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TitleEpitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.
Journal, issue, pagesNat Microbiol, Year 2026
Publish dateMar 12, 2026
AuthorsSeth J Zost / Naveenchandra Suryadevara / Lauren E Williamson / Suzanne M Scheaffer / Elad Binshtein / Cameron D Buchman / Nicole V Johnson / Nicholas J Catanzaro / Silvia Ravera / Nathaniel S Chapman / Luke Myers / Ajit R Ramamohan / Laura S Handal / Doan C Nguyen / Andrew Trivette / James R Martinez / Eduardo Villalobos / Stacey A Rutherford / F Eun-Hyung Lee / Alexandra Schäfer / Ralph S Baric / Jason S McLellan / Michael S Diamond / Robert H Carnahan / James E Crowe /
PubMed AbstractThe emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co- ...The emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co-circulation of SARS-CoV-2 variants with unique sets of antigenic substitutions has further complicated therapeutic mAb discovery. New approaches are needed to rapidly discover and characterize mAbs with preferred specificity and functional characteristics. Here we describe and perform epitope-focused mAb discovery using glycan-masked antigens. We isolated and expressed a panel of 303 mAbs, some of which potently neutralize divergent Omicron subvariants by targeting the class 3 antigenic site on SARS-CoV-2 RBD. Epitope mapping of these antibodies revealed a spectrum of cross-reactivity and differential recognition of the class 3 site, validating the utility of this enrichment approach for targeted mAb discovery. Together, this work rationally designs glycan-masked engineered RBDs and uses them to isolate mAbs that potently neutralize antigenically divergent SARS-CoV-2 variants.
External linksNat Microbiol / PubMed:41820555
MethodsEM (single particle) / X-ray diffraction
Resolution2.68 - 28.0 Å
Structure data

EMDB-43882: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3872
Method: EM (single particle) / Resolution: 18.0 Å

EMDB-43883: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3889
Method: EM (single particle) / Resolution: 24.0 Å

EMDB-43884: Negative stain EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-43885: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3892
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-43886: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3906
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-43887: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3967
Method: EM (single particle) / Resolution: 28.0 Å

EMDB-43888: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-4094
Method: EM (single particle) / Resolution: 18.0 Å

PDB-9c6y:
Crystal structure of SARS-CoV-2 XBB.1.5 RBD bound to COV2-3906 Fab
Method: X-RAY DIFFRACTION / Resolution: 2.68 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-CL:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-A2G:
2-acetamido-2-deoxy-alpha-D-galactopyranose

ChemComp-HOH:
WATER

Source
  • Severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • severe acute respiratory syndrome coronavirus
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / coronavirus / antibody / fab / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex

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