Specimen isolation data.

<p>Specimen isolation data.</p

Grouping Scan analysis.

<p>Sequence fragments of 250 bases incrementing by 100 bases with 100 bootstrap replicates, were used to compare and analyse (a) <i>P.t.troglodytes/P.t.ellioti</i> recombinant FJ98098.1 (b) <i>P.t.ellioti/P.t.troglodytes</i> recombinant FJ98099.1 (c) <i>P.t.schweinfurthii</i> isolate A498266; (d) <i>P.t.troglodytes</i> AM117396 (e) <i>P.t.troglodytes</i> recombinant AB046525 (f) study recombinant <i>Gorilla gorilla</i> HBV sequence (ECO50003); to sequence groups from <i>Gorilla gorilla</i> (red), <i>Pan troglodytes ellioti</i> (blue), <i>Pan troglodytes troglodytes</i> (green), <i>Pan troglodytes verus</i> (yellow), <i>Pan troglodytes schweinfurthii</i> (purple) and human genotype HBV/C (light blue) with respect to A498266. Values >0.5 indicate clustering within the indicated group.</p

Tree Order Scan of HBV sequences.

<p><b>Figure 2(a)</b>. TreeOrder Scan of HBV sequences, indicating positions of individual sequences (y axis) in Phylogenetic trees generated from sequential 250-base sequence fragments, incrementing by 50 bases. Changes in sequence order as a result of changes in phylogeny at the 70% bootstrap level are shown. Sequences are colour coded by genotype and host species, as indicated by the labels in left and right margin: genotype A, purple; B, light blue; C, wine; D, emerald; E, royal blue; F, orange; G, pale green; H, navy; Gorilla, blue (Gor); Chimpanzee, green (Pan); and Woolly monkey (WM-out-group on line 1), red. For comparison the Tree Order Scan has been aligned with scale genome of HBV (top panel). Recombinant sequences are highlighted as by dashed lines; black gorilla/<i>P.t.e</i> ECO50003LIP3, green FJ798099 <i>P.t.e/P.t.t</i>, pink FJ798098 <i>P.t.e/P.t.t</i>, orange AB046525 <i>P.t.t</i> and purple AF498266 <i>P.t.s </i><b>2(b).</b> Tree Order Scan of HBV sequences, indicating positions of individual sequences (y axis) in phylogenetic trees generated from sequential 250-base sequence fragments, incrementing by 50 bases. Changes in sequence order as a result of changes in phylogeny at the 70% bootstrap level are shown. Sequences are colour coded by host species and sub-species of chimpanzee, as indicated by the labels in left and right margin: <i>Gorilla gorilla</i>, blue (Gor); <i>Pan troglodytes troglodytes</i>, yellow (<i>Ptt</i>); <i>Pan troglodytes ellioti</i>, green (<i>Pte</i>); <i>Pan troglodytes verus</i>, purple (<i>Ptv</i>); <i>Pan troglodytes schweinfurthii</i>, violet (<i>Pts</i>); and <i>Hylobates pileatus</i> (<i>Hyl</i>) (out-group-line 1-GII), red. For comparison the Tree Order Scan has been aligned with scale genome of HBV (top panel). Recombinant sequences are highlighted as by dashed lines; black gorilla/<i>P.t.e</i> ECO50003LIP3, green FJ798099 <i>P.t.e/P.t.t</i>, brown FJ798098 <i>P.t.e/P.t.t</i>, orange AB046525 <i>P.t.t</i> and blue AF498266 <i>P.t.s.</i></p

Maximum likelihood tree showing the clustering of HPV_SD2 with previously documented full-length genomes of human papillomaviruses.

<p>The tree was visualized with the Interactive Tree of Life (iTOL) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone.0058404-Letunic1" target="_blank">[32]</a>. Bootstrap values with at least 50%, 75% or 100% (100 re-samplings) are indicated. Note, another HPV_SD1 from this study was added in this analysis clustered with reference HPV_49.</p

Genomic organization of the HPV_SD2 virus.

<p>Open reading frames (L2, L1, E6, E7, E1, E2, E4) and a 530 bp non-coding long control region (LCR) are shown. B. Details of the LCR region showing the TATA box (TATAAA, positions 3735–3740), a polyadenylated site (AATAAA, positions 3336–3341), 3 palindrome sites (ACCG-N₄-CGGT; positions 3483–3494, 3650–3661, 3720–3731) and 1 degenerate palindrome (ACC-N₆-GGT, positions 3524–3535). C. Metal-binding domains in deduced E6 and E7 proteins.</p

Taxonomical assignment of sequence reads convenient respiratory waste samples.

<p>A. Overall proportions of sequences with homolog in Genbank (the known, 7.8%) compared to sequences with no homolog in Genbank (Unknown, 92.2%). Unknown/Divergent indicates the proportion of highly divergent and/or novel sequences with no homology to NCBI. B. Proportion of sequences classified as eukaryotes, bacteria and viruses. Sequences were classified using BLASTn search against all non-redundant nucleotide sequences in the NCBI nt database with an E-value cutoff of 10⁻⁵.</p

Summary of known viruses detected in nasopharyngeal samples.

<p>Summary of known viruses detected in nasopharyngeal samples.</p

Composition of sample pools and methods for DNA and RNA extraction.

<p>Composition of sample pools and methods for DNA and RNA extraction.</p

Coverage plot of the circular structure of HPV-SD2.

<p>A. Screenshot of the assembly of sequences using the <i>De Novo Assembler</i> set for 98% similarity and 45 bp overlap. The coverage plot is shown in green. Overhanging sequences at the 5′ and 3′ ends are partially assembled. B. Box at 5′ end and box at 3′ end are highlighted to show the similarity between unassembled overhang reads at 5′ and 3′ ends and corresponding ends of the consensus sequence.</p

Confirmatory sequencing of full-genome amplicons generated by PCR.

<p>A. For each amplicons, the sequencing was carried out with primers other than those used for full-genome amplification. The linear sequencing template (black line), the PCR primers are shown at both ends of the amplicons. Bleu lines (amplicons 671F-892R), green lines (amplicons 6838F-6972R), red lines (amplicons 6838F-7076R) represent the sequenced regions attached to the corresponding sequencing primers. Numbers included in primer IDs represent the position relative to HPV_SD2 genome. B. Alignment of sequences generated by Sanger method along the HPV_SD2 generated by 454 sequencing. Bars in blue, green and red correspond to sequences shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058404#pone-0058404-g006" target="_blank">Figure 6A</a>. The newly generated sequences covered 4,622 nucleotides representing 63.3% of the total HPV_SD2 genome. C. Comparison of the sequences generated by Sanger method and HPV_SD2 contig generated by 454 sequencing. Size of each Sanger sequence and percentage identity are shown.</p