Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses

Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses | 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 Article Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses Kizzmekia Corbett-Helaire, Christian Dzuvor, Sydney Moak, Lindsay McManus, and 10 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7997313/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 Four seasonal endemic human coronaviruses (HCoVs), HCoV-HKU1, HCoV-OC43, HCoV-229E, and HCoV-NL63, are culprits of mild upper respiratory and periodic severe diseases in vulnerable populations. Despite their prevalence, understanding HCoVs’ antigenic and immune signatures remains elusive. SARS-CoV-2 has evolved as the fifth HCoV, requiring seasonal vaccination, and currently, no other HCoV vaccines are available. SARS-CoV-2 co-infection with HCoVs increases disease severity; thus, combined vaccination may provide increased protection against seasonal HCoVs overall. Here, we explored spike (S) receptor binding domain (RBD) vs. N-terminal domain (NTD) B-cell immunodominance in HCoV-positive convalescent donors and immunogenicity in mice. We found that while antibody and B-cell isotypes were relatively dominant to S NTD, mice immunized with S RBD elicited significantly higher binding and neutralizing antibody (nAb) responses. With that knowledge, we used computational methods to infer that HCoV S sequences evolve into two main clades and designed chimeric immunodominant domains (IDDs) from both clades for each HCoV. IDDs were scaffolded onto two-component nanoparticles (NPs) displaying each IDD separately (monovalent IDD NP); three ß-HCoV IDDs (Mosaic-3 IDD NP); or five HCoVs IDDs (Mosaic-5 IDD NP). Mice immunized with mosaic IDD NPs, but not soluble IDD antigens nor monovalent IDD NPs, elicited potent, broadly cross-reactive binding and neutralizing antibody (Ab) responses against SARS-CoV-2 variants, other HCoVs, and Sarbecoviruses. System serology revealed that all four IDD immunogens elicited distinct Ab subclasses and Fc-effector functions, with mosaic-5 IDD NPs eliciting the most de novo Ab subclasses, distributions, and broader Fc-mediated immune mechanisms. Dissection of vaccine-immune sera revealed polyclonal Ab responses against multiple non-overlapping cross-reactive S epitopes. Due to elicitation of broad Ab responses with combinatory functionality, IDD NPs open new horizons for developing first-in-class supraseasonal HCoV vaccine candidates, with potential to decrease frequent SARS-CoV-2 sequence updates and protect against other HCoVs. Moreover, elicitation of Ab breadth that spans pandemic-threat Sarbecoviruses gives mosaic IDD NPs promise towards pandemic preparedness. Biological sciences/Microbiology/Vaccines/Protein vaccines Biological sciences/Microbiology/Virology/SARS-CoV-2 Biological sciences/Biotechnology/Nanobiotechnology/Nanoparticles Biological sciences/Immunology/Infectious diseases Full Text Additional Declarations Yes there is potential Competing Interest. CKOD and KSC are inventors on a US patent “Coronavirus spike protein-based vaccines”. KSC is an inventor on a US patent entitled “Prefusion Coronavirus Spike Proteins and Their Use.” All other authors declare no competing interests. Supplementary Files 20251030EndemicIDDSupplementaryNature.pdf Supplementary Information 20251030EndemicIDDExtendedDatav2Nature.pdf Extended Data Mosaic5IDDNP1.pdf PDB Validation report 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-7997313","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":556030215,"identity":"b3e07083-2f26-491b-a7a9-fa076b2d4120","order_by":0,"name":"Kizzmekia Corbett-Helaire","email":"data:image/png;base64,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","orcid":"https://orcid.org/0000-0002-2641-4688","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":true,"prefix":"","firstName":"Kizzmekia","middleName":"","lastName":"Corbett-Helaire","suffix":""},{"id":556030216,"identity":"58a88ad7-7409-4303-980d-ca37f780e114","order_by":1,"name":"Christian Dzuvor","email":"","orcid":"https://orcid.org/0000-0002-9109-051X","institution":"Harvard University","correspondingAuthor":false,"prefix":"","firstName":"Christian","middleName":"","lastName":"Dzuvor","suffix":""},{"id":556030217,"identity":"18229cae-f406-405e-991e-2198a008fb05","order_by":2,"name":"Sydney Moak","email":"","orcid":"","institution":"Howard Hughes Medical Institute","correspondingAuthor":false,"prefix":"","firstName":"Sydney","middleName":"","lastName":"Moak","suffix":""},{"id":556030218,"identity":"8c27cc14-0df6-48af-bc12-af89cdf220ff","order_by":3,"name":"Lindsay McManus","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Lindsay","middleName":"","lastName":"McManus","suffix":""},{"id":556030219,"identity":"4f90d49d-84e9-4327-8509-b068c1aa7bce","order_by":4,"name":"Abigail Thomas","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Abigail","middleName":"","lastName":"Thomas","suffix":""},{"id":556030220,"identity":"3948a473-699a-4a26-8b03-5be37318b264","order_by":5,"name":"Abigail Dzordzorme","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Abigail","middleName":"","lastName":"Dzordzorme","suffix":""},{"id":556030221,"identity":"3059db2d-0925-458b-90fd-412a5592b14a","order_by":6,"name":"Taewoo Kim","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Taewoo","middleName":"","lastName":"Kim","suffix":""},{"id":556030222,"identity":"f897e6ef-9159-4541-acc1-534828260859","order_by":7,"name":"Jeswin Joseph","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Jeswin","middleName":"","lastName":"Joseph","suffix":""},{"id":556030223,"identity":"39ed14b1-cef2-4a76-9338-2ec2cc1af0b4","order_by":8,"name":"Valerie Foley","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Valerie","middleName":"","lastName":"Foley","suffix":""},{"id":556030224,"identity":"ab323a1a-ca56-4ccd-aa31-5e87a768ab6e","order_by":9,"name":"Ingelise Gordon","email":"","orcid":"","institution":"Vaccine Research Center, NIAID, NIH","correspondingAuthor":false,"prefix":"","firstName":"Ingelise","middleName":"","lastName":"Gordon","suffix":""},{"id":556030225,"identity":"e5656a27-8701-4dd8-b12f-d8c233297e99","order_by":10,"name":"Laura Novik","email":"","orcid":"","institution":"Vaccine Research Center; National Institutes of Allergy and Infectious Diseases; National Institutes of Health","correspondingAuthor":false,"prefix":"","firstName":"Laura","middleName":"","lastName":"Novik","suffix":""},{"id":556030226,"identity":"99fab8fc-843b-45b3-8a3c-cd8b783eb54a","order_by":11,"name":"LaSonji Holman","email":"","orcid":"","institution":"Vaccine Research Center; National Institutes of Allergy and Infectious Diseases; National Institutes of Health","correspondingAuthor":false,"prefix":"","firstName":"LaSonji","middleName":"","lastName":"Holman","suffix":""},{"id":556030227,"identity":"4276fa8c-64b2-498e-b898-a0db52388994","order_by":12,"name":"Lesia Dropulic","email":"","orcid":"https://orcid.org/0000-0003-1125-5597","institution":"National Institutes of Health","correspondingAuthor":false,"prefix":"","firstName":"Lesia","middleName":"","lastName":"Dropulic","suffix":""},{"id":556030228,"identity":"d963f4da-9b37-48e5-9a2c-3668bff8ec96","order_by":13,"name":"Ryan McNamara","email":"","orcid":"","institution":"Harvard T.H. Chan School of Public Health","correspondingAuthor":false,"prefix":"","firstName":"Ryan","middleName":"","lastName":"McNamara","suffix":""}],"badges":[],"createdAt":"2025-10-31 10:15:30","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-7997313/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-7997313/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":100547500,"identity":"43a06401-9b69-4bd3-ac46-7021266ba25e","added_by":"auto","created_at":"2026-01-19 08:15:50","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2917833,"visible":true,"origin":"","legend":"","description":"","filename":"20251031EndemicIDDv24Nature.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7997313/v1_covered_5e27c920-8612-40d5-a5da-c1c9aac17d3a.pdf"},{"id":97857925,"identity":"a10ca29b-0a01-412e-bdb8-31043581c3c9","added_by":"auto","created_at":"2025-12-10 08:10:26","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":2015150,"visible":true,"origin":"","legend":"Supplementary Information","description":"","filename":"20251030EndemicIDDSupplementaryNature.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7997313/v1/8df14e3b29f92abca8e2d0e3.pdf"},{"id":97857922,"identity":"f8400ef6-9d52-40a1-9ed5-93176180c6bf","added_by":"auto","created_at":"2025-12-10 08:10:24","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":1601034,"visible":true,"origin":"","legend":"Extended Data","description":"","filename":"20251030EndemicIDDExtendedDatav2Nature.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7997313/v1/ded20e263819beb8d81ffa70.pdf"},{"id":97857923,"identity":"10911d16-952e-4157-940d-df6583c422e1","added_by":"auto","created_at":"2025-12-10 08:10:24","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":1261712,"visible":true,"origin":"","legend":"PDB Validation report","description":"","filename":"Mosaic5IDDNP1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-7997313/v1/dc7869f8ee9d048c287cd7d7.pdf"}],"financialInterests":"\u003cb\u003eYes\u003c/b\u003e there is potential Competing Interest.\nCKOD and KSC are inventors on a US patent “Coronavirus spike protein-based vaccines”. KSC is an inventor on a US patent entitled “Prefusion Coronavirus Spike Proteins and Their Use.” All other authors declare no competing interests.","formattedTitle":"Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses","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-7997313/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7997313/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Four seasonal endemic human coronaviruses (HCoVs), HCoV-HKU1, HCoV-OC43, HCoV-229E, and HCoV-NL63, are culprits of mild upper respiratory and periodic severe diseases in vulnerable populations. Despite their prevalence, understanding HCoVs’ antigenic and immune signatures remains elusive. SARS-CoV-2 has evolved as the fifth HCoV, requiring seasonal vaccination, and currently, no other HCoV vaccines are available. SARS-CoV-2 co-infection with HCoVs increases disease severity; thus, combined vaccination may provide increased protection against seasonal HCoVs overall. Here, we explored spike (S) receptor binding domain (RBD) vs. N-terminal domain (NTD) B-cell immunodominance in HCoV-positive convalescent donors and immunogenicity in mice. We found that while antibody and B-cell isotypes were relatively dominant to S NTD, mice immunized with S RBD elicited significantly higher binding and neutralizing antibody (nAb) responses. With that knowledge, we used computational methods to infer that HCoV S sequences evolve into two main clades and designed chimeric immunodominant domains (IDDs) from both clades for each HCoV. IDDs were scaffolded onto two-component nanoparticles (NPs) displaying each IDD separately (monovalent IDD NP); three ß-HCoV IDDs (Mosaic-3 IDD NP); or five HCoVs IDDs (Mosaic-5 IDD NP). Mice immunized with mosaic IDD NPs, but not soluble IDD antigens nor monovalent IDD NPs, elicited potent, broadly cross-reactive binding and neutralizing antibody (Ab) responses against SARS-CoV-2 variants, other HCoVs, and Sarbecoviruses. System serology revealed that all four IDD immunogens elicited distinct Ab subclasses and Fc-effector functions, with mosaic-5 IDD NPs eliciting the most de novo Ab subclasses, distributions, and broader Fc-mediated immune mechanisms. Dissection of vaccine-immune sera revealed polyclonal Ab responses against multiple non-overlapping cross-reactive S epitopes. Due to elicitation of broad Ab responses with combinatory functionality, IDD NPs open new horizons for developing first-in-class supraseasonal HCoV vaccine candidates, with potential to decrease frequent SARS-CoV-2 sequence updates and protect against other HCoVs. Moreover, elicitation of Ab breadth that spans pandemic-threat Sarbecoviruses gives mosaic IDD NPs promise towards pandemic preparedness.","manuscriptTitle":"Rational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-10 08:10:19","doi":"10.21203/rs.3.rs-7997313/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":"fb368b87-1099-42ce-817f-7fbd53aa05ed","owner":[],"postedDate":"December 10th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":59183326,"name":"Biological sciences/Microbiology/Vaccines/Protein vaccines"},{"id":59183327,"name":"Biological sciences/Microbiology/Virology/SARS-CoV-2"},{"id":59183328,"name":"Biological sciences/Biotechnology/Nanobiotechnology/Nanoparticles"},{"id":59183329,"name":"Biological sciences/Immunology/Infectious diseases"}],"tags":[],"updatedAt":"2026-01-16T21:25:13+00:00","versionOfRecord":[],"versionCreatedAt":"2025-12-10 08:10:19","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7997313","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7997313","identity":"rs-7997313","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}