Signatures of the neutralizing dengue virus-reactive memory B cell repertoire identified by multiplexed envelope dimer probes
- 1National Institute of Allergy and Infectious Diseases, National Institutes of Health
Abstract
Sequential dengue virus (DENV) infection is thought to induce long-lived protection against dengue. However, little is known about the specificity, phenotype, and repertoire of the enduring B cell response due to limitations in high-throughput methods. We used stabilized DENV envelope (E) dimers as probes for in-depth memory B cell repertoire characterization using two complementary sequencing strategies. Using Rapid Assembly, Transfection, and Production of Immunoglobulins (RATP-Ig), we isolated 227 DENV2 E dimer-specific memory B cells from an immune donor, of which 87% bound at least two serotypes, 68% bound the fusion loop (FL-sensitive), and 42% were neutralizing. Among the most neutralizing, cross-binding antibodies, the FL-sensitive antibodies had weaker but broad neutralization, including to other flaviviruses, whereas FL- agnostic antibodies mapped to E domain II and III and were potently neutralizing, but only against one or two serotypes. Competitive binding of the DENV1-4 E dimers distinguished the more potently neutralizing FL-agnostic antibodies and broad and potent anti ()- envelope dimer epitope (EDE) antibodies from the low-quality FL-sensitive antibodies. Further, analysis of the heavy chain complementarity determining region 3 (CDRH3) showed FL-sensitive and -EDE antibodies were more negatively charged, but -EDE antibodies were distinguished by longer and more aromatic CDRH3s. We then demonstrated how oligonucleotide-tagged DENV1-4 dimers and proteogenomic single-cell B cell receptor sequencing (LIBRA-seq) could identify memory B cells predicted to have potent neutralization based on DENV-binding and CDRH3 physiochemical properties. This study provides insight into the secondary DENV-specific B cell repertoire and approaches for identifying protective antibodies as part of large-screening efforts.
One Sentence SummaryApproaches to define the genetic, physicochemical, and functional properties of dengue virus envelope dimer-specific memory B cells after secondary infection.
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BibTeX
@misc{lowman2026signatures,
title = {{Signatures of the neutralizing dengue virus-reactive memory B cell repertoire identified by multiplexed envelope dimer probes}},
author = {K. E. Lowman and R. A. Aogo and S. Smith and Y. Broderson and S. Firdous and G. Bhushan and D. J. Thiono and P. Mpingabo and A. R. Henry and T. S. Johnston and J. Roberts-Torres and L. Estrada and C. A. Schramm and F. Cheung and J. J. Polanco and R. Apps and K. Gangler and J. I. Cohen and S. Jacobson and E. Davidson and B. J. Doranz and J. Cherry and I. Douagi and B. A. Blacklaws and J. L. Heeney and A. M. de Silva and D. C. Douek and L. C. Katzelnick},
howpublished = {medRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.15.26363039},
url = {https://www.medrxiv.org/content/10.64898/2026.09.15.26363039v1},
note = {CC0},
}
RIS
TY - UNPB
TI - Signatures of the neutralizing dengue virus-reactive memory B cell repertoire identified by multiplexed envelope dimer probes
AU - K. E. Lowman
AU - R. A. Aogo
AU - S. Smith
AU - Y. Broderson
AU - S. Firdous
AU - G. Bhushan
AU - D. J. Thiono
AU - P. Mpingabo
AU - A. R. Henry
AU - T. S. Johnston
AU - J. Roberts-Torres
AU - L. Estrada
AU - C. A. Schramm
AU - F. Cheung
AU - J. J. Polanco
AU - R. Apps
AU - K. Gangler
AU - J. I. Cohen
AU - S. Jacobson
AU - E. Davidson
AU - B. J. Doranz
AU - J. Cherry
AU - I. Douagi
AU - B. A. Blacklaws
AU - J. L. Heeney
AU - A. M. de Silva
AU - D. C. Douek
AU - L. C. Katzelnick
PY - 2026
DA - 2026/09/15
PB - medRxiv
DO - 10.64898/2026.09.15.26363039
UR - https://www.medrxiv.org/content/10.64898/2026.09.15.26363039v1
AB - Sequential dengue virus (DENV) infection is thought to induce long-lived protection against dengue. However, little is known about the specificity, phenotype, and repertoire of the enduring B cell response due to limitations in high-throughput methods. We used stabilized DENV envelope (E) dimers as probes for in-depth memory B cell repertoire characterization using two complementary sequencing strategies. Using Rapid Assembly, Transfection, and Production of Immunoglobulins (RATP-Ig), we isolated 227 DENV2 E dimer-specific memory B cells from an immune donor, of which 87% bound at least two serotypes, 68% bound the fusion loop (FL-sensitive), and 42% were neutralizing. Among the most neutralizing, cross-binding antibodies, the FL-sensitive antibodies had weaker but broad neutralization, including to other flaviviruses, whereas FL- agnostic antibodies mapped to E domain II and III and were potently neutralizing, but only against one or two serotypes. Competitive binding of the DENV1-4 E dimers distinguished the more potently neutralizing FL-agnostic antibodies and broad and potent anti ()- envelope dimer epitope (EDE) antibodies from the low-quality FL-sensitive antibodies. Further, analysis of the heavy chain complementarity determining region 3 (CDRH3) showed FL-sensitive and -EDE antibodies were more negatively charged, but -EDE antibodies were distinguished by longer and more aromatic CDRH3s. We then demonstrated how oligonucleotide-tagged DENV1-4 dimers and proteogenomic single-cell B cell receptor sequencing (LIBRA-seq) could identify memory B cells predicted to have potent neutralization based on DENV-binding and CDRH3 physiochemical properties. This study provides insight into the secondary DENV-specific B cell repertoire and approaches for identifying protective antibodies as part of large-screening efforts. One Sentence SummaryApproaches to define the genetic, physicochemical, and functional properties of dengue virus envelope dimer-specific memory B cells after secondary infection.
ER -