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A key to this problem lies in understanding antibody affinity maturation (AM), the evolutionary process within germinal centers (GCs) that shapes the B cell and thus antibody response. Traditionally, AM has been viewed as favoring the selection of B cells with the highest-affinity B cell receptors (BCRs) through competitive interplays. However, emerging evidence suggests that GCs are more permissive, allowing B cells with a broad range of affinities to persist, thereby promoting clonal diversity and enabling the rare emergence of bnAbs. This review reassesses affinity-based selection models and proposes a new paradigm that integrates multifactorial processes, including stochastic B cell decisions within GC dynamics, antigen extraction efficiency influenced by probabilistic bond rupture, and avidity-driven BCR binding alterations and representations on multivalent antigens. We highlight how advanced AM simulations that move beyond affinity as the sole determinant provide a more realistic and predictive representation of AM, marking a major step forward in developing strategies to promote effective immune responses against highly mutable, complex antigens.<\/jats:p>","DOI":"10.3389\/fimmu.2025.1627674","type":"journal-article","created":{"date-parts":[[2025,7,1]],"date-time":"2025-07-01T05:28:09Z","timestamp":1751347689000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["A paradigm shift in simulating affinity maturation to elicit broadly neutralizing antibodies"],"prefix":"10.3389","volume":"16","author":[{"given":"Fahsai","family":"Nakarin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kayla G.","family":"Sprenger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,7,1]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.iy.12.040194.001001","article-title":"Germinal centers","volume":"12","author":"MacLennan","year":"1994","journal-title":"Annu Rev Immunol"},{"key":"B2","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-immunol-020711-075032","article-title":"Germinal centers","volume":"30","author":"Victora","year":"2012","journal-title":"Annu Rev Immunol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-immunol-120419-022408","article-title":"Germinal centers","volume":"40","year":"2022","journal-title":"Annu Rev Immunol"},{"key":"B4","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1038\/nri3804","article-title":"Dynamics of B cells in germinal centres","volume":"15","author":"De Silva","year":"2015","journal-title":"Nat Rev Immunol"},{"key":"B5","doi-asserted-by":"publisher","first-page":"162","DOI":"10.1016\/j.celrep.2012.05.010","article-title":"A theory of germinal center B cell selection, division, and exit","volume":"2","author":"Meyer-Hermann","year":"2012","journal-title":"Cell Rep"},{"key":"B6","doi-asserted-by":"publisher","DOI":"10.1126\/science.aad3439","article-title":"Visualizing antibody affinity maturation in germinal centers","volume":"351","author":"Tas","year":"2016","journal-title":"Science"},{"key":"B7","doi-asserted-by":"publisher","first-page":"e2016425118","DOI":"10.1073\/pnas.2016425118","article-title":"Permissive selection followed by affinity-based proliferation of GC light zone B cells dictates cell fate and ensures clonal breadth","volume":"118","author":"Nakagawa","year":"2021","journal-title":"Proc Natl Acad Sci"},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2021.109286","article-title":"Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells","volume":"35","author":"Mathew","year":"2021","journal-title":"Cell Rep"},{"key":"B9","doi-asserted-by":"publisher","first-page":"5486","DOI":"10.1016\/j.cell.2023.10.022","article-title":"Germinal centers output clonally diverse plasma cell populations expressing high- and low-affinity antibodies","volume":"186","author":"Sprumont","year":"2023","journal-title":"Cell"},{"key":"B10","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.immuni.2023.12.010","article-title":"Lack of affinity signature for germinal center cells that have initiated plasma cell differentiation","volume":"57","author":"Sutton","year":"2024","journal-title":"Immunity"},{"key":"B11","doi-asserted-by":"publisher","first-page":"5249","DOI":"10.1038\/s41467-023-40918-2","article-title":"Engaging an HIV vaccine target through the acquisition of low B cell affinity","volume":"14","author":"Ronsard","year":"2023","journal-title":"Nat Commun"},{"key":"B12","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1111\/imr.12661","article-title":"Germinal center responses to complex antigens","volume":"284","author":"Finney","year":"2018","journal-title":"Immunol Rev"},{"key":"B13","doi-asserted-by":"publisher","first-page":"335","DOI":"10.3390\/cells13010033","article-title":"Determination of binding affinity of antibodies to HIV-1 recombinant envelope glycoproteins, pseudoviruses, infectious molecular clones, and cell-expressed trimeric gp160 using microscale thermophoresis","volume":"13","author":"Basu","year":"2023","journal-title":"Cells"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-022-00753-w","article-title":"Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies","volume":"23","author":"Haynes","year":"2023","journal-title":"Nat Rev Immunol"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00983-17","article-title":"How germinal centers evolve broadly neutralizing antibodies: the breadth of the follicular helper T cell response. 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