Features of SARS-CoV-2 Omicron BA.2 sublineage spike protein

By Shanet Susan AlexMay 3 2022Reviewed by Aimee Molineux

In a recent study posted to the bioRxiv* preprint server, researchers assessed the traits of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.2 sublineage spike (S) protein.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Background

SARS-CoV-2 variants of concern (VOCs) are often designated so for their propensity to spread and escape host immunity. The SARS-CoV-2 Delta and Alpha VOCs surpassed the circulating viruses at the moment during the preceding coronavirus disease 2019 (COVID-19) waves. This was mainly due to their increased transmissibility when a significant part of the population had yet to acquire immunity from vaccination or natural infection, and adaptive immunity had begun to dwindle. 

Shortly, the Omicron lineages arose with a substantially higher number of mutations in the S gene than the preceding VOCs. The Omicron BA.1 subvariant quickly displaced Delta, trailed by a progressive replacement of the seemingly more contagious Omicron BA.2 sublineage.

About the study

In the present study, the authors profiled the full-length SARS-CoV-2 Omicron BA.2 sublineage S protein and analyzed its structure relative to a native sequence using cryogenic electron microscopy (cryo-EM). The structural, antigenic, and functional features of BA.2 S protein and the replication of the authentic virus in animal models and cell culture were contrasted to priorly prevalent SARS-CoV-2 variants. This was to gain molecular insights into this significantly transmissible SARS-CoV-2 mutant. The team infected cytokeratin 18 promoter (K18)-human angiotensin-converting enzyme 2 (hACE2) or transgenic mice with authentic SARS-CoV-2 viruses.

Deoxyribonucleic acid (DNA) fragments were used to assemble the full-length S protein gene from the Omicron BA.2 variant. Further, the authors carried out the purification and expression of the full-length S protein. In addition, an anti-SARS-CoV-2 S antibody was used to perform a Western blot.

Results

The study results indicated that the mutations in the S protein-induced substantial reconfigurations of the antigenic structure and surface of the N-terminal domain (NTD) and receptor-binding domain (RBD), respectively, in both the Omicron BA.2 and BA.1 sublineages. These changes resulted in high robust resistance levels to neutralizing antibodies in BA.2 and BA.2 subvariants, not detected in earlier SARS-CoV-2 variants. Despite its higher ACE2 binding affinity, numerous studies suggested that the elevated mutations in BA.1 S protein might have impaired its fusogenic capacity in return for its ability to elude host immunity.

The authors illustrated that the BA.1 S needed a significantly higher ACE2 level on the host cells for successful membrane fusion, mainly due to the N856K mutation. This mutation was not identified in the BA.2 S, which was more fusogenic than BA.1 throughout a wide range of ACE2 levels, while its S was still weaker than other VOCs. As a result, the evidence reported herein revealed a molecular foundation for BA.2's higher transmissibility than BA.1.

The researchers discovered that pulmonary viral ribonucleic acid (RNA) copy counts were 100 to 1000 times greater in the Omicron- and Delta-infected mice than in the wildtype G614-infected during the initial 24 hours after infection. This was because the intranasal administration forced the viruses straight into the lung. Despite their reduced viral entrance exhibited in cell culture, both BA.2 and BA.1 may multiply in the lungs of vulnerable animals as quickly as the Delta variant and far faster than the G614 virus before host immune responses arise.

The scientists noted that the potential of the BA.2 and BA.1 viruses to spread into extrapulmonary organs was not correlated with receptor ACE2 levels. Further, it was likely controlled by other host variables or post-infection reactions. These results imply that both replicative benefits by the replication machinery and immune elusions by the S protein might result in elevated Omicron sublineages' transmissibility.

Additionally, with just seven residue modifications, the BA.2 sublineage has evolved a method different from the previous variants to remodel the NTD. It maintained the entire RBD structure, despite 16-point mutations, due to the functional relevance of receptor adherence. Interestingly, nearly all RBD mutations were found towards the borders of the RBD-1 and 3 epitopic areas. On the contrary, there were multiple alterations in the core of the RBD-2 region, which directly intersects the ACE2 binding domain. 

The findings suggested that the BA.2's RBD-1 and 3 surfaces were drastically conserved. Therefore, the investigators mentioned that targeting the immunogenic core of the RBD-1 or 3 regions might be a potential immunogen design technique for producing widely neutralizing antibody responses that can defend against present and perhaps future SARS-CoV-2 variants. 

Conclusions

The study findings demonstrated that the Omicron BA.2 S protein could fuse membranes more proficiently than Omicron BA.1 because of the absence of a BA.1-specific mutation that might slow down receptor engagement, yet was less efficient than other SARS-CoV-2 variants. Without pre-existing immunity, both the Omicron BA.2 and BA.1 variants reproduced far quicker in animal lungs than the early SARS-CoV-2 G614 or B.1 strain, presumably explaining their enhanced transmissibility despite their functionally impaired Ss. Mutations in the BA.2 S, like in BA.1, rearrange its antigenic domains, resulting in high resistance toward neutralizing antibodies.

Overall, the present study results imply that both replicative benefit and immune escape might play a role in the increased transmissibility of the SARS-CoV-2 Omicron sublineages.

*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.