Therapeutic HBV vaccine efficacy through ancestral mismatched T cell epitopes

Therapeutic HBV vaccine efficacy through ancestral mismatched T cell epitopes | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Therapeutic HBV vaccine efficacy through ancestral mismatched T cell epitopes Antonio Bertoletti, Nina Le Bert, Akshay Binayke, Shubhankar Ambike, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8892351/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Therapeutic vaccines for the treatment of chronic viral infections, such as HBV, have been mainly designed to target conserved viral regions and to preferentially restore dysfunctional virus-specific CD8 T cells. Such vaccines have failed to deliver clinical benefit, but a recent trial combining siRNA Elabsiran and PEG-IFN-α reported a remarkable ~50% HBsAg loss rate in chronic HBV patients who responded to the therapeutic vaccine BRII-179 administered prior to the trial. To define the underlying immunological mechanisms leading to the increased HBsAg loss rate, we longitudinally characterized vaccine-induced T and B cell responses using functional assays, persistence tracking, epitope mapping, phenotyping, and analysis of vaccine and infecting HBV sequences. We found that BRII-179-mediated modulation of HBV-specific immunity did not result from recovery of pre-existing dysfunctional T cells. Instead, the vaccine primed novel IL-2-producing CD4⁺ T cells targeting epitopes that were largely mismatched to patients’ infecting HBV strains. These responses were driven by a PreS1 N-terminal domain sequence within the vaccine’s large S protein that shows high homology to HBV genotype G—a rare genotype thought to represent a remnant of an extinct prehistoric HBV lineage. These vaccine-induced CD4⁺ T cells were detected in most vaccinated patients across diverse HLA class II backgrounds and persisted with stable functionality for more than two years. Despite their lack of cross-reactivity with contemporary HBV genotypes, the presence of these epitope-mismatched CD4⁺ T cells was associated with marked, progressive maturation of HBs-specific B cells during PEG-IFN-α/siRNA treatment, consistent with intramolecular T cell help. We conclude that the ability of BRII-179 to increase HBsAg loss is associated with the expansion of epitope-mismatched CD4⁺ T cells that promote HBs-specific B cell maturation during PEG-IFN-α treatment. These findings challenge current therapeutic vaccine strategies focused on conserved viral regions and CD8⁺ T cell responses, and suggest that ancestral HBV epitopes lost during viral evolution may represent potent targets for inducing therapeutically effective antiviral immunity. Biological sciences/Immunology/Infectious diseases/Hepatitis/Viral hepatitis/Hepatitis B Biological sciences/Immunology/Adaptive immunity/Cellular immunity/Lymphocyte differentiation Biological sciences/Immunology/Applied immunology/Vaccines/Protein vaccines Full Text Additional Declarations Yes there is potential Competing Interest. Ji Y, Tan Y, and Zhu Q: Employees of and hold stock and options in Brii Biosciences. Le Bert N, Tan A and Bertoletti A are founders and hold stock of T Cell Diagnostics (TCD). Hang SK is an employee of T Cell Diagnostics (TCD). Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8892351","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":635571009,"identity":"6482964f-fc1e-4776-9642-9a15d4fcb5a0","order_by":0,"name":"Antonio Bertoletti","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+ElEQVRIiWNgGAWjYNACAwY5hgNsSFz8gBmsxphULQwMiQ1Ea+Gf3X/wcUGBTXrfjbTEB4w7DtszsDdvk2D4U4tTi8Sdw8zGMwzScmfeSDtswHjmcGIDz7EyCca247ituZHMJs1jcDh3w430Num/bYcTGCRyzCQYG47h1CEP1ZJucCO9/QdjG9Bh8m/MgA7DrcUAqiXB4EbaMQagFsYGCR6gFrYanFoMbyQbG/MYpBnOPPMsGeiF9MQ2nrRii8S2Azi1yN1IfPiY54+NPN/xNMMPjG3W9vzshzfe+PCnDrf3MQA4ehIYDpOgBQpIsWUUjIJRMAqGOQAA7U9Qn3M7uAcAAAAASUVORK5CYII=","orcid":"https://orcid.org/0000-0002-2942-0485","institution":"DUKE-NUS Medical School","correspondingAuthor":true,"prefix":"","firstName":"Antonio","middleName":"","lastName":"Bertoletti","suffix":""},{"id":635571010,"identity":"2ca8bdb1-71f2-45e6-93b5-b6b4695428df","order_by":1,"name":"Nina Le Bert","email":"","orcid":"https://orcid.org/0000-0003-0502-2527","institution":"Duke NUS Singapore","correspondingAuthor":false,"prefix":"","firstName":"Nina","middleName":"Le","lastName":"Bert","suffix":""},{"id":635571011,"identity":"fc3854be-922f-423b-b22a-65ac12212edf","order_by":2,"name":"Akshay Binayke","email":"","orcid":"","institution":"Duke-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Akshay","middleName":"","lastName":"Binayke","suffix":""},{"id":635571012,"identity":"4857e383-4ebe-4247-a571-8ef50ce0f1eb","order_by":3,"name":"Shubhankar Ambike","email":"","orcid":"","institution":"Duke-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Shubhankar","middleName":"","lastName":"Ambike","suffix":""},{"id":635571013,"identity":"9c208774-c91d-4485-ae30-d55fb96dc718","order_by":4,"name":"Shou Kit Hang","email":"","orcid":"","institution":"T Cell Diagnostics","correspondingAuthor":false,"prefix":"","firstName":"Shou","middleName":"Kit","lastName":"Hang","suffix":""},{"id":635571014,"identity":"78faf91c-15f2-43b7-9bc0-9a54609f9e5f","order_by":5,"name":"Yazhini Avaiarasi","email":"","orcid":"","institution":"Duke-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Yazhini","middleName":"","lastName":"Avaiarasi","suffix":""},{"id":635571015,"identity":"8a3e103e-def5-40f6-a707-b5f34451770a","order_by":6,"name":"Previtha Sakthi Vale","email":"","orcid":"","institution":"Duke-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Previtha","middleName":"Sakthi","lastName":"Vale","suffix":""},{"id":635571016,"identity":"513d7504-82ed-420d-9f38-926254113c67","order_by":7,"name":"Natalene Shan","email":"","orcid":"","institution":"Duke-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Natalene","middleName":"","lastName":"Shan","suffix":""},{"id":635571017,"identity":"1c8e6cca-e950-4ff7-8565-65c416be3aab","order_by":8,"name":"Nicole Tan","email":"","orcid":"","institution":"DUKE-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Nicole","middleName":"","lastName":"Tan","suffix":""},{"id":635571018,"identity":"82dc939a-beb4-4f0f-8336-9b1b9b6e235a","order_by":9,"name":"Adeline Chia","email":"","orcid":"","institution":"DUKE-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Adeline","middleName":"","lastName":"Chia","suffix":""},{"id":635571019,"identity":"d4317d85-7def-46e6-8fd0-a010090b5083","order_by":10,"name":"Anthony Tan","email":"","orcid":"https://orcid.org/0000-0003-0079-8203","institution":"DUKE-NUS Medical School","correspondingAuthor":false,"prefix":"","firstName":"Anthony","middleName":"","lastName":"Tan","suffix":""},{"id":635571020,"identity":"00d1fe2a-a241-4d25-b2ef-a0bc3cd74697","order_by":11,"name":"Ying Tan","email":"","orcid":"","institution":"Brii Biosciences Inc.","correspondingAuthor":false,"prefix":"","firstName":"Ying","middleName":"","lastName":"Tan","suffix":""},{"id":635571021,"identity":"e5dcd86b-d908-4cc2-8c03-b0405acd022c","order_by":12,"name":"Qing Zhu","email":"","orcid":"https://orcid.org/0000-0001-5148-5157","institution":"Brii Biosciences Inc.","correspondingAuthor":false,"prefix":"","firstName":"Qing","middleName":"","lastName":"Zhu","suffix":""},{"id":635571022,"identity":"6f0efe19-a043-4b4d-89e0-e4802ab1c523","order_by":13,"name":"Yun Ji","email":"","orcid":"","institution":"Brii Biosciences Inc.","correspondingAuthor":false,"prefix":"","firstName":"Yun","middleName":"","lastName":"Ji","suffix":""}],"badges":[],"createdAt":"2026-02-16 10:42:03","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8892351/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8892351/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":108805440,"identity":"07862841-3f96-4d6c-b507-d96f64a0533a","added_by":"auto","created_at":"2026-05-08 15:25:58","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3451937,"visible":true,"origin":"","legend":"Article File","description":"","filename":"WENBAHBVVaccine.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8892351/v1_covered_8b797430-11a5-4ff0-9360-3df9589c46c4.pdf"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nJi Y, Tan Y, and Zhu Q: Employees of and hold stock and options in Brii Biosciences. Le Bert N, Tan A and Bertoletti A are founders and hold stock of T Cell Diagnostics (TCD). Hang SK is an employee of T Cell Diagnostics (TCD).","formattedTitle":"Therapeutic HBV vaccine efficacy through ancestral mismatched T cell epitopes","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8892351/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8892351/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Therapeutic vaccines for the treatment of chronic viral infections, such as HBV, have been mainly designed to target conserved viral regions and to preferentially restore dysfunctional virus-specific CD8 T cells. Such vaccines have failed to deliver clinical benefit, but a recent trial combining siRNA Elabsiran and PEG-IFN-α reported a remarkable ~50% HBsAg loss rate in chronic HBV patients who responded to the therapeutic vaccine BRII-179 administered prior to the trial. To define the underlying immunological mechanisms leading to the increased HBsAg loss rate, we longitudinally characterized vaccine-induced T and B cell responses using functional assays, persistence tracking, epitope mapping, phenotyping, and analysis of vaccine and infecting HBV sequences.\r\nWe found that BRII-179-mediated modulation of HBV-specific immunity did not result from recovery of pre-existing dysfunctional T cells. Instead, the vaccine primed novel IL-2-producing CD4⁺ T cells targeting epitopes that were largely mismatched to patients’ infecting HBV strains. These responses were driven by a PreS1 N-terminal domain sequence within the vaccine’s large S protein that shows high homology to HBV genotype G—a rare genotype thought to represent a remnant of an extinct prehistoric HBV lineage.\r\nThese vaccine-induced CD4⁺ T cells were detected in most vaccinated patients across diverse HLA class II backgrounds and persisted with stable functionality for more than two years. Despite their lack of cross-reactivity with contemporary HBV genotypes, the presence of these epitope-mismatched CD4⁺ T cells was associated with marked, progressive maturation of HBs-specific B cells during PEG-IFN-α/siRNA treatment, consistent with intramolecular T cell help.\r\nWe conclude that the ability of BRII-179 to increase HBsAg loss is associated with the expansion of epitope-mismatched CD4⁺ T cells that promote HBs-specific B cell maturation during PEG-IFN-α treatment. These findings challenge current therapeutic vaccine strategies focused on conserved viral regions and CD8⁺ T cell responses, and suggest that ancestral HBV epitopes lost during viral evolution may represent potent targets for inducing therapeutically effective antiviral immunity.","manuscriptTitle":"Therapeutic HBV vaccine efficacy through ancestral mismatched T cell epitopes","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-05-07 08:21:32","doi":"10.21203/rs.3.rs-8892351/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"d27ed623-62c0-4c7a-b46c-a0ccc7455ef3","owner":[],"postedDate":"May 7th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":67644860,"name":"Biological sciences/Immunology/Infectious diseases/Hepatitis/Viral hepatitis/Hepatitis B"},{"id":67644861,"name":"Biological sciences/Immunology/Adaptive immunity/Cellular immunity/Lymphocyte differentiation"},{"id":67644862,"name":"Biological sciences/Immunology/Applied immunology/Vaccines/Protein vaccines"}],"tags":[],"updatedAt":"2026-05-07T08:21:32+00:00","versionOfRecord":[],"versionCreatedAt":"2026-05-07 08:21:32","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8892351","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8892351","identity":"rs-8892351","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}