Recombination analyses.

<p>(A) Sliding window SimPlot graph generated by using NG385 sequence against all cosavirus species with complete genomes (HCoSV-A, -B, -D, -E). (B) Bootscan analysis of NG385 in comparison to other cosaviruses. Red arrow indicates the predicted recombination site in 2B of the non-structural region P2.</p

Phylogenetic anaylsis by Maximum Likelihood method.

<p>The percentage of trees in which the associated cosavirus VP1* clustered together is shown next to the branches with 50% cutoff. A discrete Gamma distribution was used to model evolutionary rate differences among sites. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Cosaviruses sequences from this study with near full genomes are indicated by black dots and new VP1* sequences are in bold italics. The health status of individuals is included in the strain name. Pre-existing cosavirus sequences from Genbank are in regular font.</p

Phylogenetic analyses of P1 and 3D amino acid sequences of cosaviruses.

<p>Phylogenetic tree was constructed by the maximum-likelihood method. Species C was not included as no P1, and complete 3D regions are yet availabe. (A) Analysis of P1 region (B) Analysis of 3D region. Sequences from NG385 are labeled as species E/D due to its recombinant nature. Complete genomes from this study are indicated in bold. Cardiovirus D-ACG1138-Germany was used as an outgroup.</p

Phylogenetic analysis of likely simian Sapelovirus.

<p>Unrooted neighbor-joining phylogenetic relationships based on alignment of VP1 amino acid sequences, including partial simian virus genomes. Bootstrap analysis with 1000 pseudo-replicates was utilized.</p

Divergent CoxA22 genotype.

<p>Percent nucleotide identity of three VRDL2 fragments (black lines) to closest Blastn enterovirus genome. VP1 amino acid (shaded box) sequence used to create neighbor-joining phlyogenetic tree of HEV-C with bootstrap values from 1000 replicates.</p

Eyach Virus.

<p>(A) Positions of VRDL4 fragments amplified relative to segmented <i>Coltivirus</i> genome. (B) Pairwise amino acid (nucleotide) percent identities between VRDL4 and CTFV and VRDL4 and EYAV for each segment.</p

Secondary structure prediction of the sequences immediately downstream of the structural gene of different HBoV species (upper-HBoV1, middle-HBoV2 and lower-HBoV3-E1).

<p>The stems and arms are numbered for comparison, and the termination codon of the VP gene is marked by a solid line. The rabbit-ear structure (structure 3 and 4) present in all 3 HBoV species is comparable to similar conserved structures of left-hand side termini reported for animal bocaviruses (MVC and BPV) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021362#pone.0021362-Sun1" target="_blank">[44]</a>.</p

Novel Orbivirus.

<p>Alignment of VRDL3 fragments identified to genomic segments of model orbivirus sequence with amino acid identity percentages (bottom). Orbivirus VP7 amino acid neighbor-joining phylogenetic tree with bootstrap values from 1000 pseudo-replicates (top).</p

Comparative phylogenetic analysis of HBoV3-E1 and HBoV2-IB1 (filled rectangles).

<p>Nucleotide alignments were generated using the complete coding sequence of the NS, NP and VP genes. Names of sequences used for analysis are shown as Genbank accession numbers followed by the names of HBoV species and strains. The tree was constructed with the maximum likelihood method using a GTR+G substitution model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0021362#pone.0021362-Tamura1" target="_blank">[38]</a>. Bootstrap replicates (>70%) are shown above the branches and distances (>0.02) are shown below the braches.</p

Schematic representation of the HBoV3 episome, results of inverse PCR and sequence alignment of HBoV genomic termini.

<p>(A) Describes the genomic organization of the HBoV3 episome and location/orientation of PCR primers used for screening samples and inverse PCR. (B) Shows results of inverse PCR assay for three samples (B-1 to B-3) that were positive for HBoV3 screening PCR with molecular weight (MW) marker and negative (Neg) reagent PCR control. (C) Shows alignment of previously known genomic termini of HBoV3 and HBoV1 linear genomes with the non-coding region of HBoV3 episome. Unique sequence identified in this study is shown as connecting the 3′ and 5′ termini (nucleotide with no background and “-” represent sequence that remained elusive in previous studies).</p