Summary of viruses identified in this study.

(a)<p>The NCBI TaxID and name of the virus species with the highest number of hits among those viruses with BLAST hits is given.</p>(b)<p>These two samples were prepared from aliquots of the same serum sample.</p>(c)<p>In its deep sequencing dataset, Sample 168 had 9 reads matching TTV, just below our positive identification threshold.</p

Bioinformatic filtering of deep sequencing data.

<p>Average percent remaining reads after each of the filtering steps. Low-quality and low-complexity reads are removed first, followed by iterative BLAT and BLAST comparisons to human sequence. Averages were calculated for all samples (n = 130). Inset: secondary pipeline depicting post-filtering viral searches. The dashed bubble includes future methods to improve the sensitivity of viral sequence detection.</p

HHV-6B genome coverage in positive samples.

<p>Histograms of HHV-6B genome coverage generated by aligning reads with minimum 90% identity over the total read length to the genome. The depth of sequence coverage was calculated as the total Kb of aligned sequence per 1 Kb bin over the HHV-6B reference genome. Genome track representation adapted from Dominguez <i>et al </i><a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001485#pntd.0001485-Dominguez1" target="_blank">[65]</a>. The blue box represents conserved genes across the betaherpesvirus subfamily, the orange boxes represent core genes across the herpesvirus family, the green box represents the late structural genes (gp82-105), and the asterisk denotes the origin of lytic gene replication. Inset text for each histogram is the sample code. Coverage is shown for samples with greater than 80 HHV-6 reads.</p

Sequencing results and schematic representation of the EKV-1 and -2 genome organization.

<p>(<b>A</b>) Overview of the data generated for each novel rhabdovirus. (<b>B</b>) A schematic showing the assembled genomes, consisting of the following genes: <i>nucleoprotein</i> (N), <i>phosphoprotein</i> (P), <i>matrix</i> (M), <i>U1</i>/<i>U2</i>/<i>U3</i> (uncharacterized accessory proteins), <i>glycoprotein</i> (G), and <i>polymerase</i> (L). We indicate in orange (EKV-1) and blue (EKV-2) segments of the viral genomes that could not be assembled from Illumina reads and instead Sanger sequenced. (<b>C</b>) Coverage plots of the final viral genomes.</p

Sero-positivity to EKV-1 and EKV-2.

<p>A serosurvey for EKV-1 and EKV-2 was performed on Nigerian samples (n = 320). Cut-off values were based on the mean of US normals (n = 137) plus either 3xSD or 5xSD (SD = standard deviation).</p><p>Sero-positivity to EKV-1 and EKV-2.</p

Examples of rhabdoviruses reported in Africa.

<p>A map depicting examples of rhabdoviruses isolated in sub-Saharan Africa. This map does not depict the current distribution of rhabdoviruses in Sub-Saharan Africa, nor is it meant as a comprehensive listing of all rhabdoviruses isolated in Africa; rather its purpose is to illustrate that many rhabdoviruses have been discovered throughout Africa over the past half-century. Country refers to the sample’s country of origin. Abbreviations: CAR, Central African Republic; DRC, Democratic Republic of Congo.</p