Conserved Spike Epitopes Yield Antibodies That Neutralize Diverse Bat Sarbecoviruses

The ongoing evolution of SARS-CoV-2 variants of concern, together with the persistent risk that other sarbecoviruses circulating in bats could spill over into human populations, has created an urgent need for antibodies and vaccine designs that work across a broad range of these viruses. A study published in PLOS Biology by Ayush Upadhyay, Katie J. Doores and colleagues addresses this challenge by dissecting the neutralising epitopes recognised by three monoclonal antibodies that show unusually wide activity against sarbecoviruses as well as currently circulating SARS-CoV-2 variants, including XEC, JN.1 and XFG. By mapping precisely where these antibodies attach to the spike protein of WIV-1, a bat sarbecovirus closely related to the ancestor of SARS-CoV-2, the researchers provide a structural and functional blueprint for therapies and vaccines that could protect against both present and future coronaviruses.

Sarbecoviruses are a subgenus of betacoronaviruses that includes SARS-CoV-1, SARS-CoV-2 and a large diversity of viruses carried predominantly by horseshoe bats. The surface spike protein of these viruses mediates entry into host cells by binding the ACE2 receptor through its receptor-binding domain, or RBD. This domain is the principal target of neutralising antibodies, but it is also the most variable region of the spike, which allows viruses to escape immune recognition through mutation. Antibody responses against sarbecoviruses are conventionally grouped into classes depending on which part of the RBD they engage, and antibodies that target the receptor-binding motif tend to be potent but narrow, whereas those that recognise more conserved surfaces often neutralise a wider spectrum of viruses at the cost of lower potency. Understanding which epitopes remain conserved across this viral family is therefore central to designing countermeasures with durable breadth.

The three antibodies examined in the study, designated V1WT_06, V1WT_41 and VA14_26, were isolated in earlier work and shown to neutralise a panel of sarbecoviruses that spans both the SARS-CoV-1 and SARS-CoV-2 clades. In the new research, the team used the spike protein of WIV-1 as the antigenic scaffold to define the epitopes of these antibodies in molecular detail. WIV-1 is a useful reference point because it uses the same ACE2 receptor family as SARS-CoV-2 yet is distinct enough from human viruses that epitopes conserved on its spike are likely to be conserved across a wide evolutionary range. The authors combined functional assays, competition experiments and structural analysis to establish exactly where each antibody binds and how that binding translates into neutralisation of diverse viruses.

The first antibody, V1WT_06, was found to target what the researchers describe as a highly conserved site V epitope on the RBD. A striking feature of this interaction is that it is mediated entirely by the heavy chain of the antibody, without contributions from the light chain. Heavy-chain-only engagement of an epitope has practical implications for antibody engineering, because it simplifies the construction of smaller binding formats and suggests that the paratope is geometrically constrained in a way that tolerates variation in the underlying viral surface. The contact residues that V1WT_06 recognises are highly conserved among sarbecoviruses currently circulating in nature, which the authors interpret as evidence that this region of the RBD is evolutionarily and functionally constrained. In other words, the virus cannot easily alter these positions without compromising some essential aspect of its biology, most plausibly the structural integrity of the spike or its receptor interactions.

This conservation has two important consequences. First, it makes V1WT_06 an attractive candidate for therapeutic development, since an antibody directed against a site the virus struggles to mutate is less likely to be defeated by escape variants, whether those variants arise in animal reservoirs or during prolonged infection in human patients. Second, it identifies site V as a rational target for vaccine design. If immunogens can be engineered to focus the immune response onto this constrained epitope, the resulting vaccines might elicit broadly neutralising responses that protect against sarbecoviruses not yet known to science, rather than only against the strain from which the vaccine was derived.

The other two antibodies, V1WT_41 and VA14_26, bind overlapping epitopes within RBD class 4, a category of antibody targets located away from the receptor-binding motif itself. Although the two antibodies recognise substantially the same region of the spike, the study shows that they approach it at different angles, and that this difference in angle of approach has a measurable effect on the degree to which each antibody competes with ACE2 for binding to the RBD. Antibodies whose angle of approach brings them into direct steric conflict with the receptor are expected to neutralise by physically blocking attachment, whereas antibodies approaching from less obstructed angles may neutralise at other steps of the entry process, such as by preventing the conformational changes the spike undergoes after receptor binding. The finding that two antibodies to a shared epitope can differ in this mechanistically important way illustrates how the geometry of antibody binding, and not merely the location of the epitope, determines antiviral function.

Because class 4 epitopes lie outside the receptor-binding motif, antibodies targeting them are typically less sensitive to mutations that alter receptor engagement, which helps explain the breadth these antibodies display across sarbecoviruses and SARS-CoV-2 variants of concern. The demonstration that V1WT_41 and VA14_26 bind overlapping but non-identical footprints with distinct functional consequences refines the map of conserved neutralising determinants on the sarbecovirus RBD and suggests that cocktails of antibodies recognising this region from complementary angles could be particularly difficult for viruses to escape.

A central question for any broadly neutralising antibody is whether its activity extends beyond cultured pseudoviruses to entry mechanisms that operate in natural reservoir hosts. The researchers addressed this by testing whether neutralisation by the three antibodies is maintained when viral entry is mediated by the ACE2 receptors of the Japanese horseshoe bat and the Halcyon horseshoe bat, two species that host sarbecoviruses in the wild. The antibodies retained their neutralising capacity under these conditions, indicating that the epitopes they recognise remain functionally exposed and accessible across spikes adapted to different host receptors. This result strengthens the case that these antibodies would be effective against viruses circulating in bat populations, not merely against laboratory-adapted or human-adapted strains, and it supports the idea that conserved RBD epitopes can serve as anchors for pan-sarbecovirus immunity.

The authors conclude that V1WT_06, V1WT_41 and VA14_26 are ideal candidates for therapeutic antibody development. Monoclonal antibodies of this kind could be deployed prophylactically in people at high risk of exposure, such as laboratory workers, wildlife handlers and healthcare personnel during an outbreak, or therapeutically in infected patients, including immunocompromised individuals who mount weak responses to vaccination. Because the antibodies neutralise current SARS-CoV-2 variants of concern such as XEC, JN.1 and XFG alongside diverse bat viruses, a single product could in principle address both the continuing evolution of the pandemic virus and the threat of novel spillovers. Combination therapy using antibodies with non-overlapping or differently angled epitopes, as this study helps define, would further reduce the likelihood of viral escape.

Beyond therapeutics, the study contributes to the rational design of pan-betacoronavirus vaccines. Identifying conserved neutralising epitopes such as the site V region recognised by V1WT_06 tells immunogen designers exactly which molecular features a broadly protective vaccine must present to the immune system. Structure-guided vaccine strategies that display these constrained surfaces prominently, while masking or omitting more variable and immunodominant regions, could steer B cell responses toward the epitopes that matter most for cross-protection. As surveillance continues to uncover new sarbecoviruses in bats and other wildlife, and as SARS-CoV-2 itself keeps evolving, the ability to target the parts of the spike that the virus cannot easily change represents a strategic advantage. This work maps those targets with precision and demonstrates, through functional testing across host receptors from multiple bat species, that antibodies aimed at them can achieve the breadth that future coronavirus countermeasures will require.

Subject of Research: Broadly neutralising monoclonal antibodies targeting conserved sarbecovirus spike epitopes

Article Title: Targeting of conserved spike epitopes enables broad antibody neutralisation of diverse bat sarbecoviruses

Article References: Upadhyay, A., Seow, J., Alguel, Y., Newman, J., Thakur, N., Hay, A. L., Tam, J. C. H., Nans, A., Orton, R. J., Bailey, D., Cherepanov, P., & Doores, K. J. (2026). Targeting of conserved spike epitopes enables broad antibody neutralisation of diverse bat sarbecoviruses. PLOS Biology, 24(10), e3003882. https://doi.org/10.1371/journal.pbio.3003882

Image Credits: AI Generated

DOI: 10.1371/journal.pbio.3003882

Keywords: sarbecoviruses, monoclonal antibodies, spike protein, receptor-binding domain, WIV-1, SARS-CoV-2 variants, ACE2 receptor, horseshoe bats, epitope mapping, vaccine design, neutralisation, PLOS Biology