Natural variations within the glycan shield of SARS-CoV-2 impact viral spike dynamics

Abstract

The emergence of SARS-CoV-2 variants alters the efficacy of existing immunity, whether arisen naturally or through vaccination. Understanding the structure of the viral spike assists in determining the impact of mutations on the antigenic surface. One class of mutation impacts glycosylation attachment sites, which have the capacity to influence the antigenic structure beyond the immediate site of attachment. Here, we compare the glycosylation of a recombinant viral spike mimetic of the P.1 (Gamma) strain, which exhibits two additional N-linked glycan sites compared to the equivalent mimetic of the Wuhan strain. We determine the site-specific glycosylation of these variants and investigate the impact of these glycans by molecular dynamics. The N188 site is shown to exhibit very limited glycan maturation, consistent with limited enzyme accessibility. Structural modeling and molecular dynamics reveal that N188 is located within a cavity by the receptor binding domain, which influences the dynamics of these attachment domains. These observations suggest a mechanism whereby mutations affecting viral glycosylation sites have a structural impact across the antigenic surface.

The diversity of the glycan shield of sarbecoviruses closely related to SARS-CoV-2

“…This N20 site was found in both clade 3 sarbecoviruses used in this study BM4831 and BtKY72, although these strains lack site N17. The gamma variant also contains N188 (Newby et al, 2022), and whilst this site is not present in any of the strains analyzed in this study, 4 sarbecoviruses contained this site in the larger panel. Interestingly, whilst the majority of sarbecoviruses contained N370, SARS-CoV-2 did not.…”

Involvement of sialoglycans in SARS‐COV‐2 infection: Opportunities and challenges for glyco‐based inhibitors

“…The roles of the spike glycans have been proposed as: (1) a glycan shield to escape from the host immune system. 58 , 61 Mutations arising in the variant of concern, such as an additional N ‐glycan site arising in the Gamma variant, may increase the glycan shielding on the surface of spike glycoprotein, 62 (2) stabilizing favorable “up” conformation of RBD, which is required for ACE2 interaction, 63 and (3) target ligands for host attachment and viral entry through interaction with host lectins. Sialic acid‐binding immunoglobulin‐type lectins (Siglecs) are animal lectins that recognize sialic acid‐containing glycans and facilitate SARS‐CoV‐2 viral entry in an ACE2‐dependent manner.…”

Impact of mutations on the plant-based production of recombinant SARS-CoV-2 RBDs

“…The SARS-CoV-2 spike protein monomer on the surface of the virus contains 22 highly conserved N-glycosylation sites. Nglycosylation of these sites is important for expression, conformational dynamics and virus infectivity as shown for the original SARS-CoV-2 strain (Yang et al, 2020b;Zhao et al, 2020;Newby et al, 2023). Many viral envelope proteins and subunits are explored as vaccine candidates and glycosylation is critical for vaccine development (Bagdonaite and Wandall, 2018;Ozdilek and Avci, 2022).…”