Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses
Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCo...
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| Published in | Immunity (Cambridge, Mass.) Vol. 57; no. 12; pp. 2914 - 2927.e7 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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United States
Elsevier Inc
10.12.2024
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| Abstract | Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.
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•Isolation of PDCoV RBD-directed human neutralizing mAbs•Molecular basis of mAb-mediated broad PDCoV neutralization revealed by cryo-EM•Potent PDCoV neutralization involves competitive inhibition of receptor engagement•Deep-mutational scanning identification of a mAb cocktail to limit viral resistance
Porcine delta-coronavirus (PDCoV) recently spilled over to humans, and no countermeasures are approved. Rexhepaj et al. describe human mAbs that broadly neutralize PDCoV variants by inhibiting host receptor engagement to the RBD. They perform deep-mutational scanning to enhance our understanding of DCoV immunity and identify a two-mAb cocktail that could potentially limit viral resistance. |
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| AbstractList | Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.
[Display omitted]
•Isolation of PDCoV RBD-directed human neutralizing mAbs•Molecular basis of mAb-mediated broad PDCoV neutralization revealed by cryo-EM•Potent PDCoV neutralization involves competitive inhibition of receptor engagement•Deep-mutational scanning identification of a mAb cocktail to limit viral resistance
Porcine delta-coronavirus (PDCoV) recently spilled over to humans, and no countermeasures are approved. Rexhepaj et al. describe human mAbs that broadly neutralize PDCoV variants by inhibiting host receptor engagement to the RBD. They perform deep-mutational scanning to enhance our understanding of DCoV immunity and identify a two-mAb cocktail that could potentially limit viral resistance. Porcine deltacoronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent coronaviruses. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryo-electron microscopy structures of PD33 and PD41 in complex with the S receptor-binding domain and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV, and used deep mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks. Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks. Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks. |
| Author | Veesler, David Yoshiyama, Courtney N. Mccallum, Mathew Perruzza, Lisa Dickinson, Miles S. Starr, Tyler N. Saliba, Christian Leoni, Giada Tortorici, M. Alejandra Quispe, Joel Rexhepaj, Megi Asarnow, Daniel Taylor, Ashley L. Benigni, Fabio Guarino, Barbara Balmelli, Alessio Corti, Davide Culap, Katja Sprouse, Kaitlin R. Brown, Jack T. Park, Young-Jun |
| AuthorAffiliation | 1 Department of Biochemistry, University of Washington, Seattle, Washington, USA 3 Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland 2 Howard Hughes Medical Institute, Seattle, WA 98195, USA 4 Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA |
| AuthorAffiliation_xml | – name: 1 Department of Biochemistry, University of Washington, Seattle, Washington, USA – name: 4 Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA – name: 3 Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – name: 2 Howard Hughes Medical Institute, Seattle, WA 98195, USA |
| Author_xml | – sequence: 1 givenname: Megi surname: Rexhepaj fullname: Rexhepaj, Megi organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 2 givenname: Daniel surname: Asarnow fullname: Asarnow, Daniel organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 3 givenname: Lisa surname: Perruzza fullname: Perruzza, Lisa organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 4 givenname: Young-Jun surname: Park fullname: Park, Young-Jun organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 5 givenname: Barbara surname: Guarino fullname: Guarino, Barbara organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 6 givenname: Mathew surname: Mccallum fullname: Mccallum, Mathew organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 7 givenname: Katja surname: Culap fullname: Culap, Katja organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 8 givenname: Christian surname: Saliba fullname: Saliba, Christian organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 9 givenname: Giada surname: Leoni fullname: Leoni, Giada organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 10 givenname: Alessio surname: Balmelli fullname: Balmelli, Alessio organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 11 givenname: Courtney N. surname: Yoshiyama fullname: Yoshiyama, Courtney N. organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 12 givenname: Miles S. surname: Dickinson fullname: Dickinson, Miles S. organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 13 givenname: Joel surname: Quispe fullname: Quispe, Joel organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 14 givenname: Jack T. surname: Brown fullname: Brown, Jack T. organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 15 givenname: M. Alejandra surname: Tortorici fullname: Tortorici, M. Alejandra organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 16 givenname: Kaitlin R. surname: Sprouse fullname: Sprouse, Kaitlin R. organization: Department of Biochemistry, University of Washington, Seattle, WA, USA – sequence: 17 givenname: Ashley L. surname: Taylor fullname: Taylor, Ashley L. organization: Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA – sequence: 18 givenname: Davide surname: Corti fullname: Corti, Davide organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 19 givenname: Tyler N. surname: Starr fullname: Starr, Tyler N. email: tyler.starr@biochem.utah.edu organization: Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA – sequence: 20 givenname: Fabio surname: Benigni fullname: Benigni, Fabio email: fbenigni@vir.bio organization: Humabs Biomed SA, a Subsidiary of Vir. Biotechnology, 6500 Bellinzona, Switzerland – sequence: 21 givenname: David orcidid: 0000-0002-6019-8675 surname: Veesler fullname: Veesler, David email: dveesler@uw.edu organization: Department of Biochemistry, University of Washington, Seattle, WA, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/39488210$$D View this record in MEDLINE/PubMed |
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| Keywords | porcine deltacoronavirus PDCoV spike glycoprotein deep mutational scanning neutralizing antibodies zoonosis cryo-EM structures |
| Language | English |
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| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 These authors contributed equally to the work M.R., L.P., F.B., and D.V. designed the experiments. M.R., L.P. and J.T.B. recombinantly expressed and purified glycoproteins. M.M. cloned the construct and produced an initial batch of the anti-kappa light chain nanobody and M.R. purified subsequent batches. L.P., A.D., and F.B. performed immunization and monoclonal antibody isolations. K.C., C.S. and A.B. produced the recombinant antibodies. M.R. performed binding assays and performed entry assays. M.R. and C.Y. produced pseudoviruses. K.S. and C.N.Y. helped with generating hybridoma and parent pseudovirus. Y.J.P. carried out cryo-EM specimen preparation, data collection, and processing of the PD33-bound PDCoV RBD structure. Y.J.P., and D.V. built and refined the PD33-bound RBD cryoEM structure. M.R., M.S.D., and D.A. carried out cryo-EM specimen preparation and data collection of the PD41-bound PDCoV SSD2018/300. D.A. processed the PD41-bound PDCoV SSD2018/300 cryoEM dataset. M.R., D.A. and D.V. built and refined the PD41-bound RBD cryoEM structure. J.Q. helped with specimen preparation and cryoEM data collection of the PD41-bound PDCoV SSD2018/300. M.A.T. provided key reagents. A.T. and T.N.S. performed bioinformatic analysis to aid in strain selection of PDCoV and carried out DMS. B.G. evaluated mAb-mediated effector functions. M.R., Y.J.P., D.A., T.N.S. and D.V. analyzed the data and wrote the manuscript with input from all authors. D.C., T.N.S., F.B. and D.V. supervised the project. Lead contact Author contributions |
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| Snippet | Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no... Porcine deltacoronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent coronaviruses. To... |
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| SubjectTerms | Animals Antibodies, Monoclonal - immunology Antibodies, Neutralizing - immunology Antibodies, Viral - immunology Broadly Neutralizing Antibodies - immunology cryo-EM structures Cryoelectron Microscopy deep mutational scanning Epitope Mapping - methods Epitopes - immunology Humans Mice neutralizing antibodies PDCoV porcine deltacoronavirus spike glycoprotein Spike Glycoprotein, Coronavirus - chemistry Spike Glycoprotein, Coronavirus - immunology zoonosis |
| Title | Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses |
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