Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

Yasunori Watanabe; Zachary T. Berndsen; Jayna Raghwani; Gemma E. Seabright; Joel D. Allen; Jason S. McLellan; Ian A. Wilson; Thomas A. Bowden; Andrew B. Ward; Max Crispin

HIV-1 Env is a prototypic viral class I fusion protein that exhibits extensive surface glycosylation, resulting in an effective glycan shield to aid evasion from the host adaptive immune response 25, 52 . In order to visualize the structure of the respective glycan "shields" of HIV-1 and SARS coronavirus, we used single-particle cryo-electron microscopy (cryo-EM), as recently described 53 . The results for HIV-1 Env were reproduced from Berndsen et al. 53 while the previously published SARS 2P dataset 54 was reprocessed for this study. Although cryo-EM datasets of fully glycosylated MERS S 41 and chimpanzee simian immunodeficiency virus (SIVcpz) 55 are also available, only the HIV and SARS data were of sufficient quality (Fig. 5) . Using combination of low-pass filtering and thresholding, along with 3D variability analysis, we can reveal the previously hidden structure of the SARS glycan shield and compare it with the HIV-1 Env glycan shield 53 (Fig. 5) . We observe the nearly all-encompassing glycan density on HIV-1 Env and evidence for extensive glycan-glycan interactions, especially in the oligomannose patch regions, whereas the glycans on SARS S are more isolated and lack the wide-ranging glycan networks that are the hallmark of an effective glycan shield 56, 57 . The high variability around the S1 receptor binding domains is indicative of their flexibility, which is necessary for the spike to engage its receptor 58 ; however, this intrinsic property complicates the analysis of the signal from glycans in this region.