Rabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications

Rabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications | 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 Rabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications Filipa Carneiro, Margarida Cardeano, Ana Margarida Lopes, Joana Abrantes, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6364213/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 The rabbit haemorrhagic disease virus (RHDV) impacts the European rabbit and was first discovered in China in 1984. Since then, it spread globally, leading to significant rabbit population declines. To manage the vast amount of genomic data available, including of RHDV, various strategies and computational tools have been developed. These tools can automatically retrieve and curate nucleotide and amino acid information from multiple sources, enabling better identification and therapeutic approaches. This study developed an automated computational method to retrieve primers from the literature (AROLit) and design in silico primers in Python (iSOP) for the detection of RHDV. The AROLit and iSOP databases were published online under the name RHDV database ( https://rhdv-primers-identification-db.jc-biotechaiteam.com/ ). The workflows, applicable to any virus or bacterial genome, support optimal primer pair selection for PCR. Five top primers from AROLit and six from iSOP were validated in the laboratory to evaluate specificity to several RHDV strains. The RHDV database offers a unique combination of in silico and literature-derived primers optimized for PCR applications. This freely accessible database adheres to the FAIR principles and includes optimal primer pair selection workflows. The best primers in the database, validated in the lab, demonstrated promising specificity to several RHDV strains. Through the development of advanced techniques for pathogen detection, this research seeks to significantly improve the accuracy and efficiency of environmental surveillance. By enabling early and precise identification of viruses, the work aims to facilitate proactive management strategies to mitigate the impacts on both wild and domestic animal populations. Bioinformatics Evolutionary Genetics Virology Computational Biology Rabbit Haemorrhagic Disease Virus (RHDV) Automated Retrieval of Primers from Literature (AROLit) In silico oligonucleotides designed in Python (iSOP) Polymerase Chain Reaction (PCR) FAIR Principles Full Text Additional Declarations The authors declare no competing interests. Supplementary Files SupplementaryMaterial1.docx Supplementary Material 1 provides detailed information on the sequences and final PCR conditions for all tested primer pairs. This includes the specific nucleotide sequences used in the assays, along with the optimized PCR parameters applied during experimental validation. 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-6364213","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":437635406,"identity":"8506b3e9-8bbf-4202-a2e2-5ba0e0be4bc6","order_by":0,"name":"Filipa Carneiro","email":"","orcid":"https://orcid.org/0000-0001-6188-8099","institution":"CIIMAR – Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, University of Porto, Matosinhos, Portugal","correspondingAuthor":false,"prefix":"","firstName":"Filipa","middleName":"","lastName":"Carneiro","suffix":""},{"id":437635500,"identity":"8f1598af-1134-41ed-8ad2-616bc93fb3d4","order_by":1,"name":"Margarida Cardeano","email":"","orcid":"https://orcid.org/0000-0002-5188-7874","institution":"CIIMAR – Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, University of Porto, Matosinhos, Portugal","correspondingAuthor":false,"prefix":"","firstName":"Margarida","middleName":"","lastName":"Cardeano","suffix":""},{"id":437636954,"identity":"7b69a515-d917-48d7-b709-c336214ad5c2","order_by":2,"name":"Ana Margarida Lopes","email":"","orcid":"https://orcid.org/0000-0002-7176-0969","institution":"CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal","correspondingAuthor":false,"prefix":"","firstName":"Ana","middleName":"Margarida","lastName":"Lopes","suffix":""},{"id":437636955,"identity":"4dc1628a-4f0f-49a0-b394-bf058927e8a9","order_by":3,"name":"Joana Abrantes","email":"","orcid":"https://orcid.org/0000-0002-8391-7134","institution":"CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal","correspondingAuthor":false,"prefix":"","firstName":"Joana","middleName":"","lastName":"Abrantes","suffix":""},{"id":437636956,"identity":"7fb69705-9892-4242-84eb-5698e6974fc9","order_by":4,"name":"João Carneiro","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA+klEQVRIiWNgGAWjYBACxgYQaQDE7CBGBRAzMzcQqYUZxDgDYjDi14IAIC2MbQhjcCtsb3746EZBbWI/M/vDx7zzaqP524FaflRsw+2wnmPGxjkGxxNnNvMYG/NuO5474zBjA2PPmdu4tcxIMJPOMTiWuOEwD5vkzG3HchuAWpgZ2/BpSf8G1rL/MPszyZlzjuXOJ6wlB2RLTeIGZgYziY8NNbkbCGrpOVMM9MsB4xmHeYwNPhw7kLsRqOUgPr8YtrdvfJzzp062v7394YOEmrrceecPH3zwowKPlgYwdRjGhzAO4FQPBPIQqg7Gr8OlcBSMglEwCkYwAAALuF0dixgrvgAAAABJRU5ErkJggg==","orcid":"https://orcid.org/0000-0002-5153-2395","institution":"Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal","correspondingAuthor":true,"prefix":"","firstName":"João","middleName":"","lastName":"Carneiro","suffix":""}],"badges":[],"createdAt":"2025-04-02 21:23:03","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-6364213/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-6364213/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":79900715,"identity":"929396f4-1fbe-475a-b48c-f484dda525f0","added_by":"auto","created_at":"2025-04-04 09:54:23","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1008251,"visible":true,"origin":"","legend":"","description":"","filename":"MANUSCRIPTRHDVDBAOV31032025FINAL.pdf","url":"https://assets-eu.researchsquare.com/files/rs-6364213/v1_covered_03dfaafd-621a-4bdd-bd8a-746ead51018f.pdf"},{"id":79897427,"identity":"1802ab61-0083-45ae-801a-a68cc724f5d2","added_by":"auto","created_at":"2025-04-04 09:22:19","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":17627,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSupplementary Material 1\u003c/strong\u003e provides detailed information on the sequences and final PCR conditions for all tested primer pairs. This includes the specific nucleotide sequences used in the assays, along with the optimized PCR parameters applied during experimental validation.\u003c/p\u003e","description":"","filename":"SupplementaryMaterial1.docx","url":"https://assets-eu.researchsquare.com/files/rs-6364213/v1/32a1ed5dfff48e58a8744c7c.docx"}],"financialInterests":"The authors declare no competing interests.","formattedTitle":"\u003cp\u003e\u003cstrong\u003eRabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications\u003c/strong\u003e\u003c/p\u003e","fulltext":[],"fulltextSource":"","fullText":"","funders":[{"identity":"a84b24e6-3ba0-4b83-b5ce-043b5e6b9c53","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"UIDB/04423/2020 (CIIMAR)","order_by":0},{"identity":"1e034f0e-e5a0-4436-8f1f-b09a20fb35d9","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"UIDP/04423/2020 (CIIMAR)","order_by":1},{"identity":"9d8a8f11-165d-4861-b27a-ec961960f675","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"UIDB/04050/2020 (UMinho CBMA-https://doi.org/10.54499/UIDB/04050/2020)","order_by":2},{"identity":"1a4fe29e-60e8-423e-a990-8f140e420eb3","identifier":"10.13039/100010661","name":"Horizon 2020 Framework Programme","awardNumber":"LAGMED (https://www.lagmed.eu) through FCT (PRIMA/0003/2018) and PRIMA programme","order_by":3},{"identity":"60bc2c70-dca5-42b1-bcc0-d485a23dfe28","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"2021.09782.CPCA","order_by":4},{"identity":"3996c3e4-4b2f-4946-8a50-fefce3fffeed","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"CEECIND/01388/2017","order_by":5},{"identity":"ea8f7727-b8e6-475f-bd49-9112a00304a7","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"CEECIND/00078/2017","order_by":6},{"identity":"efdb908e-7cd9-4899-accd-567a7663f928","identifier":"10.13039/501100001871","name":"Fundação para a Ciência e a Tecnologia","awardNumber":"João Carneiro research contract at CIIMAR, established under the transitional rule of Decree Law 57/2016, amended by Law 57/2017","order_by":7}],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"CIIMAR – Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, University of Porto, Matosinhos, Portugal","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":"Rabbit Haemorrhagic Disease Virus (RHDV), Automated Retrieval of Primers from Literature (AROLit), In silico oligonucleotides designed in Python (iSOP), Polymerase Chain Reaction (PCR), FAIR Principles","lastPublishedDoi":"10.21203/rs.3.rs-6364213/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6364213/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe rabbit haemorrhagic disease virus (RHDV) impacts the European rabbit and was first discovered in China in 1984. Since then, it spread globally, leading to significant rabbit population declines. To manage the vast amount of genomic data available, including of RHDV, various strategies and computational tools have been developed. These tools can automatically retrieve and curate nucleotide and amino acid information from multiple sources, enabling better identification and therapeutic approaches.\u003c/p\u003e \u003cp\u003eThis study developed an automated computational method to retrieve primers from the literature (AROLit) and design in silico primers in Python (iSOP) for the detection of RHDV. The AROLit and iSOP databases were published online under the name RHDV database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://rhdv-primers-identification-db.jc-biotechaiteam.com/\u003c/span\u003e\u003cspan address=\"https://rhdv-primers-identification-db.jc-biotechaiteam.com/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e). The workflows, applicable to any virus or bacterial genome, support optimal primer pair selection for PCR. Five top primers from AROLit and six from iSOP were validated in the laboratory to evaluate specificity to several RHDV strains. The RHDV database offers a unique combination of in silico and literature-derived primers optimized for PCR applications. This freely accessible database adheres to the FAIR principles and includes optimal primer pair selection workflows. The best primers in the database, validated in the lab, demonstrated promising specificity to several RHDV strains. Through the development of advanced techniques for pathogen detection, this research seeks to significantly improve the accuracy and efficiency of environmental surveillance. By enabling early and precise identification of viruses, the work aims to facilitate proactive management strategies to mitigate the impacts on both wild and domestic animal populations.\u003c/p\u003e","manuscriptTitle":"Rabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-04-04 09:22:14","doi":"10.21203/rs.3.rs-6364213/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":"2968961a-05c8-4ea2-a21d-1a2c7a43b0c3","owner":[],"postedDate":"April 4th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":46601893,"name":"Bioinformatics"},{"id":46601894,"name":"Evolutionary Genetics"},{"id":46601895,"name":"Virology"},{"id":46601896,"name":"Computational Biology"}],"tags":[],"updatedAt":"2025-04-04T09:22:15+00:00","versionOfRecord":[],"versionCreatedAt":"2025-04-04 09:22:14","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-6364213","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6364213","identity":"rs-6364213","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}