title: Genetic typing of bovine viral diarrhoea virus in cattle on Irish farms.
abstract: The aim was to carry out a phylogenetic study of bovine viral diarrhoea viruses (BVDV) circulating in Irish cattle herds from 2011 to 2014. Three hundred and twenty five viruses from 267 herds were subtyped by nucleotide sequence analysis of the 5'UTR and/or the Nproregions. All viruses investigated in this study belonged to species BVDV-1 with BVDV-1a as the prominent subtype (97%). Subtypes BVDV-1b, BVDV-1d and BVDV-1e were also identified for the first time in Ireland. Pairwise alignments of 225 viruses with complete sequences for the 5'UTR and the Nproregions were performed to determine a low conflict threshold for virus strain demarcation. One hundred and seventy seven unique virus strains were identified. The study revealed significant levels of herd specific clustering of strains but no geographical or temporal clustering. Similar virus strains were identified in different counties, provinces and years indicating the potential to investigate the epidemiology of the disease by combining sequence analysis with animal movement data.
authors.affiliation: Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare, Ireland.
authors.forename: Eoin
authors.initials: E
authors.lastname: O'Brien
authors.affiliation: Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare, Ireland.
authors.forename: Marie
authors.initials: M
authors.lastname: Garvey
authors.affiliation: Department of Mathematics & Statistics, University of Limerick, Limerick, Ireland.
authors.forename: Cathal
authors.initials: C
authors.lastname: Walsh
authors.affiliation: Department of Life Sciences, University of Limerick, Limerick, Ireland.
authors.forename: Sean
authors.initials: S
authors.lastname: Arkins
authors.affiliation: Virology Unit, The Irish Equine Centre, Johnstown, Naas, Co. Kildare, Ireland. Electronic address: acullinane@irishequinecentre.ie.
authors.forename: Ann
authors.initials: A
authors.lastname: Cullinane
mesh_terms: D000818:Animals; D001912:Bovine Virus Diarrhea-Mucosal Disease / Q000821:virology*; D002417:Cattle; D016000:Cluster Analysis; D001908:Diarrhea Viruses, Bovine Viral / Q000235:genetics*; D000072480:Farms; D014644:Genetic Variation; D005838:Genotype; D007494:Ireland / Q000453:epidemiology; D010802:Phylogeny
keywords: Bovine viral diarrhoea; Clustering; Ireland; Subtyping