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Presently, no vaccine candidate has induced antibody responses capable of meaningful protection against the swathe of circulating, difficult to neutralize tier 2 HIV-1 viruses. However, the development of stabilized, native-like envelope (Env) trimers such as BG505.SOSIP.664.T332N (BG505 SOSIP) has marked a significant advancement in vaccine design, due to their ability to elicit NAbs that neutralize tier 2 viruses in rhesus macaques (RM). NAb development following envelope trimer immunization in RM remains poorly understood, with hypothesized contributions from genetic variation at the IG loci, naive B cell repertoire, and differential gene expression in B cell lineages. To address these knowledge gaps, we have developed a set of BG505 SOSIP probes capable of recovering paired clonotype identity, antigen specificity, and gene expression of B cells in a high throughput fashion. These probes were constructed by conjugating biotinylated BG505 SOSIP to streptavidin covalently linked to both sc-RNA-Seq compatible DNA oligonucleotides and flow cytometry compatible fluorophores. Using these reagents, we isolated and sequenced BG505 SOSIP specific memory B cells from the PBMCs of an RM that developed high titers of neutralizing antibodies. To benchmark the accuracy of our technology, we compared our recovered heavy and light chain sequences to those identified from the same animal using conventional methodology and recovered 100% of previously identified NAbs. We then applied this technology to recover BG505 SOSIP specific memory B cells from five additional vaccinated RMs, cloned 34 antibodies for functional characterization, and identified ten antibodies with autologous neutralizing activity.<\/jats:p>","DOI":"10.1371\/journal.ppat.1013831","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T17:21:49Z","timestamp":1785259309000},"page":"e1013831","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Non-human primate LIBRA-Seq accelerates neutralizing antibody discovery in RM vaccinated against HIV-1"],"prefix":"10.1371","volume":"22","author":[{"given":"Christopher T.","family":"Edwards","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aaron D.","family":"Silva-Trenkle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anusmita","family":"Sahoo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kendra","family":"Cruickshank","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney","family":"Nelson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacey A.","family":"Lapp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nagarajan","family":"Raju","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thang","family":"Ton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda","family":"Metz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emily","family":"McGhee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faith A.","family":"Mbadugha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tysheena P.","family":"Charles","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ankur","family":"Saini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiran","family":"Gill","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathryn L.","family":"Pellegrini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rui","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jens","family":"Wrammert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amit A.","family":"Upadhyay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cynthia A.","family":"Derdeyn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rama Rao","family":"Amara","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriel","family":"Kwong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2116-5061","authenticated-orcid":true,"given":"Steven E.","family":"Bosinger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"ppat.1013831.ref001","unstructured":"Unaids. 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Galeota","year":"2024","journal-title":"Clin Immunol"},{"issue":"8","key":"ppat.1013831.ref034","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1038\/s41587-022-01232-2","article-title":"Efficient discovery of SARS-CoV-2-neutralizing antibodies via B cell receptor sequencing and ligand blocking","volume":"40","author":"AR Shiakolas","year":"2022","journal-title":"Nat Biotechnol"},{"issue":"9","key":"ppat.1013831.ref035","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1012499","article-title":"Isolation and characterization of IgG3 glycan-targeting antibodies with exceptional cross-reactivity for diverse viral families","volume":"20","author":"MJ Vukovich","year":"2024","journal-title":"PLoS Pathog"},{"issue":"1","key":"ppat.1013831.ref036","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/s41392-021-00610-7","article-title":"Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via 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Zhang","year":"2016","journal-title":"Front Immunol"},{"key":"ppat.1013831.ref067","article-title":"IgBLAST: an immunoglobulin variable domain sequence analysis tool","volume":"41","author":"J Ye","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ppat.1013831.ref068","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Y Hao","year":"2024","journal-title":"Nat Biotechnol"},{"issue":"20","key":"ppat.1013831.ref069","doi-asserted-by":"crossref","first-page":"3356","DOI":"10.1093\/bioinformatics\/btv359","article-title":"Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data","volume":"31","author":"NT 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