Full-genome sequence analysis of a multirecombinant echovirus 3 strain isolated from sewage in Greece

Abstract

An echovirus 3 (Echo3) strain (strain LR31G7) was isolated from a sewage treatment plant in Greece in 2005. Full-genome molecular, phylogenetic, and SimPlot analyses were conducted in order to reveal the evolutionary pathways of the isolate. Nucleotide and phylogenetic analyses of part of the VP1 genomic region revealed that the isolated strain correlates with Echo3 strains isolated during the same year in France and Japan, implying that the same virus circulated in Europe and Asia. LR31G7 was found to be a recombinant that shares the 3' part of its genome with an Echo25 strain isolated from asymptomatic infants in Norway in 2003. Nucleotide and SimPlot analyses of the VP1-2A junction, where the recombination was located, revealed the exact recombination breakpoint (nucleotides 3357 to 3364). Moreover, there is evidence that recombination events had occurred in 3B-3D region in the evolutionary history of the isolate. Our study indicates that recombination events play major roles in enterovirus evolution and that the circulation of multirecombinant strains with unknown properties could be potentially dangerous for public health.

FIG. 1.

Phylogenetic tree of 269 nt (from nt 2692 to nt 2960) of a region of VP1 of strain LR31G7 and other Echo3 strains.

FIG. 2.

(a) SimPlot analysis of full genome of LR31G7. E, echovirus; EV, enterovirus; SVDV, swine vesicular disease virus; CBV5, serotype 5 coxsackievirus group B. (b) SimPlot analysis of recombination junction sequences between strain PicoBankDM1E3 and strain NO-519. (c) Sequence of recombination junction of LR31G7. Identities between LR31G7 and PicoBankDM1E3 are highlighted in yellow, while identities between LR31G7 and NO-519 are highlighted in green.