SARS-CoV-2 Glycosylation Suggests That Vaccines Should Have Adopted the S1 Subunit as Antigen

Abstract

Extant SARS-CoV-2 vaccines use the trimeric spike (S) protein as antigen. In the virus, the spike region is extensively glycosylated, modulating immune surveillance. Because they have been defused, many epitopes in the vaccine sidetrack the immune response. Only the receptor binding domain within the S1 subunit is well-exposed to antibody recognition. After proteolytic virus activation, the S1 subunit offers additional epitopes with antibody exposure. Thus, vaccines adopting the S1 subunit as antigen would have been more efficacious than the existing ones.

SARS-CoV-2 Glycosylation Averts Immune Surveillance

Glycosylation is a fundamental post-translational or cotranslational modification of proteins that influences the protein folding process and acts as a destination tag within the cell.¹ Viruses like SARS-CoV-2 are believed to resort to glycosylation partly to avert immune surveillance.² Thus, glycan selective attachment to the trimeric spike (S) protein is extensive and serves as camouflage to disguise the region antigenicity and consequently modulate the immune response.²

Because the ACE2-receptor-binding domain (RBD) in the S1 subunit of the S protein plays a key anchoring role enabling cell entry, this region does not get glycosylated. In fact, it constitutes essentially the only antigenic region in the spike that is exposed to immune surveillance.² The fitness cost of shielding the antigenic RBD from immune attack would simply be too high for the virus as it would impair cell penetration.³ Thus, prima facie all extant vaccines which include this epitope⁴ are likely to retain efficacy as long as the virus continues to target the same host receptor.

On the other hand, the other epitopes present in the trimeric S protein adopted as antigen in the extant vaccines⁴ are in fact immunologically defused by the virus through glycosylation.² In fact, those epitopes sidetrack the vaccine-induced immune response. Hence, the evolutionary routes of SARS-CoV-2 to evade the vaccine-induced attack are funneled to the ACE2 RBD region in the S1 subunit, a constrained region in the sense that most mutations are likely to be deleterious.⁵ However, there are predicted mutations in that region and even at the ACE2 interface that are expected to enhance the stability of the virus–receptor interface,⁵ although there is no evidence that they have been selected so far during the current Covid-19 pandemic. This is not surprising because the virus will only be under severe selection pressure during the endemic or postvaccination phase and not during the pandemic phase.⁶

In Retrospect, COVID-19 Vaccines Should Have Adopted the S1 Subunit As Antigen

Given the SARS-CoV-2 glycosylation pattern² and the fact that all extant vaccines adopted the trimeric S glycoprotein as antigen,⁴ we may expect that immune efficacy may be somewhat diminished because a portion of vaccine-induced antibodies will get steered toward epitopes that have been defused by the virus. We may say that adopting the full spike protein as antigen partly “sidetracks” the immune response. Because the only epitope not defused by the virus, the RBD, lies within the S1 subunit, we are prompted to pose the question: Would there be any benefit to efficacy in adopting the S1 subunit as antigen rather than the whole S protein trimer?

The answer is yes. By adopting the S1 subunit as antigen, we steer the immune system to launch attacks at two critical junctures of viral infection: (I) the virion phase with its spike intact, and (II) the activation phase for host-cell entry, defined by the enzymatically cleaved S1/S2 junction. This last event frees in part the ACE2-anchoring S1 subunit, thereby exposing epitopes that were occluded prior to proteolytic activation because they were part of the S1/S2 interface⁷ (Figure 1).

Figure 1.

Host-promoted proteolytic activation of glycosylated SARS-CoV-2 frees an antigenic region in the S1 subunit accessible to vaccine-induced antibodies.

Thus, by adopting the S1 subunit as vaccine antigen, we not only retain the only active epitope of extant vaccines but also incorporate other epitopes that are not defused through glycosylation by the virus and are missing from extant vaccines. Hence, if the vaccine that adopts the S1 antigen fails at juncture I, it still gets a chance to neutralize the viral infection at juncture II. This makes immune evasion routes far less likely when adopting the S1 subunit as antigen compared with the antigen that the vaccines currently use.

At the time when the current vaccines were being developed, the glycosylation-based deactivation of vaccine epitopes at the capside of SARS-CoV-2 was probably not fully delineated. Given what we now know in this regard, we should have adopted a different antigen, most likely the S1 subunit, rather than the full trimeric S protein.

The author declares no competing financial interest.