ArticleNature communications2023
Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 23 citations in OpenAlex.
- Evolutionary and structural pathways of antibody maturation reveal principles for engineering potent SARS-CoV-2 neutralizers.Journal of structural biology: X · 2026Article
- Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.Research square · 2026Article
- Prefusion-stabilized SARS-CoV-2 spike reshapes antigenic hierarchy and antibody targeting against conserved and occluded epitopes.NPJ vaccines · 2026Article
- Genomic surveillance of SARS-CoV-2 variants in hospitalized patients: a cohort study from the metropolitan area of valle de Aburrá, ColombiaBiomedica : revista del Instituto Nacional de Salud · 2026Article
- IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by a Low-Affinity Antibody.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico.Human vaccines & immunotherapeutics · 2025Review
- Structural insights into hybridoma-derived neutralizing monoclonal antibodies against Omicron BA.5 and XBB.1.16 variants of SARS-CoV-2.Journal of virology · 2025Article
- Molecular convergence of neutralizing antibodies in human revealed by repeated rabies vaccination.NPJ vaccines · 2025Article
- Computational optimization of a pan-coronavirus fusion inhibitory peptide targeting spike's heptapeptide repeat region.Biosafety and health · 2025Article
- Article
- SpatConv Enables the Accurate Prediction of Protein Binding Sites by a Pretrained Protein Language Model and an Interpretable Bio-spatial Convolution.Research (Washington, D.C.) · 2025Article
- SARS-CoV-2 evolution enhances endocytic uptake while preserving TMPRSS2-dependent fusion.Frontiers in immunology · 2025Article
- Japan-Korea collaboration on biophysical techniques for drug discovery in infectious diseases: Toward future pandemic preparedness.Biophysics and physicobiology · 2025Article
- Improved efficacy of SARS-CoV-2 isolation from COVID-19 clinical specimens using VeroE6 cells overexpressing TMPRSS2 and human ACE2.Scientific reports · 2024Article
- Locuaz: an in silico platform for protein binders optimization.Bioinformatics (Oxford, England) · 2024Article
- Overcoming antibody-resistant SARS-CoV-2 variants with bispecific antibodies constructed using non-neutralizing antibodies.iScience · 2024Article
- Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.Nature communications · 2024Article
- Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.bioRxiv : the preprint server for biology · 2024Article
- Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.GigaScience · 2024Article
- Neutralization against Omicron subvariants after BA.5/BF.7 breakthrough infection weakened as virus evolution and aging despite repeated prototype-based vaccinationEmerging microbes & infections · 2023Article
Corrections and comments
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Authors and funding
24 authors at 8 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
SARS-CoV-2 Omicron subvariants have evolved to evade receptor-binding site (RBS) antibodies that exist in diverse individuals as public antibody clones. We rationally selected RBS antibodies resilient to mutations in emerging Omicron subvariants. Y489 was identified as a site of virus vulnerability and a common footprint of broadly neutralizing antibodies against the subvariants. Multiple Y489-binding antibodies were encoded by public clonotypes and additionally recognized F486, potentially accounting for the emergence of Omicron subvariants harboring the F486V mutation. However, a subclass of antibodies broadly neutralized BA.4/BA.5 variants via hydrophobic binding sites of rare clonotypes along with high mutation-resilience under escape mutation screening. A computationally designed antibody based on one of the Y489-binding antibodies, NIV-10/FD03, was able to bind XBB with any 486 mutation and neutralized XBB.1.5. The structural basis for the mutation-resilience of this Y489-binding antibody group may provide important insights into the design of therapeutics resistant to viral escape.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.