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RNA viruses, such as rabbit hemorrhagic disease virus (RHDV), are among the viruses with the highest recombination rates. Several recombination events have been described for RHDV, mostly as a consequence of their genomic architecture. Here, we undertook phylogenetic and recombination analyses of French and Swedish RHDV strains from 1994 to 2016 and uncovered a new intergenotypic recombination event. This event occurred in the late 1990s\/early 2000s and involved nonpathogenic GI.3 strains as donors for the nonstructural part of the genome of these recombinants, while pathogenic GI.1d strains contributed to the structural part. These GI.3P\u2013GI.1d recombinant strains did not entirely replace GI.1d (nonrecombinant) strains, but became the dominant strains in France and Sweden, likely due to a fitness advantage associated with this genomic architecture. GI.3P\u2013GI.1d (P stands for polymerase) strains persisted until 2013 and 2016 in Sweden and France, respectively, and cocirculated with the new genotype GI.2 in France. Since strains from the first GI.2 outbreaks were GI.3P\u2013GI.2, we hypothesize that GI.3P\u2013GI.1d could be the parental strain. Our results confirm the outstanding recombination ability of RHDV and its importance in the evolution of lagoviruses, which was only revealed by studying complete genomic sequences.<\/jats:p>","DOI":"10.3390\/genes11080910","type":"journal-article","created":{"date-parts":[[2020,8,10]],"date-time":"2020-08-10T07:25:03Z","timestamp":1597044303000},"page":"910","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Retrospective Analysis Shows That Most RHDV GI.1 Strains Circulating Since the Late 1990s in France and Sweden Were Recombinant GI.3P\u2013GI.1d Strains"],"prefix":"10.3390","volume":"11","author":[{"given":"Joana","family":"Abrantes","sequence":"first","affiliation":[{"name":"CIBIO\/InBio-UP, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias da Universidade do Porto, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7176-0969","authenticated-orcid":false,"given":"Ana M.","family":"Lopes","sequence":"additional","affiliation":[{"name":"CIBIO\/InBio-UP, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"},{"name":"Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar\/Unidade Multidisciplinar de Investiga\u00e7\u00e3o Biom\u00e9dica, Universidade do Porto, 4050-313 Porto, Portugal"}]},{"given":"Evelyne","family":"Lemaitre","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Agence nationale de s\u00e9curit\u00e9 sanitaire, de l\u2019alimentation, de l\u2019environnement et du travail (Anses), 22440 Ploufragan, France"}]},{"given":"Harri","family":"Ahola","sequence":"additional","affiliation":[{"name":"Department of Microbiology, National Veterinary Institute (SVA), Ulls v\u00e4g 2B, SE75189 Uppsala, Sweden"}]},{"given":"Fereshteh","family":"Banihashem","sequence":"additional","affiliation":[{"name":"Department of Microbiology, National Veterinary Institute (SVA), Ulls v\u00e4g 2B, SE75189 Uppsala, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3106-6649","authenticated-orcid":false,"given":"Cl\u00e9ment","family":"Droillard","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Agence nationale de s\u00e9curit\u00e9 sanitaire, de l\u2019alimentation, de l\u2019environnement et du travail (Anses), 22440 Ploufragan, France"}]},{"given":"St\u00e9phane","family":"Marchandeau","sequence":"additional","affiliation":[{"name":"Unit\u00e9 Petite Faune S\u00e9dentaire et Esp\u00e8ces Outre-Mer, Direction de la Recherche et de l\u2019Appui Scientifique, Office Fran\u00e7ais de la Biodiversit\u00e9 (OFB), 44300 Nantes, France"}]},{"given":"Pedro J.","family":"Esteves","sequence":"additional","affiliation":[{"name":"CIBIO\/InBio-UP, Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, Universidade do Porto, 4485-661 Vair\u00e3o, Portugal"},{"name":"Departamento de Biologia, Faculdade de Ci\u00eancias da Universidade do Porto, 4169-007 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7747-2290","authenticated-orcid":false,"given":"Aleksija","family":"Neimanis","sequence":"additional","affiliation":[{"name":"Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), Ulls v\u00e4g 2B, SE75189 Uppsala, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4557-6532","authenticated-orcid":false,"given":"Ghislaine","family":"Le Gall-Recul\u00e9","sequence":"additional","affiliation":[{"name":"Unit\u00e9 de Virologie, Immunologie, Parasitologie, Aviaires et Cunicoles, Laboratoire de Ploufragan-Plouzan\u00e9-Niort, Agence nationale de s\u00e9curit\u00e9 sanitaire, de l\u2019alimentation, de l\u2019environnement et du travail (Anses), 22440 Ploufragan, France"}]}],"member":"1968","published-online":{"date-parts":[[2020,8,9]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.meegid.2017.09.029","article-title":"Mutation and recombination in pathogen evolution: Relevance, methods and controversies","volume":"63","author":"Arenas","year":"2018","journal-title":"Infect. 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