1. Immunology and Inflammation
  2. Microbiology and Infectious Disease
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High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post HIV Env trimer vaccination

  1. Adam S Dingens  Is a corresponding author
  2. Payal Pratap
  3. Keara D Malone
  4. Sarah K Hilton
  5. Thomas Ketas
  6. Christopher A Cottrell
  7. Julie M Overbaugh
  8. John P Moore
  9. P J Klasse
  10. Andrew B Ward
  11. Jesse D Bloom  Is a corresponding author
  1. Fred Hutchinson Cancer Research Center, United States
  2. The Scripps Research Institute, United States
  3. Weill Cornell Medicine, United States
Research Article
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Cite this article as: eLife 2021;10:e64281 doi: 10.7554/eLife.64281

Abstract

Mapping polyclonal serum responses is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual antibodies, which incompletely defines the 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. We used mutational antigenic profiling to determine how all mutations in Env affected viral neutralization and electron microscopy polyclonal epitope mapping (EMPEM) to directly visualize serum Fabs bound to Env trimers. The dominant neutralizing specificities were generally only a subset of the more diverse binding specificities. Additional differences between binding and neutralization reflected antigenicity differences between virus and soluble Env trimer. Further, we refined residue-level epitope specificity directly from sera, revealing subtle differences across sera. Together, mutational antigenic profiling and EMPEM yield a holistic view of the binding and neutralizing specificity of polyclonal sera.

Data availability

The entire mutational antigenic profiling analysis pipeline, as well as processed data are available as https://github.com/jbloomlab/Vacc_Rabbit_Sera_MAP. Illumina sequencing read were uploaded to the NCBI SRA as BioProject PRJNA656582 with sample identifiers SRR12431153-SRR12431189. EMPEM 3D maps are being processed to be deposited into EMDB. Figure 2-Source Data 1 contains csv files with all median site- and mutation- level differential selection values, as well as logoplots plotting escape profiles for the entire mutagenized portion of env

The following data sets were generated

Article and author information

Author details

  1. Adam S Dingens

    Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    adingens@fredhutch.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9603-9409
  2. Payal Pratap

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7170-6866
  3. Keara D Malone

    Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  4. Sarah K Hilton

    Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  5. Thomas Ketas

    Department of Microbiology and Immunology, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
  6. Christopher A Cottrell

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    No competing interests declared.
  7. Julie M Overbaugh

    Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    Julie M Overbaugh, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0239-9444
  8. John P Moore

    Department of Microbiology and Immunology, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
  9. P J Klasse

    Department of Microbiology and Immunology, Weill Cornell Medicine, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8222-278X
  10. Andrew B Ward

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7153-3769
  11. Jesse D Bloom

    Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    jbloom@fredhutch.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1267-3408

Funding

National Institute of Allergy and Infectious Diseases (R01 AI140891)

  • Jesse D Bloom

National Institute of Allergy and Infectious Diseases (P01 AI110657)

  • John P Moore
  • Andrew B Ward

National Institute of Allergy and Infectious Diseases (R01 AI12096)

  • Julie M Overbaugh

Howard Hughes Medical Institute

  • Jesse D Bloom

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Pamela J Bjorkman, California Institute of Technology, United States

Publication history

  1. Received: October 22, 2020
  2. Accepted: January 12, 2021
  3. Accepted Manuscript published: January 13, 2021 (version 1)
  4. Version of Record published: February 4, 2021 (version 2)

Copyright

© 2021, Dingens et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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