Temporal dynamics and turnover of rabbit hemorrhagic disease virus 2 (RHDV2/GI.2) in wild lagomorphs from northeastern Spain

Temporal dynamics and turnover of rabbit hemorrhagic disease virus 2 (RHDV2/GI.2) in wild lagomorphs from northeastern Spain | 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 Research Article Temporal dynamics and turnover of rabbit hemorrhagic disease virus 2 (RHDV2/GI.2) in wild lagomorphs from northeastern Spain Josep Estruch, Tereza Almeida, Emmanuel Serrano, Lorena Pereira, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8310298/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 21 Mar, 2026 Read the published version in Microbial Ecology → Version 1 posted 11 You are reading this latest preprint version Abstract In Mediterranean ecosystems, emerging lagoviruses, particularly rabbit hemorrhagic disease virus 2 (RHDV2/GI.2), have caused substantial mortality in European rabbits ( Oryctolagus cuniculus ) and, sporadically, hares ( Lepus spp.). Recombination is common among RNA viruses, including lagoviruses, and shapes their evolution, influencing pathogenicity, epidemiology, and host range. However, the viral dynamics of recombinant strains in wild populations remain largely unknown. In this work, we analyse 66 RHDV2/GI.2 coding sequences from European rabbits (n = 44), European brown hares (n = 21) and one Iberian hare collected in Catalonia (NE Spain) between 2014–2024, to characterise temporal patterns and turnover of the different recombinant lineages. All strains shared the GI.2 capsid backbone but with four distinct non-structural genomic profiles: GI.3P–GI.2, GI.1bP–GI.2, GI.4(p16)–GI.1bP–GI.2, and GI.4P–GI.2. The four recombinants were detected in European brown hares, whereas rabbits were infected by only three, with the same recombinant present in areas where both species coexist. The Iberian hare was infected by a GI.4P-GI.2 recombinant, where rabbits showed the same lineage. Generalised additive models revealed significant interactions between recombinant type and year of detection, indicating contrasting turnover and temporal dynamics. Over the decade, GI.3P-GI.2 appeared transiently in 2014, GI.1bP-GI.2 strains dominated until 2019, and GI.4-related recombinants progressively replaced them, with GI.4P-GI.2 prevailing from 2020 onwards. Our findings reveal that recombinant strains have been successively replaced over time in leporid species from northeastern Iberia, likely due to the selective advantages provided by the non-structural genomic region, highlighting recombination as a major driver of viral dynamics. Lepus europaeus Oryctolagus cuniculus rabbit hemorrhagic disease viral recombination viral evolution Wildlife disease surveillance Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementarymaterialV2.docx Cite Share Download PDF Status: Published Journal Publication published 21 Mar, 2026 Read the published version in Microbial Ecology → Version 1 posted Editorial decision: Revision requested 27 Jan, 2026 Reviews received at journal 27 Jan, 2026 Reviewers agreed at journal 20 Jan, 2026 Reviewers agreed at journal 15 Jan, 2026 Reviews received at journal 06 Jan, 2026 Reviewers agreed at journal 16 Dec, 2025 Reviewers agreed at journal 16 Dec, 2025 Reviewers invited by journal 10 Dec, 2025 Editor assigned by journal 10 Dec, 2025 Submission checks completed at journal 10 Dec, 2025 First submitted to journal 08 Dec, 2025 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-8310298","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":559500008,"identity":"2a6f9426-3384-4f7c-b19d-36502de2589c","order_by":0,"name":"Josep Estruch","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA6UlEQVRIiWNgGAWjYBACxgYkDjNDBQODAdFaeMBazkC1HCDGOrAWxjYitDC3tz98XMBgY28vfcbwc+G8w/LmDMwPP3/A57CeM8bGMxjSEnv4coylZ247bLizgc1YAp8tjDNy2KR5GA4n8PDwmDHzbjvMuOEADwMBLenPf/Mw/LeHaJlz2B6ohfkHfi0JZsw8DAcYe8BaGg4nArWw4bcF6BfpGQbJiT1n2IqleY6lJ+9sZjOzOINHiyEwxD4XVNjZs/cwb/zMU2Ntu529+fGNCnxaGkAxiBLjzHiUg4A8EWpGwSgYBaNgpAMAoWhFPEEwY04AAAAASUVORK5CYII=","orcid":"","institution":"Autonomous University of Barcelona","correspondingAuthor":true,"prefix":"","firstName":"Josep","middleName":"","lastName":"Estruch","suffix":""},{"id":559500009,"identity":"7dde5119-14d0-47e4-9f05-bc6d5c1cdea4","order_by":1,"name":"Tereza Almeida","email":"","orcid":"","institution":"University of Porto","correspondingAuthor":false,"prefix":"","firstName":"Tereza","middleName":"","lastName":"Almeida","suffix":""},{"id":559500011,"identity":"104cd78b-e30e-4334-8f07-38e49f55659e","order_by":2,"name":"Emmanuel Serrano","email":"","orcid":"","institution":"Autonomous University of Barcelona","correspondingAuthor":false,"prefix":"","firstName":"Emmanuel","middleName":"","lastName":"Serrano","suffix":""},{"id":559500015,"identity":"9c62c5d5-0ff2-49b8-a2a9-e42f91627839","order_by":3,"name":"Lorena Pereira","email":"","orcid":"","institution":"University of Porto","correspondingAuthor":false,"prefix":"","firstName":"Lorena","middleName":"","lastName":"Pereira","suffix":""},{"id":559500016,"identity":"be920f01-233b-4938-82ba-e814c9e0153e","order_by":4,"name":"Carlos Rouco","email":"","orcid":"","institution":"University of Seville","correspondingAuthor":false,"prefix":"","firstName":"Carlos","middleName":"","lastName":"Rouco","suffix":""},{"id":559500017,"identity":"e8349e8f-33a1-4865-bc03-97e4358db0de","order_by":5,"name":"Santiago Lavín","email":"","orcid":"","institution":"Autonomous University of Barcelona","correspondingAuthor":false,"prefix":"","firstName":"Santiago","middleName":"","lastName":"Lavín","suffix":""},{"id":559500018,"identity":"b8a7ae75-74ef-4595-a357-372d0605f149","order_by":6,"name":"Joana Abrantes","email":"","orcid":"","institution":"University of Porto","correspondingAuthor":false,"prefix":"","firstName":"Joana","middleName":"","lastName":"Abrantes","suffix":""},{"id":559500019,"identity":"b18fa41d-240f-4d1c-99aa-786a54f3b629","order_by":7,"name":"Roser Velarde","email":"","orcid":"","institution":"Autonomous University of Barcelona","correspondingAuthor":false,"prefix":"","firstName":"Roser","middleName":"","lastName":"Velarde","suffix":""},{"id":559500020,"identity":"46dcd2b3-1067-46fc-865e-d712d26ef066","order_by":8,"name":"Ana M. Lopes","email":"","orcid":"","institution":"University of Porto","correspondingAuthor":false,"prefix":"","firstName":"Ana","middleName":"M.","lastName":"Lopes","suffix":""}],"badges":[],"createdAt":"2025-12-08 18:08:14","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8310298/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8310298/v1","draftVersion":[],"editorialEvents":[{"content":"https://doi.org/10.1007/s00248-026-02746-x","type":"published","date":"2026-03-21T15:57:33+00:00"}],"editorialNote":"","failedWorkflow":false,"files":[{"id":98433610,"identity":"00425e98-1eab-4596-8def-96ddf97c426c","added_by":"auto","created_at":"2025-12-17 16:50:56","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":647658,"visible":true,"origin":"","legend":"","description":"","filename":"EstruchetalTemporalDynamicsV4.docx","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/a65633e5be155d1edbc4bb3a.docx"},{"id":98266034,"identity":"87bb0235-3d45-4c1c-963e-5b7baf085ab2","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"json","order_by":1,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":10771,"visible":true,"origin":"","legend":"","description":"","filename":"fcb6a247c29f4ea9bb84ff98353d0d53.json","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/a6527feaf231fa7456e426cc.json"},{"id":98266039,"identity":"85f16c0d-83a2-465c-b463-b2654d8e3c16","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":45365,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementarymaterialV2.docx","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/ed7649096c630b032f3214f9.docx"},{"id":98435300,"identity":"8fb3bbce-2b98-469d-8255-e9fb1cb6c257","added_by":"auto","created_at":"2025-12-17 16:53:26","extension":"xml","order_by":3,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":124506,"visible":true,"origin":"","legend":"","description":"","filename":"fcb6a247c29f4ea9bb84ff98353d0d531enriched.xml","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/7afcc1191ca1af9157e310ce.xml"},{"id":98435441,"identity":"1dadd8af-0ea9-470d-ad8a-18a377f455f6","added_by":"auto","created_at":"2025-12-17 16:53:48","extension":"jpeg","order_by":4,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":308815,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage1.jpeg","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/1a64d7541b9fc81a5924f284.jpeg"},{"id":98435727,"identity":"61cad0a5-2302-45cf-aecd-c17ef4ff3af5","added_by":"auto","created_at":"2025-12-17 16:54:19","extension":"png","order_by":5,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":33627,"visible":true,"origin":"","legend":"","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/686ab6ca9b56204d6cacfb0f.png"},{"id":98266042,"identity":"18f8a16d-7fca-4cd8-826f-6183a829fa13","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"png","order_by":6,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":75325,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/76e467ddbd6df2cfcc2963cb.png"},{"id":98266040,"identity":"b3f55625-d533-4c21-b9fb-eb3a1facfdc7","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"png","order_by":7,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":16110,"visible":true,"origin":"","legend":"","description":"","filename":"Onlinefloatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/d4288303667059b472602520.png"},{"id":98434327,"identity":"83c3320a-f8c4-4974-a6f4-576af8dba4b5","added_by":"auto","created_at":"2025-12-17 16:51:54","extension":"xml","order_by":8,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":124649,"visible":true,"origin":"","legend":"","description":"","filename":"fcb6a247c29f4ea9bb84ff98353d0d531structuring.xml","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/dc407fe72cf25e2ed630e27a.xml"},{"id":98266044,"identity":"bce39bd2-bdcc-4f7c-8526-4353769528ea","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"html","order_by":9,"title":"","display":"","copyAsset":false,"role":"acdc-reference","size":138669,"visible":true,"origin":"","legend":"","description":"","filename":"earlyproof.html","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/1318941b9778bd93b4c1352c.html"},{"id":105223417,"identity":"ca2789bd-f975-4966-8c45-ef9e0270fd3d","added_by":"auto","created_at":"2026-03-23 16:06:06","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":685102,"visible":true,"origin":"","legend":"","description":"","filename":"EstruchetalTemporalDynamicsV4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1_covered_e4f8fff8-a319-4efd-8109-e079fd146c2f.pdf"},{"id":98266035,"identity":"fc06b9bf-3f39-44a2-8a9b-8d01aa0e717a","added_by":"auto","created_at":"2025-12-15 22:54:30","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":45365,"visible":true,"origin":"","legend":"","description":"","filename":"SupplementarymaterialV2.docx","url":"https://assets-eu.researchsquare.com/files/rs-8310298/v1/f17148213b8a6b2ceca9737c.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Temporal dynamics and turnover of rabbit hemorrhagic disease virus 2 (RHDV2/GI.2) in wild lagomorphs from northeastern Spain","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"Lepus europaeus, Oryctolagus cuniculus, rabbit hemorrhagic disease, viral recombination, viral evolution, Wildlife disease surveillance","lastPublishedDoi":"10.21203/rs.3.rs-8310298/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8310298/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eIn Mediterranean ecosystems, emerging lagoviruses, particularly rabbit hemorrhagic disease virus 2 (RHDV2/GI.2), have caused substantial mortality in European rabbits (\u003cem\u003eOryctolagus cuniculus\u003c/em\u003e) and, sporadically, hares (\u003cem\u003eLepus\u003c/em\u003e spp.). Recombination is common among RNA viruses, including lagoviruses, and shapes their evolution, influencing pathogenicity, epidemiology, and host range. However, the viral dynamics of recombinant strains in wild populations remain largely unknown. In this work, we analyse 66 RHDV2/GI.2 coding sequences from European rabbits (n\u0026thinsp;=\u0026thinsp;44), European brown hares (n\u0026thinsp;=\u0026thinsp;21) and one Iberian hare collected in Catalonia (NE Spain) between 2014\u0026ndash;2024, to characterise temporal patterns and turnover of the different recombinant lineages. All strains shared the GI.2 capsid backbone but with four distinct non-structural genomic profiles: GI.3P\u0026ndash;GI.2, GI.1bP\u0026ndash;GI.2, GI.4(p16)\u0026ndash;GI.1bP\u0026ndash;GI.2, and GI.4P\u0026ndash;GI.2. The four recombinants were detected in European brown hares, whereas rabbits were infected by only three, with the same recombinant present in areas where both species coexist. The Iberian hare was infected by a GI.4P-GI.2 recombinant, where rabbits showed the same lineage. Generalised additive models revealed significant interactions between recombinant type and year of detection, indicating contrasting turnover and temporal dynamics. Over the decade, GI.3P-GI.2 appeared transiently in 2014, GI.1bP-GI.2 strains dominated until 2019, and GI.4-related recombinants progressively replaced them, with GI.4P-GI.2 prevailing from 2020 onwards. Our findings reveal that recombinant strains have been successively replaced over time in leporid species from northeastern Iberia, likely due to the selective advantages provided by the non-structural genomic region, highlighting recombination as a major driver of viral dynamics.\u003c/p\u003e","manuscriptTitle":"Temporal dynamics and turnover of rabbit hemorrhagic disease virus 2 (RHDV2/GI.2) in wild lagomorphs from northeastern Spain","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-12-15 22:54:25","doi":"10.21203/rs.3.rs-8310298/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2026-01-27T14:10:16+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-01-27T11:59:31+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"59261314606760543933306162947137859974","date":"2026-01-20T14:47:03+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"334601592334054144051731600636389355196","date":"2026-01-15T15:28:18+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2026-01-06T18:19:27+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"11927957707264726590920277296098435508","date":"2025-12-16T16:05:18+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"49975365104200291994312462014415797735","date":"2025-12-16T16:04:34+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-12-10T15:24:33+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-12-10T06:08:23+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-12-10T06:08:06+00:00","index":"","fulltext":""},{"type":"submitted","content":"Microbial Ecology","date":"2025-12-08T17:59:31+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"microbial-ecology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"meco","sideBox":"Learn more about [Microbial Ecology](https://www.springer.com/journal/248)","snPcode":"248","submissionUrl":"https://submission.nature.com/new-submission/248/3","title":"Microbial Ecology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"em","reportingPortfolio":"Springer Hybrid","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"2ac1d642-05a2-472f-b178-1e28a92627f3","owner":[],"postedDate":"December 15th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[],"tags":[],"updatedAt":"2026-03-23T16:02:53+00:00","versionOfRecord":{"articleIdentity":"rs-8310298","link":"https://doi.org/10.1007/s00248-026-02746-x","journal":{"identity":"microbial-ecology","isVorOnly":false,"title":"Microbial Ecology"},"publishedOn":"2026-03-21 15:57:33","publishedOnDateReadable":"March 21st, 2026"},"versionCreatedAt":"2025-12-15 22:54:25","video":"","vorDoi":"10.1007/s00248-026-02746-x","vorDoiUrl":"https://doi.org/10.1007/s00248-026-02746-x","workflowStages":[]},"version":"v1","identity":"rs-8310298","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8310298","identity":"rs-8310298","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}