Fig 1.
Reconstructed maximum likelihood whole-genome phylogeny for TBEV variants with 200 bootstrap replicates.
Blue circles indicate bootstrap support of corresponding branches. Leaves are colored by group: red, Siberian subtype of TBEV (Sib); blue, Far-Eastern subtype of TBEV (FE); green, European subtype of TBEV (EU); black, Omsk hemorrhagic fever virus (OHFV) used as the outgroup species; orange, Baikal subtype of TBEV; gray, TBEV variants 2871 and 178–79 excluded from the GS analysis. Newly sequenced Baikal TBEV variants are marked with purple dots.
Fig 2.
Evidence for recombination at origin of the Baikal subtype.
Each analysis compared five consensus sequences: of the Baikal subtype (used as the query), and of the four other subtypes. (A) TOPAL/DSS score, reflecting the difference in shapes of the phylogenies between the adjacent alignment windows (dark gray), against the background of the same values calculated for bootstrap replicates of simulated non-recombinant sequences (light gray); the two dashed lines indicate the expected 99% and 95% confidence intervals of expected scores [36]. (B) SIMPLOT score, reflecting the nucleotide sequence distance between the query and the four consensus sequences [35]; the Far-Eastern subtype is the closest to the Baikal subtype throughout most of the alignment, but the Siberian subtype is more closely related in some of the alignment regions. (C) Bootscan plot is based on reconstructing the neighbor joining trees for each sequence window, and calculating the bootstrap support for the clade uniting the query subtype and each of the four other subtypes [34]; again, the clade uniting the Baikal subtype with the Far-Eastern subtype has the highest support for the bulk of the alignment, but the clade uniting it with the Siberian subtype has a higher support for some regions. (D) GS analysis. Joint characteristic fragments (JCFs) used for subsequent phylogenetic reconstruction are shown below the GS scores plot. The 0.5 threshold is shown as a dashed gray line. For (A)-(C), default parameters were used, namely, sliding window of length 200, step 20 (for (A), step 10 + smoothing step 10). For (D), we used the sliding window length of 250, and step size of 40.
Fig 3.
Phylogenetic evidence for recombinant origin of the Baikal subtype.
The plots show the dependence of the p-value for the GSAUC statistic on the GS score threshold (with threshold increments of 0.01), relative to each of the four TBEV subtypes. While no GS score thresholds result in p<0.05 for the European subtype and the OHFV (an outgroup species), for the Far-Eastern and Siberian subtypes, some of the GS score thresholds correspond to p<0.05, indicating that both these subtypes contributed to the Baikal subtype.
Fig 4.
Reconstructed Bayesian phylogenies of TBEV based on the characteristic fragments.
Each panel is based on the alignment segment of the corresponding JCF.