112 research outputs found
Viruses detected by sequencing that were not screened by PCR.
<p>The bars represent the number of samples in which each virus was detected by sequencing. *Indicates viruses that were not assayed by PCR in NP samples. **Indicates a virus that was not assayed by PCR but belongs to a genus with members that were.</p
Sequence analysis identifies a variety of viruses in samples from febrile and afebrile children.
<p>Analysis of 176 plasma and NP samples on the Illumina GAIIX and HiSeq 2000 platforms identified approximately 50,000 sequences with similarity to 25 known (A) DNA and (B) RNA virus genera.</p
Prevalence of viruses in samples from febrile compared with afebrile children.
<p>The total number of reads per sample was scaled to 3 million to make samples more comparable, and all counts of ≥1 virus sequence were reported. The percent virus-positive samples are graphed for plasma and NP samples, respectively (A and B). P-values were determined using Fisher’s exact test. Heatmaps representing the number of virus reads for each virus detected (x-axis) and each sample evaluated (y-axis) are presented for plasma and NP samples, respectively (C and D). The light yellow area is 0 reads, with more intense red representing larger numbers of reads.</p
Febrile children have more viral sequences from a greater range of viruses than do afebrile children.
<p>The number of sequences was scaled to 3 million per sample before comparisons were made between groups. (A) The average numbers of viral sequences found in plasma and NP samples from the subjects are represented by gray bars for samples from afebrile children and black bars for samples from febrile children. The percentage of samples in each group for which 0, 1, 2, 3, 4, or 5 viruses was detected is plotted for (B) sequencing data and (C) PCR data.</p
Detection of viruses with next generation sequencing.
<p>Detection of viruses with next generation sequencing.</p
Illumina sequences with remote homologies to astroviruses.
<p>The top alignment from tblastx, excluding MLB1 and MLB2, is reported if the alignment was to an astrovirus.</p
Comparison of sequencing results with Ct values from real-time PCR assays.
<p>The average Ct values from real-time PCR assays for (A) adenovirus and (B) bocavirus are graphed. Each PCR experiment was repeated at least twice per sample. Samples are grouped from left to right according to whether they were detected by sequencing, not detected by sequencing, or only detected when the number of sequence reads was increased to 21 or 51 million sequences for A and B, respectively.</p
Genome coverage.
*<p>Full genome sequence not available. Largest Genbank sequence used.</p
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