Vulnerabilities in coronavirus glycan shields despite extensive glycosylation

Yasunori Watanabe,Joel D Allen,Gemma E Seabright,Ian A Wilson,Jason S Mclellan,Zachary T Berndsen,Max Crispin,Jayna Raghwani,Andrew B Ward,Thomas A Bowden,Oliver G Pybus

doi:10.1038/s41467-020-16567-0

Abstract

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. Vaccine development focuses on the principal target of the neutralizing humoral immune response, the spike (S) glycoprotein. Coronavirus S proteins are extensively glycosylated, encoding around 66–87 N-linked glycosylation sites per trimeric spike. Here, we reveal a specific area of high glycan density on MERS S that results in the formation of oligomannose-type glycan clusters, which were absent on SARS and HKU1 CoVs. We provide a comparison of the global glycan density of coronavirus spikes with other viral proteins including HIV-1 envelope, Lassa virus glycoprotein complex, and influenza hemagglutinin, where glycosylation plays a known role in shielding immunogenic epitopes. Overall, our data reveal how organisation of glycosylation across class I viral fusion proteins influence not only individual glycan compositions but also the immunological pressure across the protein surface.

Highlights

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential
N-linked glycan sequons per trimeric spike with SARS-CoV-2 containing 66 sites. These modifications often mask immunogenic protein epitopes from the host humoral immune system by occluding them with host-derived glycans[16,17,18]. This phenomenon of immune evasion by molecular mimicry and glycan shielding has been well characterised across other viral glycoproteins, such as HIV-1 envelope protein (Env)[19,20,21], influenza hemagglutinin (HA)[22,23] and Lassa virus glycoprotein complex (LASV GPC)[24,25,26]
It is interesting to note that the distribution of oligomannose-type glycans was broad, with Man5GlcNAc2 to Man9GlcNAc2 glycans all present, without one particular dominant peak, as is the case for some viral glycoproteins, such as HIV-1 Env[36]

Summary

Introduction

Severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) coronaviruses (CoVs) are zoonotic pathogens with high fatality rates and pandemic potential. We provide global and site-specific analyses of N-linked glycosylation on soluble SARS, MERS and HKU1 CoV S glycoproteins and reveal extensive heterogeneity, ranging from oligomannose-type glycans to highly-processed complex-type glycosylation.

Results

Conclusion