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

Abstract

Ljungan virus (LV) was discovered 20 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, indicates that this strain represents a genotype that is 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 north-eastern 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 the evolutionary relationship between the 64-7855 strain and other viruses within the family 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 with other LV strains, indicating that previous recombination events have been involved in the evolution of this virus. INTRODUCTIONLjungan virus (LV) is one of two species within the genus Parechovirus, family Picornaviridae, a large family consisting of more than 300 virus serotypes divided into nine different genera (Stanway et al., 2005). Human parechovirus (HPeV), the other species in the genus Parechovirus, is a human pathogen often isolated from children with diarrhoea and gastroenteritis (Stanway & Hyypiä, 1999). Recently, several new HPeV genotypes have been characterized (Al-Sunaidi et al., 2007;Watanabe et al., 2007) and one of these genotypes, HPeV3, seems to be widely distributed Benschop et al., 2006;Boivin et al., 2005;Ito et al., 2004). LV was first isolated from bank voles (Myodes glareolus) trapped in Medelpad and Västerbotten counties in Sweden during the search for an infectious agent causing human disease (Niklasson et al., 1998(Niklasson et al., , 1999. LV has been suggested as an aetiological agent of several human diseases, based on coinciding fluctuations of vole populations in northern Sweden and increasing incidences of type I diabetes mellitus, myocarditis and Guillain-Barré syndrome (Niklasson et al., 1998). Recently, LV antigens were detected by immunohistochemistry in fetal tissue samples in cases of human intrauterine fetal death (Niklasson et al., 2007). However, more information is needed before the role of LV as a possible zoonotic agent can be evaluated.Three LV strains were initially isolated from Swedish bank voles: the prototype strain 87-012 and the strains 174F and 145SL. Genome sequence analyses showed that the 87-012 and 174F strain constitute genotype 1, since ...

Isolation of a sp. nov. Ljungan virus from wild birds in Japan

“…Genetic analyses of these strains showed that LVs can be divided into four genotypes (genotypes 1-4) (Johansson et al, 2003;Pounder et al, 2015;Tolf et al, 2009). Previous studies have also shown the geographical distribution of the four genotypes of LV strains: LVs isolated in Sweden belong to genotypes 1 and 2, while North American strains are classified as genotypes 3 and 4 (Pounder et al, 2015;Tolf et al, 2009). In this study, we isolated LV from wild bird faeces collected in Japan, where the virus had not been identified.…”

“…Only seven LV strains isolated in Sweden and the USA have been completely or nearly completely sequenced (Johansson et al, 2003(Johansson et al, , 2002Tolf et al, 2009). Genetic analyses of these strains showed that LVs can be divided into four genotypes (genotypes 1-4) (Johansson et al, 2003;Pounder et al, 2015;Tolf et al, 2009). Previous studies have also shown the geographical distribution of the four genotypes of LV strains: LVs isolated in Sweden belong to genotypes 1 and 2, while North American strains are classified as genotypes 3 and 4 (Pounder et al, 2015;Tolf et al, 2009).…”

“…LVs have so far been detected/isolated in a limited number of countries including Sweden, the UK, Denmark, Italy and the USA (Hauffe et al, 2010;Johansson et al, 2003;Niklasson et al, 1999Niklasson et al, , 2007bSalisbury et al, 2014;Tolf et al, 2009). Only seven LV strains isolated in Sweden and the USA have been completely or nearly completely sequenced (Johansson et al, 2003(Johansson et al, , 2002Tolf et al, 2009).…”

“…Only seven LV strains isolated in Sweden and the USA have been completely or nearly completely sequenced (Johansson et al, 2003(Johansson et al, , 2002Tolf et al, 2009). Genetic analyses of these strains showed that LVs can be divided into four genotypes (genotypes 1-4) (Johansson et al, 2003;Pounder et al, 2015;Tolf et al, 2009).…”

Ljungan/Sebokele-like picornavirus in birds of prey, common kestrel ( Falco tinnunculus ) and red-footed falcon ( F. vespertinus )

“…internal ribosomal entry site (IRES) (Martínez-Salas et al, 2015) and cis-acting replication element (cre) (Tolf et al, 2009). Generally, the viral polyprotein (VP) processed to form three or four capsid monomer proteins (VP0-VP3-VP1 or VP4-VP2-VP3-VP1), and at least seven non-structural proteins: 2A-2B-2C-3A-3B-3C-3D; however, differences occur in picornaviruses of different genera.…”