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Molecular characterization of a novel Ljungan virus (Parechovirus; Picornaviridae) reveals a fourth genotype and indications of ancestral recombination

¹ University of Kalmar, Sweden;
² Discipline of Immunology and Microbiology, Faculty of Health, The University of Newcastle, Australia;
³ 3Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA;
⁴ 4Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden;
⁵ University of Kalmar, Dept of Chemistry and Biomedical Sciences

⁶ E-mail: michael.lindberg{at}hik.se

Ljungan virus (LV) was discovered twenty years ago in Swedish bank voles (Myodes glareolus, previously referred to as Clethrionomys glareolus), during the search for an infectious agent causing lethal myocarditis in young athletes. To date, the genomes of four LV isolates, including the prototype 87-012 strain, have been characterized. Three of these LV strains were isolated from bank voles trapped in Sweden. Sequence analysis of an American virus (M1146), isolated from a montane vole (Microtus montanus) in western USA, represent a genotype different from the Swedish strains. Here we present genomic analyses of a fifth LV strain (64-7855) isolated from a southern red-backed vole (Myodes gapperi) trapped during arbovirus studies in New York state in the northeastern USA in the 1960s. Sequence analysis of the 64-7855 genome showed an LV-like genome organization and sequence similarity to other LV strains. Genetic and phylogenetic analyses of evolutionary relationship between the 64-7855 strain and other viruses within the Picornaviridae, including previously published LV strains, demonstrated that the 64-7855 strain constitutes a new genotype within the LV species. Analyses also showed that different regions of the 64-7855 genome have different phylogenetic relationships towards other LV strains indicating that previous recombination events have been involved in the evolution of this virus.

Received 15 October 2008; accepted 22 December 2008.