title: Genome characterisation of two Ljungan virus isolates from wild bank voles (Myodes glareolus) in Sweden.
abstract: Ljungan virus (LV) (family Picornaviridae, genus Parechovirus) is a suspected zoonotic pathogen with associations to human disease in Sweden. LV is a single-stranded RNA virus with a positive sense genome. There are five published Ljungan virus strains, three isolated from Sweden and two from America, and are classified into four genotypes. A further two strains described here were isolated from wild bank voles (Myodes glareolus) caught in Västmanlands county, Sweden in 1994. These strains were sequenced using next generation pyrosequencing technology on the GS454flx platform. Genetic and phylogenetic analysis of the obtained genomes confirms isolates LV340 and LV342 as two new putative members of genotype 2 along with LV145SL, with 92% and 99% nucleotide identities respectively. Only two codon sites throughout the entire genome were identified as undergoing positive selection, both situated within the VP3 structural region, in or near to major antigenic sites. Whilst these two strains do not constitute new genotypes they provide evidence, though weakly supported, which suggests the evolution of Ljungan viruses to be relatively slow, a characteristic unlike other picornaviruses. Additional genomic sequences are urgently required for Ljungan virus strains, particularly from different locations or hosts, to fully understand the evolutionary and epidemiological properties of this potentially zoonotic virus.
authors.affiliation: University of Liverpool, Institute of Integrative Biology, Liverpool L69 7ZB, UK.
authors.forename: Kieran C
authors.initials: KC
authors.lastname: Pounder
authors.affiliation: University of Liverpool, Institute of Integrative Biology, Liverpool L69 7ZB, UK; University of Oulu, Department of Ecology, FI-90014, Finland.
authors.forename: Phillip C
authors.initials: PC
authors.lastname: Watts
authors.affiliation: Apodemus AB, Nobels väg 3, 17165 Solna, Stockholm, Sweden.
authors.forename: Bo
authors.initials: B
authors.lastname: Niklasson
authors.affiliation: University of Liverpool, Institute of Integrative Biology, Liverpool L69 7ZB, UK; University of Jyvaskyla, Department of Biological and Environmental Science, P.O. Box 35, FI-40014, University of Jyvaskyla, Finland.
authors.forename: Eva R K
authors.initials: ERK
authors.lastname: Kallio
authors.affiliation: Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency (APHA), New Haw, Addlestone, Surrey KT15 3NB, UK.
authors.forename: Denise A
authors.initials: DA
authors.lastname: Marston
authors.affiliation: Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency (APHA), New Haw, Addlestone, Surrey KT15 3NB, UK; University of Liverpool Institute of Infection and Global Health, L69 7BE, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK.
authors.forename: Anthony R
authors.initials: AR
authors.lastname: Fooks
authors.affiliation: University of Liverpool, Institute of Integrative Biology, Liverpool L69 7ZB, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK.
authors.forename: Michael
authors.initials: M
authors.lastname: Begon
authors.affiliation: Wildlife Zoonoses and Vector-borne Diseases Research Group, Animal and Plant Health Agency (APHA), New Haw, Addlestone, Surrey KT15 3NB, UK; University of Liverpool Institute of Infection and Global Health, L69 7BE, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, L69 7BE, UK. Electronic address: lorraine.mcelhinney@apha.gsi.gov.uk.
authors.forename: Lorraine M
authors.initials: LM
authors.lastname: McElhinney
mesh_terms: D000818:Animals; D003411:Arvicolinae / Q000821:virology*; D019143:Evolution, Molecular; D005814:Genes, Viral; D016679:Genome, Viral; D005838:Genotype; D009690:Nucleic Acid Conformation; D030061:Parechovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D010850:Picornaviridae Infections / Q000662:veterinary*; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D012641:Selection, Genetic; D013548:Sweden; D020506:Untranslated Regions
chemical_list: D012367:RNA, Viral; D020506:Untranslated Regions
keywords: Evolution; GS454; Ljungan virus; Myodes glareolus; Positive selection; VP3