{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"Research Square"}],"indexed":{"date-parts":[[2025,4,5]],"date-time":"2025-04-05T04:06:27Z","timestamp":1743825987840,"version":"3.40.3"},"posted":{"date-parts":[[2025,4,4]]},"group-title":"In Review","reference-count":39,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T00:00:00Z","timestamp":1743724800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04423\/2020 (CIIMAR)"],"award-info":[{"award-number":["UIDB\/04423\/2020 (CIIMAR)"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDP\/04423\/2020 (CIIMAR)"],"award-info":[{"award-number":["UIDP\/04423\/2020 (CIIMAR)"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["UIDB\/04050\/2020 (UMinho CBMA-https:\/\/doi.org\/10.54499\/UIDB\/04050\/2020)"],"award-info":[{"award-number":["UIDB\/04050\/2020 (UMinho CBMA-https:\/\/doi.org\/10.54499\/UIDB\/04050\/2020)"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["LAGMED (https:\/\/www.lagmed.eu) through FCT (PRIMA\/0003\/2018) and PRIMA programme"],"award-info":[{"award-number":["LAGMED (https:\/\/www.lagmed.eu) through FCT (PRIMA\/0003\/2018) and PRIMA programme"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["2021.09782.CPCA"],"award-info":[{"award-number":["2021.09782.CPCA"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["CEECIND\/01388\/2017"],"award-info":[{"award-number":["CEECIND\/01388\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["CEECIND\/00078\/2017"],"award-info":[{"award-number":["CEECIND\/00078\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","doi-asserted-by":"publisher","award":["Jo\u00e3o Carneiro research contract at CIIMAR, established under the transitional rule of Decree Law 57\/2016, amended by Law 57\/2017"],"award-info":[{"award-number":["Jo\u00e3o Carneiro research contract at CIIMAR, established under the transitional rule of Decree Law 57\/2016, amended by Law 57\/2017"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,4,2]]},"abstract":"<title>Abstract<\/title>\n        <p>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.<\/p>","DOI":"10.21203\/rs.3.rs-6364213\/v1","type":"posted-content","created":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T09:25:21Z","timestamp":1743758721000},"source":"Crossref","is-referenced-by-count":0,"title":["Rabbit Haemorrhagic Disease Virus Database: Enhancing Environmental Surveillance with In Silico and Literature-Derived Primers for PCR Applications"],"prefix":"10.21203","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6188-8099","authenticated-orcid":false,"given":"Filipa","family":"Carneiro","sequence":"first","affiliation":[{"name":"CIIMAR \u2013 Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, University of Porto, Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5188-7874","authenticated-orcid":false,"given":"Margarida","family":"Cardeano","sequence":"additional","affiliation":[{"name":"CIIMAR \u2013 Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, University of Porto, Matosinhos, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7176-0969","authenticated-orcid":false,"given":"Ana Margarida","family":"Lopes","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8391-7134","authenticated-orcid":false,"given":"Joana","family":"Abrantes","sequence":"additional","affiliation":[{"name":"CIBIO, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Campus de Vair\u00e3o, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5153-2395","authenticated-orcid":false,"given":"Jo\u00e3o","family":"Carneiro","sequence":"additional","affiliation":[{"name":"Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057 Braga, Portugal"}]}],"member":"297","reference":[{"issue":"12","key":"ref1","doi-asserted-by":"publisher","DOI":"10.1186\/1297-9716-43-12","article-title":"Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review","volume":"43","author":"Abrantes J","year":"2012","unstructured":"Abrantes J, van der Loo W, Le Pendu J, Esteves PJ (2012) Rabbit haemorrhagic disease (RHD) and rabbit haemorrhagic disease virus (RHDV): a review. Vet Res 43(12). 10.1186\/1297-9716-43-12","journal-title":"Vet Res"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-71303-4","article-title":"Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus\/GI.2","author":"Abrantes J","year":"2020","unstructured":"Abrantes J, Droillard C, Lopes AM, Lemaitre E, Lucas P, Blanchard Y, Marchandeau S, Esteves PJ, Le Gall-Recul\u00e9 G (2020) Recombination at the emergence of the pathogenic rabbit haemorrhagic disease virus\/GI.2. https:\/\/doi.org\/10.1038\/s41598-020-71303-4. Sci Rep-Uk 10 Doi:"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9050972","article-title":"A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV)","author":"Abrantes J","year":"2021","unstructured":"Abrantes J, Lopes AM (2021) A Review on the Methods Used for the Detection and Diagnosis of Rabbit Hemorrhagic Disease Virus (RHDV). Microorganisms 9 Doi https:\/\/doi.org\/10.3390\/microorganisms9050972"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1016\/j.meegid.2015.07.010","article-title":"Tracking the evolution of the G1\/RHDVb recombinant strains introduced from the Iberian Peninsula to the Azores islands, Portugal","volume":"34","author":"Almeida T","year":"2015","unstructured":"Almeida T, Lopes AM, Magalh\u00e3es MJ, Neves F, Pinheiro A, Gon\u00e7alves D, Leit\u00e3o M, Esteves PJ, Abrantes J (2015) Tracking the evolution of the G1\/RHDVb recombinant strains introduced from the Iberian Peninsula to the Azores islands, Portugal. Infect Genet Evol 34:307\u2013313. 10.1016\/j.meegid.2015.07.010","journal-title":"Infect Genet Evol"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul SF","year":"1997","unstructured":"Altschul SF, Madden TL, Sch\u00e4ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389\u20133402. 10.1093\/nar\/25.17.3389","journal-title":"Nucleic Acids Res"},{"issue":"447","key":"ref6","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2452-3","article-title":"PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization","volume":"19","author":"Burger F","year":"2018","unstructured":"Burger F, Angioni M, Russo G, Schad M, Kallarackal J (2018) PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization. BMC Bioinformatics 19(447). 10.1186\/s12859-018-2452-3","journal-title":"BMC Bioinformatics"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"409","DOI":"10.20506\/rst.10.2.558","article-title":"Epidemiology and current situation of viral haemorrhagic disease of rabbits and the European brown hare syndrome in Italy","volume":"10","author":"Cancellotti F","year":"1991","unstructured":"Cancellotti F, Renzi M (1991) Epidemiology and current situation of viral haemorrhagic disease of rabbits and the European brown hare syndrome in Italy. Revue Scientifique et Technique (International Office Epizootics) 10:409\u2013422. 10.20506\/rst.10.2.558","journal-title":"Revue Scientifique et Technique (International Office Epizootics)"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e0004757","DOI":"10.1371\/journal.pntd.0004757","article-title":"EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment","volume":"10","author":"Carneiro J","year":"2016","unstructured":"Carneiro J, Pereira F (2016) EbolaID: An Online Database of Informative Genomic Regions for Ebola Identification and Treatment. PLoS Negl Trop Dis 10:e0004757. 10.1371\/journal.pntd.0004757","journal-title":"PLoS Negl Trop Dis"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1093\/database\/bax005","author":"Carneiro J","year":"2017","unstructured":"Carneiro J, Resende A, Pereira F (2017) The HIV oligonucleotide database (HIVoligoDB). Database (Oxford) 2017 10.1093\/database\/bax005"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1101\/2020.04.19.048991","article-title":"CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2. bioRxiv:2020.2004.2019.048991","author":"Carneiro J","year":"2020","unstructured":"Carneiro J, Gomes C, Couto C, Pereira F (2020) CoV2ID: Detection and Therapeutics Oligo Database for SARS-CoV-2. bioRxiv:2020.2004.2019.048991. 10.1101\/2020.04.19.048991"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1111\/tbed.13706","article-title":"Widespread occurrence of the non-pathogenic hare calicivirus (HaCV Lagovirus GII.2) in captive-reared and free-living wild hares in Europe","volume":"68","author":"Cavadini P","year":"2021","unstructured":"Cavadini P, Molinari S, Merzoni F, Vismarra A, Posautz A, Alzaga Gil V, Chiari M, Giannini F, Capucci L, Lavazza A (2021) Widespread occurrence of the non-pathogenic hare calicivirus (HaCV Lagovirus GII.2) in captive-reared and free-living wild hares in Europe. Transbound Emerg Dis 68:509\u2013518. 10.1111\/tbed.13706","journal-title":"Transbound Emerg Dis"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1007\/978-1-0716-1799-1_13","article-title":"qPrimerDB: A Powerful and User-Friendly Database for qPCR Primer Design","volume":"2392","author":"Chang W","year":"2022","unstructured":"Chang W, Niu Y, Yu M, Li T, Li J, Lu K (2022) qPrimerDB: A Powerful and User-Friendly Database for qPCR Primer Design. Methods Mol Biol 2392:173\u2013182. 10.1007\/978-1-0716-1799-1_13","journal-title":"Methods Mol Biol"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e00050","DOI":"10.1128\/spectrum.00050-23","article-title":"Dynamics of Humoral Immunity to Myxoma and Rabbit Hemorrhagic Disease Viruses in Wild European Rabbits Assessed by Longitudinal Semiquantitative Serology","volume":"11","author":"Coelho J","year":"2023","unstructured":"Coelho J, Pacheco H, Rafael M, Jim\u00e9nez-Ruiz S, Alves PC, Santos N (2023) Dynamics of Humoral Immunity to Myxoma and Rabbit Hemorrhagic Disease Viruses in Wild European Rabbits Assessed by Longitudinal Semiquantitative Serology. Microbiol Spectr 11:e00050\u2013e00023. 10.1128\/spectrum.00050-23","journal-title":"Microbiol Spectr"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1111\/j.1365-2907.2009.00140.x","article-title":"European rabbit population trends and associated factors: a review of the situation in the Iberian Peninsula","volume":"39","author":"Delibes-Mateos M","year":"2009","unstructured":"Delibes-Mateos M, Ferreras P, Villafuerte R (2009) European rabbit population trends and associated factors: a review of the situation in the Iberian Peninsula. Mammal Rev 39:124\u2013140. https:\/\/doi.org\/10.1111\/j.1365-2907.2009.00140.x","journal-title":"Mammal Rev"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.14202\/vetworld.2020.1098-1107","article-title":"Genotyping of rabbit hemorrhagic disease virus detected in diseased rabbits in Egyptian Provinces by VP60 sequencing","volume":"13","author":"Erfan AM","year":"2020","unstructured":"Erfan AM, Shalaby AG (2020) Genotyping of rabbit hemorrhagic disease virus detected in diseased rabbits in Egyptian Provinces by VP60 sequencing. Vet World 13:1098\u20131107. 10.14202\/vetworld.2020.1098-1107","journal-title":"Vet World"},{"issue":"Suppl 2","key":"ref16","doi-asserted-by":"publisher","first-page":"S322","DOI":"10.1086\/315591","article-title":"Taxonomy of the caliciviruses","volume":"181","author":"Green KY","year":"2000","unstructured":"Green KY, Ando T, Balayan MS, Berke T, Clarke IN, Estes MK, Matson DO, Nakata S, Neill JD, Studdert MJ, Thiel HJ (2000) Taxonomy of the caliciviruses. J Infect Dis 181(Suppl 2):S322\u2013330. 10.1086\/315591","journal-title":"J Infect Dis"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"5951","DOI":"10.1007\/s00253-015-6571-8","article-title":"Identification of two novel rabbit hemorrhagic disease virus (RHDV) B cell epitopes and evaluation of its immunoprotection against RHDV","volume":"99","author":"Kong DS","year":"2015","unstructured":"Kong DS, Liu HR, Liu JS, Yu Z, Jiang Q, Guo DC, Hu XL, Wang FJ, Huang QQ, Qu LD (2015) Identification of two novel rabbit hemorrhagic disease virus (RHDV) B cell epitopes and evaluation of its immunoprotection against RHDV. Appl Microbiol Biot 99:5951\u20135966. 10.1007\/s00253-015-6571-8","journal-title":"Appl Microbiol Biot"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1136\/vr.d697","article-title":"Detection of a new variant of rabbit haemorrhagic disease virus in France","volume":"168","author":"Gall-Recul\u00e9 G","year":"2011","unstructured":"Le Gall-Recul\u00e9 G, Zwingelstein F, Boucher S, Le Normand B, Plassiart G, Portejoie Y, Decors A, Bertagnoli S, Gu\u00e9rin JL, Marchandeau S (2011) Detection of a new variant of rabbit haemorrhagic disease virus in France. Vet Rec 168:137\u2013138. 10.1136\/vr.d697","journal-title":"Vet Rec"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1016\/j.virol.2010.12.001","article-title":"Characterisation of a non-pathogenic and non-protective infectious rabbit lagovirus related to RHDV","volume":"410","author":"Gall-Recul\u00e9 G","year":"2011","unstructured":"Le Gall-Recul\u00e9 G, Zwingelstein F, Fages MP, Bertagnoli S, Gelfi J, Aubineau J, Roobrouck A, Botti G, Lavazza A, Marchandeau S (2011) Characterisation of a non-pathogenic and non-protective infectious rabbit lagovirus related to RHDV. Virology 410:395\u2013402. 10.1016\/j.virol.2010.12.001","journal-title":"Virology"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"1658","DOI":"10.1099\/jgv.0.000840","article-title":"Proposal for a unified classification system and nomenclature of lagoviruses","volume":"98","author":"Pendu J","year":"2017","unstructured":"Le Pendu J, Abrantes J, Bertagnoli S, Guitton JS, Le Gall-Recul\u00e9 G, Lopes AM, Marchandeau S, Alda F, Almeida T, C\u00e9lio AP, B\u00e1rcena J, Burmakina G, Blanco E, Calvete C, Cavadini P, Cooke B, Dalton K, Delibes Mateos M, Deptula W, Eden JS, Wang F, Ferreira CC, Ferreira P, Foronda P, Gon\u00e7alves D, Gavier-Wid\u00e9n D, Hall R, Hukowska-Szematowicz B, Kerr P, Kovaliski J, Lavazza A, Mahar J, Malogolovkin A, Marques RM, Marques S, Martin-Alonso A, Monterroso P, Moreno S, Mutze G, Neimanis A, Niedzwiedzka-Rystwej P, Peacock D, Parra F, Rocchi M, Rouco C, Ruvo\u00ebn-Clouet N, Silva E, Silv\u00e9rio D, Strive T, Thompson G, Tokarz-Deptula B, Esteves P (2017) Proposal for a unified classification system and nomenclature of lagoviruses. J Gen Virol 98:1658\u20131666. 10.1099\/jgv.0.000840","journal-title":"J Gen Virol"},{"key":"ref21","first-page":"253","article-title":"A new viral disease in rabbits","volume":"16","author":"Liu S","year":"1984","unstructured":"Liu S, Xue H, Pu B, Qian NH (1984) A new viral disease in rabbits. Anim Husb Veterinary Med (Xumu yu Shouyi) 16:253\u2013255","journal-title":"Anim Husb Veterinary Med (Xumu yu Shouyi)"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1099\/vir.0.000070","article-title":"Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events","volume":"96","author":"Lopes AM","year":"2015","unstructured":"Lopes AM, Dalton KP, Magalhaes MJ, Parra F, Esteves PJ, Holmes EC, Abrantes J (2015) Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events. J Gen Virol 96:1309\u20131319. 10.1099\/vir.0.000070","journal-title":"J Gen Virol"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1007\/s00705-018-4052-y","article-title":"GI.1b\/GI.1b\/GI.2 recombinant rabbit hemorrhagic disease virus 2 (Lagovirus europaeus\/GI.2) in Morocco, Africa","volume":"164","author":"Lopes AM","year":"2019","unstructured":"Lopes AM, Rouco C, Esteves PJ, Abrantes J (2019) GI.1b\/GI.1b\/GI.2 recombinant rabbit hemorrhagic disease virus 2 (Lagovirus europaeus\/GI.2) in Morocco, Africa. Arch Virol 164:279\u2013283. 10.1007\/s00705-018-4052-y","journal-title":"Arch Virol"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"27787","DOI":"10.1074\/jbc.M100707200","article-title":"Identification of the amino acid residue involved in rabbit hemorrhagic disease virus VPg uridylylation","volume":"276","author":"Mach\u00edn A","year":"2001","unstructured":"Mach\u00edn A, Mart\u00edn Alonso JM, Parra F (2001) Identification of the amino acid residue involved in rabbit hemorrhagic disease virus VPg uridylylation. J Biol Chem 276:27787\u201327792. 10.1074\/jbc.M100707200","journal-title":"J Biol Chem"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.01374\u2009\u2013\u200901317","article-title":"Rabbit Hemorrhagic Disease Virus 2 (RHDV2; GI.2) Is Replacing Endemic Strains of RHDV in the Australian Landscape within 18 Months of Its Arrival","volume":"92","author":"Mahar JE","year":"2018","unstructured":"Mahar JE, Hall RN, Peacock D, Kovaliski J, Piper M, Mourant R, Huang N, Campbell S, Gu X, Read A, Urakova N, Cox T, Holmes EC, Strive T (2018) Rabbit Hemorrhagic Disease Virus 2 (RHDV2; GI.2) Is Replacing Endemic Strains of RHDV in the Australian Landscape within 18 Months of Its Arrival. J Virol 92. 10.1128\/jvi.01374\u2009\u2013\u200901317","journal-title":"J Virol"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veab080","article-title":"Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses","author":"Mahar JE","year":"2021","unstructured":"Mahar JE, Jenckel M, Huang NN, Smertina E, Holmes EC, Strive T, Hall RN (2021) Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses. Virus Evol 7. https:\/\/doi.org\/10.1093\/ve\/veab080","journal-title":"Virus Evol 7"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1016\/0042-6822(91)90437-g","article-title":"Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles","volume":"184","author":"Meyers G","year":"1991","unstructured":"Meyers G, Wirblich C, Thiel HJ (1991) Genomic and subgenomic RNAs of rabbit hemorrhagic disease virus are both protein-linked and packaged into particles. Virology 184:677\u2013686. 10.1016\/0042-6822(91)90437-g","journal-title":"Virology"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1016\/0042-6822(91)90436-f","article-title":"Rabbit hemorrhagic disease virus\u2013molecular cloning and nucleotide sequencing of a calicivirus genome","volume":"184","author":"Meyers G","year":"1991","unstructured":"Meyers G, Wirblich C, Thiel HJ (1991) Rabbit hemorrhagic disease virus\u2013molecular cloning and nucleotide sequencing of a calicivirus genome. Virology 184:664\u2013676. 10.1016\/0042-6822(91)90436-f","journal-title":"Virology"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1006\/viro.2000.0545","article-title":"Rabbit hemorrhagic disease virus: genome organization and polyprotein processing of a calicivirus studied after transient expression of cDNA constructs","volume":"276","author":"Meyers G","year":"2000","unstructured":"Meyers G, Wirblich C, Thiel HJ, Thumfart JO (2000) Rabbit hemorrhagic disease virus: genome organization and polyprotein processing of a calicivirus studied after transient expression of cDNA constructs. Virology 276:349\u2013363. 10.1006\/viro.2000.0545","journal-title":"Virology"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"221","DOI":"10.7589\/0090-3558-34.2.221","article-title":"The initial impact of rabbit hemorrhagic disease on European rabbit populations in South Australia","volume":"34","author":"Mutze G","year":"1998","unstructured":"Mutze G, Cooke B, Alexander P (1998) The initial impact of rabbit hemorrhagic disease on European rabbit populations in South Australia. J Wildl Dis 34:221\u2013227. 10.7589\/0090-3558-34.2.221","journal-title":"J Wildl Dis"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"5336","DOI":"10.1021\/bi702363u","article-title":"Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations","volume":"47","author":"Owczarzy R","year":"2008","unstructured":"Owczarzy R, Moreira BG, You Y, Behlke MA, Walder JA (2008) Predicting Stability of DNA Duplexes in Solutions Containing Magnesium and Monovalent Cations. Biochemistry 47:5336\u20135353. 10.1021\/bi702363u","journal-title":"Biochemistry"},{"key":"ref32","author":"Scientific TF","year":"2019","unstructured":"Scientific TF (2019) PCR Primer Design Tips. https:\/\/wwwthermofishercom\/blog\/behindthebench\/pcr-primer-design-tips\/"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"5812","DOI":"10.1128\/jvi.69.9.5812-5815.1995","article-title":"Two independent pathways of expression lead to self-assembly of the rabbit hemorrhagic disease virus capsid protein","volume":"69","author":"Sibilia M","year":"1995","unstructured":"Sibilia M, Boniotti MB, Angoscini P, Capucci L, Rossi C (1995) Two independent pathways of expression lead to self-assembly of the rabbit hemorrhagic disease virus capsid protein. J Virol 69:5812\u20135815. 10.1128\/jvi.69.9.5812-5815.1995","journal-title":"J Virol"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"983","DOI":"10.1111\/tbed.12830","article-title":"Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains","volume":"65","author":"Silv\u00e9rio D","year":"2018","unstructured":"Silv\u00e9rio D, Lopes AM, Melo-Ferreira J, Magalh\u00e3es MJ, Monterroso P, Serronha A, Maio E, Alves PC, Esteves PJ, Abrantes J (2018) Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains. Transbound Emerg Dis 65:983\u2013992. 10.1111\/tbed.12830","journal-title":"Transbound Emerg Dis"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.virol.2008.11.004","article-title":"Identification and partial characterisation of a new Lagovirus in Australian wild rabbits","volume":"384","author":"Strive T","year":"2009","unstructured":"Strive T, Wright JD, Robinson AJ (2009) Identification and partial characterisation of a new Lagovirus in Australian wild rabbits. Virology 384:97\u2013105. 10.1016\/j.virol.2008.11.004","journal-title":"Virology"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1093\/ve\/veaa080","article-title":"Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1)","author":"Szillat KP","year":"2020","unstructured":"Szillat KP, H\u00f6per D, Beer M, K\u00f6nig P (2020) Full-genome sequencing of German rabbit haemorrhagic disease virus uncovers recombination between RHDV (GI.2) and EBHSV (GII.1). https:\/\/doi.org\/10.1093\/ve\/veaa080. Virus Evol 6 Doi"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.1099\/jgv.0.001332","article-title":"ICTV Virus Taxonomy Profile: Caliciviridae","volume":"100","author":"Vinje J","year":"2019","unstructured":"Vinje J, Estes MK, Esteves P, Green KY, Katayama K, Knowles NJ, L'Homme Y, Martella V, Vennema H, White PA, Ictv Report C (2019) ICTV Virus Taxonomy Profile: Caliciviridae. J Gen Virol 100:1469\u20131470. 10.1099\/jgv.0.001332","journal-title":"J Gen Virol"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR Guiding Principles for scientific data management and stewardship","volume":"3","author":"Wilkinson MD","year":"2016","unstructured":"Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten J-W, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJG, Groth P, Goble C, Grethe JS, Heringa J, \u2019t Hoen PAC, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone S-A, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3:160018. 10.1038\/sdata.2016.18","journal-title":"Sci Data"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"2458","DOI":"10.1128\/jb.00330-15","article-title":"Databases for Microbiologists","volume":"197","author":"Zhulin IB","year":"2015","unstructured":"Zhulin IB (2015) Databases for Microbiologists. J Bacteriol 197:2458\u20132467. 10.1128\/jb.00330-15","journal-title":"J Bacteriol"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/www.researchsquare.com\/article\/rs-6364213\/v1","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.researchsquare.com\/article\/rs-6364213\/v1.html","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,4,4]],"date-time":"2025-04-04T09:25:37Z","timestamp":1743758737000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.researchsquare.com\/article\/rs-6364213\/v1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,4,4]]},"references-count":39,"URL":"https:\/\/doi.org\/10.21203\/rs.3.rs-6364213\/v1","relation":{},"subject":[],"published":{"date-parts":[[2025,4,4]]},"subtype":"preprint"}}