{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T18:45:35Z","timestamp":1792003535704,"version":"4.4.0"},"update-to":[{"DOI":"10.1371\/journal.pbio.3003996","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000}}],"reference-count":70,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Prevention and Control of Emerging and Major Infectious Diseases-National Science and Technology Major Project","award":["2026ZD01999601"],"award-info":[{"award-number":["2026ZD01999601"]}]},{"name":"the Major Project of Guangzhou National Laboratory","award":["SRPG22-002"],"award-info":[{"award-number":["SRPG22-002"]}],"id":[{"id":"https:\/\/ror.org\/03ybmxt82","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the Major Project of Guangzhou National Laboratory","award":["GZNL2026C01003"],"award-info":[{"award-number":["GZNL2026C01003"]}],"id":[{"id":"https:\/\/ror.org\/03ybmxt82","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the Major Project of Guangzhou National Laboratory","award":["EKPG21-30-2"],"award-info":[{"award-number":["EKPG21-30-2"]}],"id":[{"id":"https:\/\/ror.org\/03ybmxt82","id-type":"ROR","asserted-by":"crossref"}]},{"name":"the Major Project of Guangzhou National Laboratory","award":["GZNL2025A0009"],"award-info":[{"award-number":["GZNL2025A0009"]}],"id":[{"id":"https:\/\/ror.org\/03ybmxt82","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Key Research and Development Program of China","award":["2021YFA1300903"],"award-info":[{"award-number":["2021YFA1300903"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82341085"],"award-info":[{"award-number":["82341085"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32570199"],"award-info":[{"award-number":["32570199"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82495200"],"award-info":[{"award-number":["82495200"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82495203"],"award-info":[{"award-number":["82495203"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32361163669"],"award-info":[{"award-number":["32361163669"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170189"],"award-info":[{"award-number":["32170189"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32241021"],"award-info":[{"award-number":["32241021"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["92469301"],"award-info":[{"award-number":["92469301"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82201932"],"award-info":[{"award-number":["82201932"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012245","name":"Science and Technology Planning Project of Guangdong Province","doi-asserted-by":"publisher","award":["2023B1212060050"],"award-info":[{"award-number":["2023B1212060050"]}],"id":[{"id":"10.13039\/501100012245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012245","name":"Science and Technology Planning Project of Guangdong Province","doi-asserted-by":"publisher","award":["2023B1212120009"],"award-info":[{"award-number":["2023B1212120009"]}],"id":[{"id":"10.13039\/501100012245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100017692","name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["GIBHBRP24-02"],"award-info":[{"award-number":["GIBHBRP24-02"]}],"id":[{"id":"10.13039\/501100017692","id-type":"DOI","asserted-by":"publisher"}]},{"name":"the 111 Project","award":["D18010"],"award-info":[{"award-number":["D18010"]}]},{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2025A1515011245"],"award-info":[{"award-number":["2025A1515011245"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosbiology.org"],"crossmark-restriction":false},"short-container-title":["PLoS Biol"],"abstract":"<jats:p>\n                    R1-32-like public antibodies, characterized by shared IGHV1-69\/IGLV1-40 usage, are elicited in more than 50% of individuals with COVID-19 and have been implicated in driving recurrent mutations at L452\n                    <jats:sub>SARS2<\/jats:sub>\n                    and F490\n                    <jats:sub>SARS2<\/jats:sub>\n                    within their convergent epitope in the SARS-CoV-2 spike receptor-binding domain. These mutations effectively mediate escape from non-affinity-matured R1-32-like antibodies with germline-like sequences. Here, we characterize four affinity-matured human R1-32-like antibodies, C092, C807, BD56-104, and BD56-597, that tolerate L452\n                    <jats:sub>SARS2<\/jats:sub>\n                    and F490\n                    <jats:sub>SARS2<\/jats:sub>\n                    mutations. We show that this tolerance arises from residues introduced by somatic hypermutation at convergent positions across multiple CDR loops and surrounding regions, thereby creating additional contacts that reinforce epitope binding. An unusual N354\n                    <jats:sub>SARS2<\/jats:sub>\n                    glycosylation site, which emerged in BA.2.86 and became fixed in its descendants, is linked to escape from affinity-matured R1-32-like antibodies, implying ongoing selection by this public antibody class. Using an AI model trained on extensive neutralization data, we further identified ZL525, an ultrapotent human R1-32-like antibody with pan-SARS-CoV-2 variant activity, including against the highly evasive KP.3 variant carrying the N354\n                    <jats:sub>SARS2<\/jats:sub>\n                    glycosylation, and broad sarbecovirus cross-reactivity extending to SARS-CoV-1. Together, these findings show how affinity maturation enables public antibodies to adapt to viral antigenic drift, reveal how public antibody responses contribute to shaping SARS-CoV-2 antigenic evolution, and demonstrate the potential of AI-empowered strategies for discovering broadly neutralizing antibodies.\n                  <\/jats:p>","DOI":"10.1371\/journal.pbio.3003996","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T17:59:12Z","timestamp":1789495152000},"page":"e3003996","update-policy":"https:\/\/doi.org\/10.1371\/journal.pbio.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["R1-32-like public antibodies acquire tolerance to SARS-CoV-2 antigenic drift through somatic hypermutation"],"prefix":"10.1371","volume":"24","author":[{"given":"Chuanying","family":"Niu","sequence":"first","affiliation":[{"name":"University of Science and Technology of China","place":["Hefei, China"],"department":["Division of Life Sciences and Medicine"]},{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaohan","family":"Huang","sequence":"additional","affiliation":[{"name":"Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1645-8764","authenticated-orcid":true,"given":"Qihong","family":"Yan","sequence":"additional","affiliation":[{"name":"Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Banghui","family":"Liu","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]},{"name":"Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences","place":["Chengdu, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xijie","family":"Gao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yidong","family":"Song","sequence":"additional","affiliation":[{"name":"Nankai University","place":["Tianjin, China"],"department":["School of Statistics and Data Science"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjing","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]},{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zimu","family":"Li","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huiran","family":"Zheng","sequence":"additional","affiliation":[{"name":"Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"He","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaodong","family":"Huang","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Yuan","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Binqian","family":"Zou","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuedong","family":"Yang","sequence":"additional","affiliation":[{"name":"Sun Yat-sen University","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fandi","family":"Wu","sequence":"additional","affiliation":[{"name":"Tencent, AI for Life Sciences Lab","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yicheng","family":"Yao","sequence":"additional","affiliation":[{"name":"Sun Yat-sen University","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gul","family":"Habib","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinwen","family":"Chen","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling","family":"Chen","sequence":"additional","affiliation":[{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"He","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianhua","family":"Yao","sequence":"additional","affiliation":[{"name":"Tencent, AI for Life Sciences Lab","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jincun","family":"Zhao","sequence":"additional","affiliation":[{"name":"Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4632-9122","authenticated-orcid":true,"given":"Xiaoli","family":"Xiong","sequence":"additional","affiliation":[{"name":"Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences","place":["Guangzhou, China"],"department":["State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Laboratory for Stem Cell and Regenerative Medicine"]},{"name":"Guangzhou National Laboratory","place":["Guangzhou, China"]},{"name":"Guangzhou Medical University","place":["Guangzhou, China"],"department":["The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, GMU-GIBH Joint School of Life Sciences, Guangdong Provincial Key Laboratory of Protein Modification and Disease"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"issue":"7948","key":"pbio.3003996.ref001","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/s41586-022-05644-7","article-title":"Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution","volume":"614","author":"Y Cao","year":"2023","journal-title":"Nature"},{"issue":"5","key":"pbio.3003996.ref002","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1038\/s41564-019-0392-y","article-title":"Antibody responses to viral infections: a structural perspective across three different enveloped viruses","volume":"4","author":"CD Murin","year":"2019","journal-title":"Nat Microbiol"},{"issue":"1","key":"pbio.3003996.ref003","article-title":"Potent neutralizing antibodies against SARS-CoV-2 identified by high-throughput single-cell sequencing of convalescent patients\u2019 B cells","volume":"182","author":"Y Cao","year":"2020","journal-title":"Cell"},{"issue":"7896","key":"pbio.3003996.ref004","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/s41586-021-04245-0","article-title":"The N501Y spike substitution enhances SARS-CoV-2 infection and transmission","volume":"602","author":"Y Liu","year":"2022","journal-title":"Nature"},{"issue":"12","key":"pbio.3003996.ref005","doi-asserted-by":"crossref","first-page":"110156","DOI":"10.1016\/j.celrep.2021.110156","article-title":"Structural analysis of receptor binding domain mutations in SARS-CoV-2 variants of concern that modulate ACE2 and antibody binding","volume":"37","author":"D Mannar","year":"2021","journal-title":"Cell Rep"},{"issue":"7","key":"pbio.3003996.ref006","doi-asserted-by":"crossref","DOI":"10.1016\/j.immuni.2021.06.003","article-title":"Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species","volume":"54","author":"R Wang","year":"2021","journal-title":"Immunity"},{"key":"pbio.3003996.ref007","article-title":"Structural and functional ramifications of antigenic drift in recent SARS-CoV-2 variants","author":"M Yuan","year":"2021","journal-title":"Science"},{"issue":"6582","key":"pbio.3003996.ref008","doi-asserted-by":"crossref","first-page":"760","DOI":"10.1126\/science.abn7760","article-title":"SARS-CoV-2 Omicron variant: Antibody evasion and cryo-EM structure of spike protein-ACE2 complex","volume":"375","author":"D Mannar","year":"2022","journal-title":"Science"},{"issue":"7839","key":"pbio.3003996.ref009","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1038\/s41586-020-2852-1","article-title":"SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies","volume":"588","author":"CO Barnes","year":"2020","journal-title":"Nature"},{"issue":"5","key":"pbio.3003996.ref010","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2021.01.050","article-title":"Maturation and persistence of the anti-SARS-CoV-2 memory B cell response","volume":"184","author":"A Sokal","year":"2021","journal-title":"Cell"},{"issue":"6507","key":"pbio.3003996.ref011","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1126\/science.abd2321","article-title":"Structural basis of a shared antibody response to SARS-CoV-2","volume":"369","author":"M Yuan","year":"2020","journal-title":"Science"},{"issue":"8","key":"pbio.3003996.ref012","doi-asserted-by":"crossref","DOI":"10.1016\/j.immuni.2021.07.008","article-title":"Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations","volume":"54","author":"F Muecksch","year":"2021","journal-title":"Immunity"},{"issue":"8","key":"pbio.3003996.ref013","doi-asserted-by":"crossref","first-page":"109604","DOI":"10.1016\/j.celrep.2021.109604","article-title":"Convergent antibody responses to the SARS-CoV-2 spike protein in convalescent and vaccinated individuals","volume":"36","author":"EC Chen","year":"2021","journal-title":"Cell Rep"},{"issue":"1","key":"pbio.3003996.ref014","doi-asserted-by":"crossref","first-page":"7585","DOI":"10.1038\/s41467-024-51770-3","article-title":"Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants","volume":"15","author":"Q Yan","year":"2024","journal-title":"Nat Commun"},{"issue":"4","key":"pbio.3003996.ref015","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01600-21","article-title":"Analysis of B cell receptor repertoires reveals key signatures of the systemic B cell response after SARS-CoV-2 infection","volume":"96","author":"Y Zhang","year":"2022","journal-title":"J Virol"},{"issue":"1","key":"pbio.3003996.ref016","doi-asserted-by":"crossref","first-page":"2749","DOI":"10.1080\/22221751.2022.2140611","article-title":"Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants","volume":"11","author":"Q Yan","year":"2022","journal-title":"Emerg Microbes Infect"},{"issue":"7","key":"pbio.3003996.ref017","doi-asserted-by":"crossref","DOI":"10.1016\/j.str.2023.04.010","article-title":"Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response","volume":"31","author":"A Patel","year":"2023","journal-title":"Structure"},{"issue":"1","key":"pbio.3003996.ref018","doi-asserted-by":"crossref","first-page":"2751","DOI":"10.1038\/s41467-023-38345-4","article-title":"Evolution of antibody immunity following Omicron BA.1 breakthrough infection","volume":"14","author":"CI Kaku","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3003996.ref019","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1080\/22221751.2021.1925594","article-title":"Germline IGHV3-53-encoded RBD-targeting neutralizing antibodies are commonly present in the antibody repertoires of COVID-19 patients","volume":"10","author":"Q Yan","year":"2021","journal-title":"Emerg Microbes Infect"},{"issue":"1","key":"pbio.3003996.ref020","doi-asserted-by":"crossref","first-page":"4210","DOI":"10.1038\/s41467-021-24514-w","article-title":"Potent and protective IGHV3-53\/3-66 public antibodies and their shared escape mutant on the spike of SARS-CoV-2","volume":"12","author":"Q Zhang","year":"2021","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3003996.ref021","doi-asserted-by":"crossref","first-page":"108950","DOI":"10.1016\/j.celrep.2021.108950","article-title":"Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class","volume":"35","author":"M Rapp","year":"2021","journal-title":"Cell Rep"},{"issue":"6","key":"pbio.3003996.ref022","doi-asserted-by":"crossref","first-page":"114265","DOI":"10.1016\/j.celrep.2024.114265","article-title":"An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike","volume":"43","author":"B Liu","year":"2024","journal-title":"Cell Rep"},{"issue":"10","key":"pbio.3003996.ref023","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1038\/s41564-021-00972-2","article-title":"Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail","volume":"6","author":"J Dong","year":"2021","journal-title":"Nat Microbiol"},{"issue":"7","key":"pbio.3003996.ref024","doi-asserted-by":"crossref","first-page":"111650","DOI":"10.1016\/j.celrep.2022.111650","article-title":"Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2","volume":"41","author":"M Yuan","year":"2022","journal-title":"Cell Rep"},{"key":"pbio.3003996.ref025","doi-asserted-by":"crossref","DOI":"10.1016\/j.immuni.2022.03.019","article-title":"A large-scale systematic survey reveals recurring molecular features of public antibody responses to SARS-CoV-2","volume":"55","author":"Y Wang","year":"2022","journal-title":"Immunity"},{"issue":"7","key":"pbio.3003996.ref026","doi-asserted-by":"crossref","first-page":"110812","DOI":"10.1016\/j.celrep.2022.110812","article-title":"LY-CoV1404 (bebtelovimab) potently neutralizes SARS-CoV-2 variants","volume":"39","author":"K Westendorf","year":"2022","journal-title":"Cell Rep"},{"issue":"10","key":"pbio.3003996.ref027","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1038\/s41564-022-01235-4","article-title":"SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope","volume":"7","author":"P He","year":"2022","journal-title":"Nat Microbiol"},{"issue":"7923","key":"pbio.3003996.ref028","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/s41586-022-04980-y","article-title":"BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection","volume":"608","author":"Y Cao","year":"2022","journal-title":"Nature"},{"issue":"2","key":"pbio.3003996.ref029","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2022.12.018","article-title":"Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants","volume":"186","author":"Q Wang","year":"2023","journal-title":"Cell"},{"issue":"9","key":"pbio.3003996.ref030","doi-asserted-by":"crossref","first-page":"1785","DOI":"10.1038\/s41591-022-01911-2","article-title":"Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa","volume":"28","author":"H Tegally","year":"2022","journal-title":"Nat Med"},{"issue":"7851","key":"pbio.3003996.ref031","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41586-021-03207-w","article-title":"Evolution of antibody immunity to SARS-CoV-2","volume":"591","author":"C Gaebler","year":"2021","journal-title":"Nature"},{"issue":"7855","key":"pbio.3003996.ref032","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/s41586-021-03324-6","article-title":"mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants","volume":"592","author":"Z Wang","year":"2021","journal-title":"Nature"},{"issue":"1","key":"pbio.3003996.ref033","doi-asserted-by":"crossref","first-page":"6867","DOI":"10.1038\/s41467-024-50903-y","article-title":"De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model","volume":"15","author":"H He","year":"2024","journal-title":"Nat Commun"},{"issue":"7867","key":"pbio.3003996.ref034","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/s41586-021-03696-9","article-title":"Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection","volume":"595","author":"Z Wang","year":"2021","journal-title":"Nature"},{"issue":"8","key":"pbio.3003996.ref035","article-title":"A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2","volume":"8","author":"L Zhang","year":"2021","journal-title":"Natl Sci Rev"},{"issue":"11","key":"pbio.3003996.ref036","doi-asserted-by":"crossref","first-page":"3699","DOI":"10.1038\/s41596-020-0394-5","article-title":"Quantification of SARS-CoV-2 neutralizing antibody by a pseudotyped virus-based assay","volume":"15","author":"J Nie","year":"2020","journal-title":"Nat Protoc"},{"issue":"1","key":"pbio.3003996.ref037","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1038\/s41467-023-36761-0","article-title":"Somatically hypermutated antibodies isolated from SARS-CoV-2 Delta infected patients cross-neutralize heterologous variants","volume":"14","author":"H Yu","year":"2023","journal-title":"Nat Commun"},{"issue":"11","key":"pbio.3003996.ref038","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adr8772","article-title":"SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding","volume":"11","author":"J Wang","year":"2025","journal-title":"Sci Adv"},{"issue":"1","key":"pbio.3003996.ref039","doi-asserted-by":"crossref","first-page":"2402880","DOI":"10.1080\/22221751.2024.2402880","article-title":"Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages","volume":"13","author":"Q Wang","year":"2024","journal-title":"Emerg Microbes Infect"},{"key":"pbio.3003996.ref040","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btz328","article-title":"Multifaceted protein-protein interaction prediction based on Siamese residual RCNN","volume":"35","author":"M Chen","year":"2019","journal-title":"Bioinformatics"},{"key":"pbio.3003996.ref041","article-title":"AI recognizes convergent somatic hypermutation signatures to allow the discovery of variant-resilient broadly neutralizing antibodies","author":"Q Yan","year":"2025","journal-title":"bioRxiv"},{"key":"pbio.3003996.ref042","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1016\/j.str.2024.06.012","article-title":"Spike structures, receptor binding, and immune escape of recently circulating SARS-CoV-2 Omicron BA.2.86, JN.1, EG.5, EG.5.1, and HV.1 sub-variants","volume":"32","author":"L Li","year":"2024","journal-title":"Structure"},{"key":"pbio.3003996.ref043","doi-asserted-by":"crossref","first-page":"7715","DOI":"10.1038\/s41467-024-51973-8","article-title":"Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants","volume":"15","author":"H Yang","year":"2024","journal-title":"Nat Commun"},{"issue":"7","key":"pbio.3003996.ref044","article-title":"Spike N354 glycosylation augments SARS-CoV-2 fitness for human adaptation through structural plasticity","volume":"11","author":"P Liu","year":"2024","journal-title":"Natl Sci Rev"},{"issue":"1","key":"pbio.3003996.ref045","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/s41467-021-21006-9","article-title":"Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2","volume":"12","author":"AG Wrobel","year":"2021","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3003996.ref046","doi-asserted-by":"crossref","first-page":"1607","DOI":"10.1038\/s41467-021-21767-3","article-title":"Bat and pangolin coronavirus spike glycoprotein structures provide insights into SARS-CoV-2 evolution","volume":"12","author":"S Zhang","year":"2021","journal-title":"Nat Commun"},{"issue":"1","key":"pbio.3003996.ref047","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/s41421-023-00581-9","article-title":"Host susceptibility and structural and immunological insight of S proteins of two SARS-CoV-2 closely related bat coronaviruses","volume":"9","author":"X Ou","year":"2023","journal-title":"Cell Discov"},{"issue":"8","key":"pbio.3003996.ref048","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.00342-24","article-title":"Structural determinants of spike infectivity in bat SARS-like coronaviruses RsSHC014 and WIV1","volume":"98","author":"S Qiao","year":"2024","journal-title":"J Virol"},{"issue":"9","key":"pbio.3003996.ref049","doi-asserted-by":"crossref","DOI":"10.26508\/lsa.202201796","article-title":"Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes","volume":"6","author":"X Zhang","year":"2023","journal-title":"Life Sci Alliance"},{"key":"pbio.3003996.ref050","doi-asserted-by":"crossref","first-page":"15092","DOI":"10.1038\/ncomms15092","article-title":"Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains","volume":"8","author":"Y Yuan","year":"2017","journal-title":"Nat Commun"},{"key":"pbio.3003996.ref051","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.sbi.2020.11.008","article-title":"Progress toward improved understanding of antibody maturation","volume":"67","author":"S Vajda","year":"2021","journal-title":"Curr Opin Struct Biol"},{"key":"pbio.3003996.ref052","article-title":"Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies","author":"P Pushparaj","year":"2022","journal-title":"Immunity"},{"issue":"4","key":"pbio.3003996.ref053","doi-asserted-by":"crossref","first-page":"100255","DOI":"10.1016\/j.xcrm.2021.100255","article-title":"Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016","volume":"2","author":"TN Starr","year":"2021","journal-title":"Cell Rep Med"},{"issue":"11","key":"pbio.3003996.ref054","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2122954119","article-title":"Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization","volume":"119","author":"S Shan","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"8013","key":"pbio.3003996.ref055","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1038\/s41586-024-07385-1","article-title":"Computationally restoring the potency of a clinical antibody against Omicron","volume":"629","author":"TA Desautels","year":"2024","journal-title":"Nature"},{"issue":"6704","key":"pbio.3003996.ref056","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1126\/science.adk8946","article-title":"Unsupervised evolution of protein and antibody complexes with a structure-informed language model","volume":"385","author":"VR Shanker","year":"2024","journal-title":"Science"},{"issue":"6510","key":"pbio.3003996.ref057","doi-asserted-by":"crossref","first-page":"1501","DOI":"10.1126\/science.abd0826","article-title":"Structure-based design of prefusion-stabilized SARS-CoV-2 spikes","volume":"369","author":"C-L Hsieh","year":"2020","journal-title":"Science"},{"issue":"10","key":"pbio.3003996.ref058","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/s41594-020-0478-5","article-title":"A thermostable, closed SARS-CoV-2 spike protein trimer","volume":"27","author":"X Xiong","year":"2020","journal-title":"Nat Struct Mol Biol"},{"issue":"7","key":"pbio.3003996.ref059","article-title":"Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike","volume":"18","author":"K Qu","year":"2022","journal-title":"PLoS Pathog"},{"issue":"28","key":"pbio.3003996.ref060","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.adv7296","article-title":"Structures and receptor binding activities of merbecovirus spike proteins reveal key signatures for human DPP4 adaptation","volume":"11","author":"H Yuan","year":"2025","journal-title":"Sci Adv"},{"issue":"1","key":"pbio.3003996.ref061","doi-asserted-by":"crossref","first-page":"63","DOI":"10.1038\/nmeth.2727","article-title":"Quantifying the local resolution of cryo-EM density maps","volume":"11","author":"A Kucukelbir","year":"2014","journal-title":"Nat Methods"},{"issue":"13","key":"pbio.3003996.ref062","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera--a visualization system for exploratory research and analysis","volume":"25","author":"EF Pettersen","year":"2004","journal-title":"J Comput Chem"},{"key":"pbio.3003996.ref063","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"P Emsley","year":"2010","journal-title":"Acta Crystallogr D Biol Crystallogr"},{"key":"pbio.3003996.ref064","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1107\/S2059798318006551","article-title":"Real-space refinement in PHENIX for cryo-EM and crystallography","volume":"74","author":"PV Afonine","year":"2018","journal-title":"Acta Crystallogr D Struct Biol"},{"issue":"6","key":"pbio.3003996.ref065","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"UniProt Consortium","year":"2015","journal-title":"Bioinformatics"},{"key":"pbio.3003996.ref066","doi-asserted-by":"crossref","first-page":"127063","DOI":"10.1016\/j.neucom.2023.127063","article-title":"RoFormer: enhanced transformer with rotary position embedding","volume":"568","author":"J Su","year":"2024","journal-title":"Neurocomputing"},{"issue":"7898","key":"pbio.3003996.ref067","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1038\/s41586-021-04385-3","article-title":"Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies","volume":"602","author":"Y Cao","year":"2022","journal-title":"Nature"},{"issue":"12","key":"pbio.3003996.ref068","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20221006","article-title":"Memory B cell responses to Omicron subvariants after SARS-CoV-2 mRNA breakthrough infection in humans","volume":"219","author":"Z Wang","year":"2022","journal-title":"J Exp Med"},{"issue":"1","key":"pbio.3003996.ref069","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1038\/s41467-023-35927-0","article-title":"Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape","volume":"14","author":"L Witte","year":"2023","journal-title":"Nat Commun"},{"issue":"73","key":"pbio.3003996.ref070","doi-asserted-by":"crossref","DOI":"10.1101\/2022.04.01.486726","article-title":"Recall of preexisting cross-reactive B cell memory after Omicron BA.1 breakthrough infection","volume":"7","author":"CI Kaku","year":"2022","journal-title":"Sci Immunol"}],"updated-by":[{"DOI":"10.1371\/journal.pbio.3003996","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T00:00:00Z","timestamp":1791936000000}}],"container-title":["PLOS Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003996","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T17:53:14Z","timestamp":1792000394000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pbio.3003996"}},"subtitle":[],"editor":[{"given":"Ali H.","family":"Ellebedy","sequence":"first","affiliation":[{"name":"Washington University School of Medicine","place":["UNITED STATES OF AMERICA"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":70,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9,15]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pbio.3003996","relation":{},"ISSN":["1545-7885"],"issn-type":[{"value":"1545-7885","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]}}}