Aug 2026· PLoS Pathogens· Vol 22, pp. e1014393 - e1014393· 0 citations· 54 references
Medicine
TL;DR
The isolation of a human monoclonal antibody from a SARS-CoV-2 convalescent donor that targets the conserved S2 stem helix region is reported, demonstrating the potential of in vitro affinity maturation to expand the neutralization breadth of stem-helix-targeting antibodies across divergent betacoronaviruses.
Abstract
Broadly neutralizing antibodies (bnAbs) targeting conserved regions of the betacoronavirus spike are important for pan-betacoronavirus protection and pandemic preparedness. Here, we report the isolation of a human monoclonal antibody, CC65.1, from a SARS-CoV-2 convalescent donor that targets the conserved S2 stem helix region. CC65.1 neutralizes various sarbecoviruses, including SARS-CoV-2, and binds to the MERS-CoV spike but lacks MERS-CoV-neutralizing activity due to insufficient binding affinity. We utilized directed evolution to enhance the binding affinity of CC65.1 for the MERS-CoV S2 stem helix, yielding engineered antibody variants with newly acquired MERS-CoV-neutralizing activity. High-resolution structural analysis reveals key paratope mutations that enhance binding and stabilize epitope engagement. Our findings demonstrate the potential of in vitro affinity maturation to expand the neutralization breadth of stem-helix-targeting antibodies across divergent betacoronaviruses. This work supports the development of engineered bnAbs for broadly protective betacoronavirus countermeasures and provides a strategy for achieving cross-lineage neutralization.
Two human-derived monoclonal antibodies are characterized that recognize conserved epitopes on the SARS-CoV-2 RBD and retain activity across antigenically distinct variants, and conserved, mutationally constrained epitopes may serve as targets for vaccines designed to elicit antibody responses resilient to ongoing SARS-CoV-2 evolution and future sarbecovirus emergence.
M. Abernathy, William B. Foreman, Jasmyn A. Lopez et al.· bioRxiv· 0 citations
Understanding the potential for resistance to antibodies targeting conserved epitopes on the coronavirus spike protein is essential for developing broad-spectrum antivirals. The S2′-helix and stem helix represent two key conserved epitopes across multiple coronaviruses, with the S2′-helix being broadly conserved throughout the coronavirus subfamily and the stem helix primarily conserved among betacoronaviruses. Here, we demonstrate that the S2′-helix in SARS-CoV-2 possesses a higher genetic barrier to antibody resistance than the stem helix. Potent escape mutations in the stem helix, including D1153G, Y1155S, F1156L and F1156V, were selected under antibody pressure, and variants such as S1147L, E1151D, D1153G, D1153H, D1153Y and Y1155H were frequently identified in naturally circulating strains. These mutations completely abolished neutralization by some stem helix-targeting antibodies. In contrast, under pressure from S2′-helix-targeting antibodies, we did not detect clear viral escape. Only one naturally occurring mutation in the S2′-helix, L822F, was observed at considerable frequency; it weakly or mildly reduced but did not abolish neutralizing activity. Furthermore, combination therapy with S2′-helix-targeting antibodies synergistically suppressed the emergence of escape mutants selected by stem helix-directed antibodies. Our findings underscore the S2′-helix as a promising target for the design of broadly protective coronavirus therapeutics with a reduced risk of viral escape.
Xuanjian Wang, Shitong Qiao, Zhiheng Bao et al.· PLoS Pathogens· 0 citations
The rapid evolution of SARS-CoV-2 and the ongoing risk of zoonotic spillover highlight the need for vaccines that provide broad protection beyond strain-specific immunity. Here, we present a structure-guided, AI-enabled strategy for rational antigen design that enhances cross-reactive B-cell epitope recognition across betacoronaviruses. By integrating comparative sequence analysis with conformational epitope prediction, we identified conserved epitope hotspots within the Spike receptor-binding domain and introduced targeted motif-level substitutions into a SARS-CoV-2 BA.2 backbone. Engineered Spike immunogens, delivered as mRNA-lipid nanoparticle vaccines, elicited robust antibody responses in mice and demonstrated broad neutralizing activity against antigenically diverse SARS-CoV-2 variants, including BA.5 and XBB.1.5, as well as zoonotic sarbecoviruses. Selected designs reached neutralisation breadth comparable to an Omicron-adapted clinical benchmark for shared SARS-CoV-2 antigens, while extending neutralising activity to divergent zoonotic sarbecoviruses. These findings show that minimal, structure-guided epitope remodeling can enhance the presentation of conserved epitopes and improve antibody breadth, providing a generalizable framework for designing vaccines resilient to viral evolution and future pandemic threats.
A. Odainic, Ioannis Vardaxis, M. Ferraz et al.· Frontiers in Immunology· 0 citations
The continued emergence of betacoronaviruses underscores the urgent need for vaccines that provide broadly protective immunity. Here, we present an epitope-focused vaccine strategy targeting the conserved S2 stem-helix region of the spike fusion machinery, a broadly neutralizing antibody-(bnAb) epitope shared across betacoronaviruses yet partially occluded on the native spike. Immunization of non-human primates with engineered S2 stem-helix nanoparticle immunogens, alone or followed by a SARS-CoV-2 BA.1 spike mRNA boost, elicited broadly cross-reactive antibody responses against sarbecoviruses, merbecoviruses, and embecoviruses and neutralized SARS-CoV-2, multiple variants, other sarbecoviruses, and MERS-CoV. Vaccine-elicited monoclonal antibodies displayed broad in-vitro neutralizing activity and protected against both SARS-CoV-2 and MERS-CoV in-vivo. Structural analyses revealed conserved features between rhesus and human stem-helix bnAbs, supporting the translational potential. Overall, our findings provide proof-of-concept that epitope-focused nanoparticle immunogens can target partially occluded, immunoquiescent bnAb epitopes, laying the groundwork for pan-betacoronavirus vaccines that provide broad protection and strengthen pandemic preparedness. ONE SENTENCE SUMMARY Epitope-focused S2 stem-helix nanoparticle immunogens elicit protective broadly neutralizing antibodies (bnAbs) against diverse betacoronaviruses in non-human primates, establishing a framework for development of pan-betacoronavirus vaccines.
Panpan Zhou, Ziqi Feng, Wan-ting He et al.· bioRxiv· 0 citations
Monoclonal antibodies from COVID-19 convalescent donors are identified that target two conserved epitopes in the S2 domain of the coronavirus Spike glycoprotein: the central helix and the lower stalk, advancing knowledge of two conserved and structurally vulnerable sites within the coronavirus S2 subunit.
Adonis A. Rubio, M. Abernathy, Davide F. Robbiani et al.· Journal of Immunology· 0 citations
Comparing wild-type XG83 and modified MuXG83 shows how allosteric tuning affects antibody-antigen compatibility in developing variations like Omicron, and indicates that non-epitope (potentially allosteric) changes to CDRH3 are also important while investigating potential development and neutralization before advancement.
Muhammad Waqas Nasir, Qi-Yun Liang, Jun He et al.· Microbiology spectrum· 0 citations
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