Clinical symptoms reported in subjects with PARV4 infection.

<p>Papers are listed in alphabetical order by first author.</p>a<p>Denominator presented is the number of individuals positive for PARV4 (extrapolated from total number of subjects studied in each paper), except for Simmons et al. <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004036#ppat.1004036-Simmons1" target="_blank">[9]</a>, where denominator is number with HIV.</p>b<p>Other infectious causes of the clinical syndrome were excluded.</p>c<p>Other pathogens were also present which may have explained the clinical syndrome.</p><p>CNS = central nervous system; CSF = cerebrospinal fluid; IDU = injecting drug user; LFTs = liver function tests.</p

Oxford Screening of CSF and Respiratory Samples ('OSCAR'): Supplementary resources for a project using Next Generation Sequencing (NGS) for identification of viruses from clinical laboratory samples

<p>This is a file set that describes the methods used in a small pilot study to investigate 'next generation sequencing' (NGS) derived from an Illumina platform, applied to clinical diagnostic samples following routine testing in a UK microbiology laboratory.</p><p>We briefly summarise the benefits and challenges of an NGS approach to diagnostics, and conclude with some potential methodological improvements.</p><p>The file set includes anonymised metadata for the samples tested (10 respiratory and 10 CSF).</p><p>Results have been made available through a separate DOI: 10.6084/m9.figshare.5712091 and the entire genomic metadata have been submitted to European Nucleotide Archive (ENA); (primary accession PRJEB22949). </p><p>This study was approved through the UK integrated research application system (REC reference 14/LO/1077).</p

Oxford Screening of CSF and Respiratory Samples ('OSCAR'): interactive data visualisation using Krona to display results from a pilot project using Next Generation Sequencing (NGS) for identification of viruses from clinical laboratory samples

This is an html file that allows visualisation of metagenomic dataset from a pilot project to screen CSF and respiratory samples using Illumina HiSeq after completion of routine diagnostic testing in a UK microbiology laboratory.<div><br></div><div>Methods and underlying metadata are available through a separate DOI (<a rel="noreferrer noopener" target="_blank">10.6084/m9.figshare.5670007). The entire metagenomic dataset has been uploaded to the European Nucleotide Archive (</a>primary accession PRJEB22949). <a rel="noreferrer noopener" target="_blank">A subset of these data have been used for a project to identify human herpesvirus 6 (HHV-6) in clinical samples; this manuscript is available on BioRxiv (</a>https://doi.org/10.1101/236083).</div><div><div><div><div><br></div></div><div>This study was approved through the UK integrated research application system (REC reference 14/LO/1077).</div></div></div

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

Specimen isolation data.

<p>Specimen isolation data.</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