alpha variant, the residue E484 is known to weaken receptor binding. Omicron avoids this by expressing A484, matching the equivalent SARS-CoV-2 residue A471 – located next to the L472 residue that comes into direct contact with ACE2. Another residue, K493, in the RBM of Omicron is positioned where N479 is found in SARS-CoV-1. N479 is another residue that contacts ACE2 and is also considered essential for binding and infectivity. An N479K exchange results in steric hindrance and weakening of ACE2 binding. S496 and R498 are rare mutations in the RBM, likely as they are assumed to have adverse effects on binding due to the introduction of charge repulsion. Y501 is thought to strengthen binding and increase replication rates. H505 is located where Y491 is on SARS-CoV-1 – replacing Y505 seen in the wild-type. Y505 is directly involved in hACE2 binding, and the residue exchange is assumed to weaken binding.

The researchers performed free energy difference calculations to confirm their hypothesis: that the Omicron RBM binding to ACE2 was weaker than the wild-type. They examined the energy difference for the RBMs if either the wild-type, Alpha, Delta or Omicron variants were bound to ACE2, and compared them to respective RBM DPP-IV interactions as a negative control. According to ΔΔG calculations on amino acid exchanges and their contributions to receptor binding, the Alpha RBM is the only variant that should show stronger binding to ACE2 than the wild-type. The Delta RBM shows roughly equivalent binding strength compared to the wild-type, but the Omicron RBM-ACE2 complex is less energetically favored.

Conclusion

The authors highlight that their study shows that Omicron binds to the ACE2 receptor in a significantly weaker manner than other variants and the wild-type. They suggest that the increased transmission of Omicron results from mutations outside of the RBM, and imply that the virus is beginning to adapt more to the host, with less severe disease outcomes and higher transmission.

However, there are some issues - the negative control used can be bound by SARS-CoV-2, making it inappropriate for use in this circumstance. While the binding of the Omicron variant appears to be lower, this has not been confirmed by more physical experimentation, such as binding assays, and the conclusions may somewhat overreach the evidence gathered. The best example of this would be the assumptions the authors make of the severity of disease outcome – of which there is currently very little solid data – compared to RBM-ACE2 binding. There is currently little indication that a change of this size in RBM binding and disease severity are significantly linked.

*Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information

Journal reference:
Sam Hancock

Written by

Sam Hancock

Sam completed his MSci in Genetics at the University of Nottingham in 2019, fuelled initially by an interest in genetic ageing. As part of his degree, he also investigated the role of rnh genes in originless replication in archaea.

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