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High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization

View ORCID ProfileAdam S. Dingens, Payal Pratap, Keara Malone, View ORCID ProfileSarah K. Hilton, Thomas Ketas, View ORCID ProfileChristopher A. Cottrell, View ORCID ProfileJulie Overbaugh, John P. Moore, P.J. Klasse, View ORCID ProfileAndrew B. Ward, View ORCID ProfileJesse D. Bloom
doi: https://doi.org/10.1101/2020.10.21.348623
Adam S. Dingens
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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  • For correspondence: adingens@fredhutch.org jbloom@fredhutch.org
Payal Pratap
2Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Keara Malone
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Sarah K. Hilton
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Thomas Ketas
3Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
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Christopher A. Cottrell
2Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Julie Overbaugh
4Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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John P. Moore
3Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
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P.J. Klasse
3Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
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Andrew B. Ward
2Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Jesse D. Bloom
1Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
5Howard Hughes Medical Institute, Seattle, WA 98109, USA
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  • For correspondence: adingens@fredhutch.org jbloom@fredhutch.org
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Abstract

Mapping the epitope specificities of polyclonal serum is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual monoclonal antibodies, which incompletely defines the full polyclonal response. Here we use two complementary approaches to directly map the specificities of the neutralizing and binding antibodies of polyclonal anti-HIV-1 sera from rabbits immunized with BG505 Env SOSIP trimers. To map the neutralizing specificity, we used mutational antigenic profiling to determine how all amino-acid mutations in Env affected viral neutralization. To map the binding specificity, we used electron microscopy polyclonal epitope mapping (EMPEM) to directly visualize the Fabs in serum bound to Env trimers. Mutational antigenic profiling showed that the dominant neutralizing specificities were the C3/V5 and/or 241/289 glycan hole epitopes, which were generally only a subset of the more diverse binding specificities mapped with EMPEM. Additional differences between binding and neutralization reflected antigenicity differences between virus and soluble Env trimer. Further, mutational antigenic profiling was able to refine epitope specificity in residue-level detail directly from sera, revealing subtle differences across rabbits. Together, mutational antigenic profiling and EMPEM allow for a holistic view of the binding and neutralizing specificity of polyclonal sera and could be used to finely evaluate and guide vaccine design.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 21, 2020.
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High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization
Adam S. Dingens, Payal Pratap, Keara Malone, Sarah K. Hilton, Thomas Ketas, Christopher A. Cottrell, Julie Overbaugh, John P. Moore, P.J. Klasse, Andrew B. Ward, Jesse D. Bloom
bioRxiv 2020.10.21.348623; doi: https://doi.org/10.1101/2020.10.21.348623
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High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization
Adam S. Dingens, Payal Pratap, Keara Malone, Sarah K. Hilton, Thomas Ketas, Christopher A. Cottrell, Julie Overbaugh, John P. Moore, P.J. Klasse, Andrew B. Ward, Jesse D. Bloom
bioRxiv 2020.10.21.348623; doi: https://doi.org/10.1101/2020.10.21.348623

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