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
Article and author information
Author details
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
- Pamela J Bjorkman, California Institute of Technology, United States
Publication history
- Received: October 22, 2020
- Accepted: January 12, 2021
- Accepted Manuscript published: January 13, 2021 (version 1)
- 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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