Discovery and characterization of a pan-betacoronavirus S2-binding antibody

Nicole V Johnson¹, Steven C Wall², Kevin J Kramer², Clinton M Holt³, Sivakumar Periasamy⁴, Simone I Richardson⁵, Nelia P Manamela⁵, Naveenchandra Suryadevara⁶, Emanuele Andreano⁷, Ida Paciello⁷, Giulio Pierleoni⁷, Giulia Piccini⁸, Ying Huang⁹, Pan Ge¹⁰, James D Allen¹⁰, Naoko Uno¹¹, Andrea R Shiakolas², Kelsey A Pilewski², Rachel S Nargi⁶, Rachel E Sutton⁶, Alexandria A Abu-Shmais², Robert Parks¹², Barton F Haynes¹³, Robert H Carnahan¹⁴, James E Crowe Jr¹⁵, Emanuele Montomoli¹⁶, Rino Rappuoli¹⁷, Alexander Bukreyev⁴, Ted M Ross¹⁸, Giuseppe A Sautto¹⁹, Jason S McLellan²⁰, Ivelin S Georgiev²¹

Affiliations

¹ Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
² Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA.
³ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁴ Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
⁵ National Institute for Communicable Diseases of the National Health Laboratory Service, 2131 Johannesburg, South Africa; South African MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
⁶ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁷ Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy.
⁸ VisMederi Research S.r.l., 53100 Siena, Italy.
⁹ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
¹⁰ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA.
¹¹ Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA.
¹² Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
¹³ Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA.
¹⁴ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁵ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁶ VisMederi Research S.r.l., 53100 Siena, Italy; VisMederi S.r.l, 53100 Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy.
¹⁷ Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
¹⁸ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
¹⁹ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA. Electronic address: sauttog@ccf.org.
²⁰ Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jmclellan@austin.utexas.edu.
²¹ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: ivelin.georgiev@vanderbilt.edu.

PMID: 39326419
PMCID: PMC11560675 (available on 2025-11-07)
DOI: 10.1016/j.str.2024.08.022

Discovery and characterization of a pan-betacoronavirus S2-binding antibody

Nicole V Johnson et al. Structure. 2024.

. 2024 Nov 7;32(11):1893-1909.e11.

doi: 10.1016/j.str.2024.08.022. Epub 2024 Sep 25.

Authors

Affiliations

¹ Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
² Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA.
³ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁴ Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA; Galveston National Laboratory, University of Texas Medical Branch at Galveston, Galveston, TX 77555, USA.
⁵ National Institute for Communicable Diseases of the National Health Laboratory Service, 2131 Johannesburg, South Africa; South African MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
⁶ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
⁷ Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy.
⁸ VisMederi Research S.r.l., 53100 Siena, Italy.
⁹ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
¹⁰ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA.
¹¹ Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA.
¹² Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA.
¹³ Duke Human Vaccine Institute, Duke University, Durham, NC 27710, USA; Departments of Medicine and Immunology, Duke University, Durham, NC 27710, USA.
¹⁴ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁵ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
¹⁶ VisMederi Research S.r.l., 53100 Siena, Italy; VisMederi S.r.l, 53100 Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy.
¹⁷ Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, 53100 Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
¹⁸ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Department of Infection Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44196, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA; Department of Infectious Diseases, University of Georgia, Athens, GA 30602, USA.
¹⁹ Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA; Center for Vaccines and Immunology, University of Georgia, Athens, GA 30602, USA. Electronic address: sauttog@ccf.org.
²⁰ Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA. Electronic address: jmclellan@austin.utexas.edu.
²¹ Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 73232, USA; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA; Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA. Electronic address: ivelin.georgiev@vanderbilt.edu.

PMID: 39326419
PMCID: PMC11560675 (available on 2025-11-07)
DOI: 10.1016/j.str.2024.08.022

Abstract

The continued emergence of deadly human coronaviruses from animal reservoirs highlights the need for pan-coronavirus interventions for effective pandemic preparedness. Here, using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq), we report a panel of 50 coronavirus antibodies isolated from human B cells. Of these, 54043-5 was shown to bind the S2 subunit of spike proteins from alpha-, beta-, and deltacoronaviruses. A cryoelectron microscopy (cryo-EM) structure of 54043-5 bound to the prefusion S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike defined an epitope at the apex of S2 that is highly conserved among betacoronaviruses. Although non-neutralizing, 54043-5 induced Fc-dependent antiviral responses in vitro, including antibody-dependent cellular cytotoxicity (ADCC) and antibody-dependent cellular phagocytosis (ADCP). In murine SARS-CoV-2 challenge studies, protection against disease was observed after introduction of Leu234Ala, Leu235Ala, and Pro329Gly (LALA-PG) substitutions in the Fc region of 54043-5. Together, these data provide new insights into the protective mechanisms of non-neutralizing antibodies and define a broadly conserved epitope within the S2 subunit.

Keywords: LALA-PG; LIBRA-seq; S2 subunit; antibodies; betacoronaviruses; coronaviruses; cryo-EM; spike protein.

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Conflict of interest statement

Declaration of interests A.R.S. and I.S.G. are co-founders of AbSeek Bio. K.J.K., A.R.S., N.V.J., I.S.G., J.S.M., R.H.C., and J.E.C. are listed as inventors on patents filed describing the antibodies discovered here. R.H.C. is an inventor on patents related to other SARS-CoV-2 antibodies. J.E.C. has served as a consultant for Luna Biologics, is a member of the Scientific Advisory Board of Meissa Vaccines and is Founder of IDBiologics. The Crowe laboratory has received funding support in sponsored research agreements from AstraZeneca, IDBiologics, and Takeda. The Georgiev laboratory at VUMC has received unrelated funding from Takeda Pharmaceuticals.

Update of

Discovery and Characterization of a Pan-betacoronavirus S2-binding antibody.
Johnson NV, Wall SC, Kramer KJ, Holt CM, Periasamy S, Richardson S, Suryadevara N, Andreano E, Paciello I, Pierleoni G, Piccini G, Huang Y, Ge P, Allen JD, Uno N, Shiakolas AR, Pilewski KA, Nargi RS, Sutton RE, Abu-Shmais AA, Parks R, Haynes BF, Carnahan RH, Crowe JE Jr, Montomoli E, Rappuoli R, Bukreyev A, Ross TM, Sautto GA, McLellan JS, Georgiev IS. Johnson NV, et al. bioRxiv [Preprint]. 2024 Jan 16:2024.01.15.575741. doi: 10.1101/2024.01.15.575741. bioRxiv. 2024. Update in: Structure. 2024 Nov 7;32(11):1893-1909.e11. doi: 10.1016/j.str.2024.08.022. PMID: 38293237 Free PMC article. Updated. Preprint.

References

1. Li F (2016). Structure, Function, and Evolution of Coronavirus Spike Proteins. Annu Rev Virol 3, 237–261. 10.1146/annurev-virology-110615-042301. - DOI - PMC - PubMed
1. Su S, Wong G, Shi W, Liu J, Lai ACK, Zhou J, Liu W, Bi Y, and Gao GF (2016). Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol 24, 490–502. 10.1016/j.tim.2016.03.003. - DOI - PMC - PubMed
1. Amoutzias GD, Nikolaidis M, Tryfonopoulou E, Chlichlia K, Markoulatos P, and Oliver SG (2022). The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2. Viruses 14. 10.3390/v14010078. - DOI - PMC - PubMed
1. Nickbakhsh S, Ho A, Marques DFP, McMenamin J, Gunson RN, and Murcia PR (2020). Epidemiology of Seasonal Coronaviruses: Establishing the Context for the Emergence of Coronavirus Disease 2019. J Infect Dis 222, 17–25. 10.1093/infdis/jiaa185. - DOI - PMC - PubMed
1. Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, et al. (2003). A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med 348, 1953–1966. 10.1056/NEJMoa030781. - DOI - PubMed

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Discovery and characterization of a pan-betacoronavirus S2-binding antibody

Affiliations

Discovery and characterization of a pan-betacoronavirus S2-binding antibody

Authors

Affiliations

Abstract

Conflict of interest statement

Update of

References

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Molecular Biology Databases

Miscellaneous