Molecular Analysis of Three Ljungan Virus Isolates Reveals a New, Close-to-Root Lineage of the Picornaviridae with a Cluster of Two Unrelated 2A Proteins

Abstract

Ljungan virus (LV) is a suspected human pathogen recently isolated from bank voles (Clethrionomys glareolus).In the present study, it is revealed through comparative sequence analysis that three newly determined Swedish LV genomes are closely related and possess a deviant picornavirus-like organization: 5 untranslated region-VP0-VP3-VP1-2A1-2A2-2B-2C-3A-3B-3C-3D-3 untranslated region. The LV genomes and the polyproteins encoded by them exhibit several exceptional features, such as the absence of a predicted maturation cleavage of VP0, a conserved sequence determinant in VP0 that is typically found in VP1 of other picornaviruses, and a cluster of two unrelated 2A proteins. The 2A1 protein is related to the 2A protein of cardio-, erbo-, tescho-, and aphthoviruses, and the 2A2 protein is related to the 2A protein of parechoviruses, kobuviruses, and avian encephalomyelitis virus. The unprecedented association of two structurally different 2A proteins is a feature never previously observed among picornaviruses and implies that their functions are not mutually exclusive. Secondary polyprotein processing of the LV polyprotein is mediated by proteinase 3C (3C pro ) possessing canonical affinity to Glu and Gln at the P1 position and small amino acid residues at the P1 position. In addition, LV 3C pro appears to have unique substrate specificity to Asn, Gln, and Asp and to bulky hydrophobic residues at the P2 and P4 positions, respectively. Phylogenetic analysis suggests that LVs form a separate division, which, together with the Parechovirus genus, has branched off the picornavirus tree most closely to its root. The presence of two 2A proteins indicates that some contemporary picornaviruses with a single 2A may have evolved from the ancestral multi-2A picornavirus.

Ljungan Virus Detected in Bank Voles (Myodes glareolus) and Yellow-Necked Mice (Apodemus flavicollis) from Northern Italy

“…The other two sequences were identical to these except where five to eight nucleotides were missing. A nucleotide megaBLAST suggested that our one complete 147-bp sequence is most similar to LV strain 174F (accession number: AF327921; Johansson et al, 2002), and confirms that the PCR assay developed by Donoso Mantke et al (2007) This short communication significantly extends the known geographic distribution of LV to southern Europe, previously only reported from northern European countries and the United States. Our results suggest that in northern Italy, LV is present in a proportion of bank voles similar to that found in northern Sweden (Niklasson, unpubl.…”

Prenatal viral exposure followed by adult stress produces glucose intolerance in a mouse model

“…This and other findings initiated an effort to isolate novel infectious agents from small rodents in an attempt to find an aetiological agent for type 1 diabetes in humans. As a result of these efforts, we isolated a new picornavirus (Ljungan virus [LV]) from bank voles trapped in Sweden [10,11]. Moreover, it has been shown that more than one-third of wild-caught bank voles and their offspring develop diabetes when kept under laboratory conditions [12].…”

Relationship Between Ljungan Virus Antibodies, HLA-DQ8, and Insulin Autoantibodies in Newly Diagnosed Type 1 Diabetes Children

“…The Ljungan virus (LV), a parechovirus, possibly pathogenic to humans (8,23,28) has been proposed to contribute to T1D. The LV was defined (23,29) as a separate species in the family picornaviridae of the parechovirus genus, that formerly was classified as an enterovirus but later reclassified as a separate genus containing both human parechoviruses (HPeV) and the LV. Similar to LV, both HPeV, type 1 and 2, formerly named echovirus 22 and 23, respectively, have been considered for associations to T1D (10,36).…”

“…A fluctuating pattern of infectious diseases, including zoonoses (29), has been suggested to contribute to the appearance of either islet autoimmunity, T1D, or both (4,34). The Ljungan virus (LV), a parechovirus, possibly pathogenic to humans (8,23,28) has been proposed to contribute to T1D. The LV was defined (23,29) as a separate species in the family picornaviridae of the parechovirus genus, that formerly was classified as an enterovirus but later reclassified as a separate genus containing both human parechoviruses (HPeV) and the LV.…”