Analysis of the genomic homologous recombination in Theilovirus based on complete genomes

Abstract

At present, Theilovirus is considered to comprise four distinct serotypes, including Theiler's murine encephalomyelitis virus, Vilyuisk human encephalomyelitis virus, Thera virus, and Saffold virus. So far, there is no systematical study that investigated the genomic recombination of Theilovirus. The present study performed the phylogenetic and recombination analysis of Theilovirus over the complete genomes. Seven potentially significant recombination events were identified. However, according to the strains information and references related to the recombinants and their parental strains, four of the recombination events might happen non-naturally. These results will provide valuable hints for future research on evolution and antigenic variability of Theilovirus.

Figure 1

Phylogenetic tree for the 21 complete Theilovirus genomes. Phylogenetic analysis were performed using the neighbor-joining method and evaluated using the interior branch test method with Mega 4 software. Values for various branches are percentages of the tree obtained from 1000 resamplings of the data. Percent bootstrap supports are indicated at nodes.

Figure 2

Identification of the 7 recombination events. The recombination events were indicated in red word "event"; GenBank No. of each strain was indicated at the left end; the minor parental strain of each recombinant was shown at the recombination region. The solid triangles indicated the naturally occurred recombination events.

Figure 3

Identification of recombination between EU681177 and EF165067. (A) BOOTSCAN evidence for the recombination origin on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates; (B) Neighbor joining tree (2,000 replicates, Kimura 2-parameter distance) constructed using the non-recombinant region (Position 1-575 + 3945-end); (C) Neighbor joining tree (2,000 replicates, Kimura 2-parameter distance) constructed using the recombinant region (Position 576-3944).

Figure 4

BOOTSCAN evidence for recombination between two TMEV strains, which led to a recombinant TMEV strain. Analysis were based on the basis of pairwise distance, modeled with a window size 200, step size 20, and 100 Bootstrap replicates.

Figure 5

RDP screenshots displaying the possible recombinant (GenBank:M20301). The y-axis indicates the pairwise identity that refers to the average pairwise sequence identity within a 30nt sliding window moved one nucleotide at a time. The area outlined in gray demarcates the potential recombinant regions.