A recent study published on the preprint server bioRxiv* explored the diversity of the glycan shield of sarbecoviruses, increasing knowledge for developing broad-spectrum pan-coronavirus vaccines.
Study: The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2. Image credit: Andrii Vodolazhskyi/Shutterstock
background
The various coronavirus outbreaks, starting with the severe acute respiratory syndrome coronavirus (SARS-CoV-1) epidemic in 2003 to the latest severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in 2020 , have emphasized the importance of vaccines in limiting the severity of these zoonotic diseases. Many vaccines developed to combat the COVID-19 pandemic targeted the glycoprotein (S) of SARS-CoV-2 and were based on existing knowledge of protein structure and protein engineering techniques.
Sarbecoviruses belong to the genus Betacoronavirus and include SARS-CoV-1 and SARS-CoV-2. Many sarbecoviruses with high similarity to the SARS-CoV-2 virus have been found circulating in various animal populations, such as bats and pangolins, and present a high risk of zoonotic disease. Understanding the similarities and differences in the glycan shield of various sarbecoviruses would help develop vaccines to combat a wide range of sarbecoviruses.
About the study
The S protein, which allows the virus to enter the host cell, undergoes several modifications inside the host cell, including proteolytic cleavage, maturation, and N-linked glycosylation. The major components of the S protein includes an N-terminal domain (NTD), a receptor-binding domain (RBD) and a C-terminal transmembrane domain, together with the fusion peptide and heptad repeats 1 and 2. Proteolytic cleavage separates protein S. Protein S into S1 (NTD and RBD) and S2. Approximately one-third of the mass of the S protein is made up of N-linked glycans, which play an important role in the proper folding and stabilization of the protein. N-linked glycans also play an important role in neutralizing antibody epitopes, and modified N-linked glycans, such as oligomannose-type N-linked glycans, contribute to the density of the glycan shield.
In this study, the researchers selected 78 sarbecoviruses that share similar sequences with SARS-CoV-2 and investigated the conserved and variable N-linked glycosylation sites. To explore the variability of the glycan shield, they selected 11 sarbecovirus spike protein genes and introduced mutations similar to those used in current SARS-CoV-2 vaccines.
The soluble native trimers of the S proteins that were produced were purified and analyzed by liquid chromatography mass spectrometry. Aliquots of tip glycoproteins were also subjected to trypsin, chymotrypsin, and alpha-lytic protease to investigate the glycan processing status of each site. They then modeled the N-linked glycan sites in structural models of sarbecoviruses to study the three-dimensional environment of these sites.
results
Comparison of the N-linked glycan sites of several sarbecoviruses with those of SARS-CoV-2 revealed that some glycosylation sites were highly conserved while others were highly variable. The researchers found that all strains contained highly conserved regions in the S2 subunit. Most strains also contained conserved sites in an oligomannose-type glycan-rich site and two sites in the SARS-CoV-2 RBD.
Divergent sites were found in or near the RBD and also showed restricted glycan processing. Later variants of the SAR-CoV-2 virus have shown that the RBD is under immune selection pressure and that antibody binding is greatly reduced with only a few regional mutations. The results indicate that glycan shields are highly conserved and play a role in maintaining the structure and function of protein S. However, determination of glycan processing states revealed that they were highly variable , despite the fact that many N-linked glycosylation sites are conserved in all sarbecoviruses. The researchers also inferred that the glycan shield around the RBD of all analyzed sarbecoviruses is sparse.
Conclusions
Overall, the results of the study showed that most N-linked glycosylation sites were conserved across multiple clades of sarbecoviruses. SARS-CoV-2 variants showed variability in the N-terminal regions, with the gamma variant containing a glycosylation site (N20) not found in the original Wuhan strain, but found in two other sarbecoviruses. In addition, the S2 region of the protein contained many conserved sites and expressed low levels of oligomannose-type glycans. Certain regions that expressed high variability in terms of glycan processing were found to be highly conserved sites, indicating heterogeneity.
The study provides new insights into potentially novel target regions of the spike glycoprotein for developing broad-spectrum sarbecovirus vaccines. It also highlights the highly variable regions of the RBD, indicating potential pitfalls of developing vaccines targeting these sites.
With the rapid rate at which SAR-CoV-2 variants have emerged, combined with the discovery of several highly similar sarbecoviruses circulating in nature that are potential zoonotic pathogens, there is an urgent need to develop a pan-coronavirus vaccine . Although the researchers mentioned that antibodies generated to these conserved target sites lack the potency of RBD-specific antibodies, the study emphasizes the importance and potential of exploring conserved regions for vaccine design.
*Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health-related behavior, or be treated as established information.