title: Full genomic analysis of new variant rabbit hemorrhagic disease virus revealed multiple recombination events.
abstract: Rabbit hemorrhagic disease virus (RHDV), a Lagovirus of the family Caliciviridae, causes rabbit hemorrhagic disease (RHD) in the European rabbit (Oryctolagus cuniculus). The disease was first documented in 1984 in China and rapidly spread worldwide. In 2010, a new RHDV variant emerged, tentatively classified as 'RHDVb'. RHDVb is characterized by affecting vaccinated rabbits and those <2 months old, and is genetically distinct (~20 %) from older strains. To determine the evolution of RHDV, including the new variant, we generated 28 full-genome sequences from samples collected between 1994 and 2014. Phylogenetic analysis of the gene encoding the major capsid protein, VP60, indicated that all viruses sampled from 2012 to 2014 were RHDVb. Multiple recombination events were detected in the more recent RHDVb genomes, with a single major breakpoint located in the 5' region of VP60. This breakpoint divides the genome into two regions: one that encodes the non-structural proteins and another that encodes the major and minor structural proteins, VP60 and VP10, respectively. Additional phylogenetic analysis of each region revealed two types of recombinants with distinct genomic backgrounds. Recombinants always include the structural proteins of RHDVb, with non-structural proteins from non-pathogenic lagoviruses or from pathogenic genogroup 1 strains. Our results show that in contrast to the evolutionary history of older RHDV strains, recombination plays an important role in generating diversity in the newly emerged RHDVb.
authors: INSERM, UMR892, Université de Nantes, Nantes, France.|Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.|CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors: Ana M
authors: AM
authors: Lopes
authors: Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain.
authors: Kevin P
authors: KP
authors: Dalton
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors: Maria J
authors: MJ
authors: Magalhães
authors: Instituto Universitario de Biotecnología de Asturias, Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo, Oviedo, Spain.
authors: Francisco
authors: F
authors: Parra
authors: CITS, Centro de Investigação em Tecnologias da Saúde, IPSN, CESPU, Gandra, Portugal.|Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.|CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors: Pedro J
authors: PJ
authors: Esteves
authors: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.
authors: Edward C
authors: EC
authors: Holmes
authors: CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Campus de Vairão, Rua Padre Armando Quintas, 4485-661 Vairão, Portugal.
authors: Joana
authors: J
authors: Abrantes
mesh_terms: D000818:Animals; D002681:China; D016000:Cluster Analysis; D019143:Evolution, Molecular; D016679:Genome, Viral; D017929:Hemorrhagic Disease Virus, Rabbit / Q000235:genetics* / Q000302:isolation & purification; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D011817:Rabbits; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D012367:RNA, Viral