Study reveals surfaces of SARS-CoV-2 spike most resistant to antibody escape

A team of international scientists has formed a consortium to map the epitope landscape of a range of therapeutic monoclonal antibodies on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Moreover, the scientists characterized the neutralization potency of these antibodies and have investigated how emerging viral variants with spike mutations can impact antibody-mediated neutralization. They have recently published the consortium findings in the journal Science.

The coronavirus Immunotherapeutic Consortium, which was formed to structurally and functionally characterize candidate therapeutic antibodies, currently includes more than 350 monoclonal antibodies against the spike proteins of 56 different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These antibodies were tested in various in vivo and in vitro assays, and findings were uploaded to a publicly available database.  

The majority of these antibodies were developed against the spike receptor-binding domain (RBD). In addition, some antibodies targeting the N terminal domain (NTD) and S2 subunit of the spike protein were developed. A total of 186 anti-RBD antibodies were grouped into seven core communities (RBD 1 to 7) based on the competition profiles between antibodies. These communities were further divided into fine clusters based on the competition profiles between clusters and/or the ability of antibodies to compete with angiotensin-converting enzyme 2 (ACE2).

The neutralization ability of a set of 41 representative anti-RBD antibodies was assessed against a variety of spike protein variants containing globally dominant G614 mutation, 15 substitution or deletion mutations observed in circulating variants, a group of related mutations observed in four VOCs (alpha, beta, gamma, and delta), or mutations responsible for human-to-animal spillover events.   

Characterization of antibodies belonging to RBD 1, 2, and 3 communities

The analysis revealed that the antibodies belonging to these communities primarily target the receptor-binding motif (RBM) to compete with ACE2. For binding, these antibodies required the “up” conformation of the RBD. Furthermore, it was observed that the antibodies in the RBD-1 community bind all three RBDs on the spike protein and frequently crosslink two spike trimers. In contrast, RBD-2 antibodies mostly interacted with a single spike trimer bivalently. The RBD-3 antibodies exhibited both bivalent binding patterns and the ability to crosslink spike trimers.

Mutations affecting antibody-mediated neutralization

A strong correlation was observed between the epitope position and spike mutations, collectively impacting antibody-mediated neutralization.

While some RBD-2 antibodies were significantly impacted by the K417N and E484K mutations, some remained unaffected. Similarly, some RBD-2 antibodies were resistant to the L452R mutation and some were sensitive. In RBD-3 antibodies, a heavy impact of both N501T/Y and E484K mutations was observed. In RBD-1 antibodies, a variable impact of particular mutations on neutralization was observed.

An overall reduction in neutralization potency of RBD-1 and RBD-2 antibodies was observed against the spike protein containing mutations found in four VOCs. Both beta and gamma variants showed complete resistance to RBD-1 and RBD-2 antibodies. In contrast, the delta and epsilon variants showed sensitivity towards the majority of these antibodies.

Characterization of antibodies belonging to RBD-4 and RBD-5 communities

The analysis revealed that the antibodies belonging to these communities bind to the RBD outer surface irrespective of its structural positioning (“up” or “down” conformation). Unlike RBD-5 antibodies, RBD-4 antibodies exhibited ACE2 blocking potency. The RBD-5 antibodies with spike-crosslinking ability exhibited virus neutralization potency, despite the absence of ACE2 blocking ability.  

Mutations affecting antibody-mediated neutralization

A significant impact of E484K and L452R mutations was observed on the majority of RBD-4 antibodies. In contrast, almost all RBD-5 antibodies showed a broad-spectrum resistance to all tested mutations. Only two antibodies from this community were moderately impacted by the V367F and N439K mutations.    

Characterization of antibodies belonging to RBD-6 and RBD-7 communities

The analysis revealed that the antibodies belonging to these communities bind to the RBD inner surface, with two RBDs in the “up” conformation. These antibodies showed high potency in crosslinking spike trimers. Except antibodies belonging to two RBD-7 sub-clusters, all showed potent ACE2 blocking and virus-neutralizing abilities. All RBD-6 and RBD-7 antibodies showed resistance to the tested mutations because of their location away from the RBM.

Characterization of anti-NTD antibodies

Four anti-NTD antibodies were analyzed in the study and grouped as NTD-1, NTD-2, and NTD-3 communities. Two NTD-1 antibodies interacted with the top side of NTD to cover its N terminus and residue Y144. Similarly, the NTD-2 antibody interacted with the front side of NTD, covering a number of residues that are mutated in emerging viral variants. Importantly, the NTD-3 antibody that bound to the left side of NTD represented a novel epitope.

Mutations affecting antibody-mediated neutralization

The neutralization potency of all anti-NTD antibodies was severely affected by the NTD deletion or substitution mutations found in circulating VOCs. Mutations that alter disulfide bonding in the NTD also impacted the neutralization potency of antibodies.

Study significance

The study provides a detailed landscape of the spike binding sites of a large number of therapeutic monoclonal antibody candidates. The study findings can be extensively used to predict the impact of emerging spike mutations on antibody-mediated neutralization and identify therapeutic antibody combinations with durable and potent activity against emerging VOCs.

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