Site-Specific Steric Control of SARS-CoV-2 Spike Glycosylation

Allen, Joel D.; Chawla, Himanshi; Samsudin, Firdaus; Zuzic, Lorena; Shivgan, Aishwary Tukaram; Watanabe, Yasunori; He, Wan-ting; Callaghan, Sean; Song, Ge; Yong, Peter; Brouwer, Philip J. M.; Song, Yutong; Cai, Yongfei; Duyvesteyn, Helen M. E.; Malinauskas, Tomas; Kint, Joeri; Pino, Paco; Wurm, Maria J.; Frank, Martin; Chen, Bing; Stuart, David I.; Sanders, Rogier W.; Andrabi, Raiees; Burton, Dennis R.; Li, Sai; Bond, Peter J.; Crispin, Max

[Image: see text] A central tenet in the design of vaccines is the display of native-like antigens in the elicitation of protective immunity. The abundance of N-linked glycans across the SARS-CoV-2 spike protein is a potential source of heterogeneity among the many different vaccine candidates under investigation. Here, we investigate the glycosylation of recombinant SARS-CoV-2 spike proteins from five different laboratories and compare them against S protein from infectious virus, cultured in Vero cells. We find patterns that are conserved across all samples, and this can be associated with site-specific stalling of glycan maturation that acts as a highly sensitive reporter of protein structure. Molecular dynamics simulations of a fully glycosylated spike support a model of steric restrictions that shape enzymatic processing of the glycans. These results suggest that recombinant spike-based SARS-CoV-2 immunogen glycosylation reproducibly recapitulates signatures of viral glycosylation.