The glycan shields of HIV-1 and SARS-CoV-2 spike proteins and their differential importance in vaccine design.

Abstract

Viral infections are responsible for major global pandemics, causing millions of deaths and greatly impacting human societies across the globe. Two of the viruses responsible for some of the worst pandemics over the last century are human immunodeficiency virus-1 (HIV-1) and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Whilst symptoms of the diseases they cause are distinct, there are features of the virions which are shared across both viruses. Proteins on the surface of the virion mediate interactions with host receptors and act as fusion machinery to enable the virus to enter the host cell. As these are exposed, they are key targets of the human immune system, particularly for neutralizing antibodies. The elicitation of broadly neutralizing antibodies is an attractive target for vaccination as these antibodies, in combination with other parts of the immune system, protect against viral exposure.
Whilst the immune system is able to target the receptor binding proteins on the virion, viruses employ a range of strategies to avoid clearance. One such strategy is to shield the antigenic viral protein surface with glycans. During egress through the host cell, spike proteins hijack the host’s post translational machinery and attach polysaccharide chains, known as glycans, which cover the protein surface. As these are host-derived it can be difficult for the immune system to recognize these glycans as foreign and can aid the virus in avoiding immune detection. Vaccine design must capture the native-like display of glycans when trying to elicit an antibody-based response so as to avoid the recognition of vaccine-specific epitopes that are not present on the virus. The attachment of glycans to viral spikes is a heterogeneous process, as glycan maturation is not genetically encoded, as it is for amino acids. To this end bespoke strategies are required to understand glycan presentation on viruses and their corresponding vaccine candidates. Mass spectrometry is ideal for studying glycans as it can handle extremely heterogeneous mixtures. In this thesis I demonstrate how mass spectrometry can be used to inform vaccine design efforts by comparing and contrasting the glycosylation of SARS-CoV-2 and HIV-1 spike proteins, by studying the glycosylation of leading vaccine candidates for both viruses and their viral counterparts.
This thesis demonstrates that whilst key regions of the HIV-1 Env glycan shield are conserved between recombinant protein and the corresponding virus, there are differences in glycosylation regarding the composition and glycan occupancy at particular regions of the glycan shield. These differences result in the elicitation of undesirable antibodies however, this thesis demonstrates that the glycan occupancy of recombinant Env can be improved by engineering the N-linked glycan attachment sequon. Comparable analyses of SARS-CoV-2 S protein revealed that whilst under processed oligomannose-type glycans are present on the spike glycoprotein, their abundance is much less than that of HIV-1 Env, indicating a less dense glycan shield. Additionally, the glycan shield of recombinant and viral-derived S protein were in closer agreement than observed for HIV-1 Env. This work indicates that the extensive glycan shield of HIV-1 is more of a hinderance to vaccine design efforts compared to SARS-CoV-2.

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Identifiers

ORCID for Joel Allen: orcid.org/0000-0003-2547-968X

ORCID for Matthew Crispin: orcid.org/0000-0002-1072-2694

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