35 research outputs found

    Many patient specimens contained DNA from multiple human anellovirus species.

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    <p><b>A–B</b>. Patient plasma (<b>A</b>) and NP (<b>B</b>) specimens were assayed for TTV, TTMDV, and TTV DNA by PCR and the percentage of specimens with 3, 2, 1, or no anellovirus species were determined.</p

    Anellovirus DNA was more prevalent in specimens from febrile children by high-throughput sequencing.

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    <p><b>A–B</b>. High-throughput sequencing analysis of plasma (<b>A</b>) and NP (<b>B</b>) specimens showed that a higher percentage of specimens from febrile children contained anellovirus DNA compared to specimens from afebrile children (plasma, p = 0.034; NP, p = 0.002). <b>C</b>. The trend was the same, but not statistically significant at the patient level of analysis. <b>D–E</b>. Afebrile and febrile patients had a similar median number of anellovirus sequence reads in their plasma (10.2 vs. 15.6) (<b>D</b>) and NP (2.9 vs. 1.7) (<b>E</b>) specimens. <b>F</b>. Anellovirus sequences detected by high-throughput sequencing were more prevalent in plasma compared to NP specimens (p<0.0001; Chi-squared test).</p

    Detection of anellovirus DNA correlates with increasingly elevated temperatures in children.

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    <p><b>A–B</b>. The percent of patients infected with detectable TTV (<b>A</b>) and TTMDV (<b>B</b>) rises as patient's temperature increases. <b>C</b>. The percentage of patients with TTMV DNA detected is independent of temperature.</p

    Anellovirus association with patient age, race, and gender.

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    <p><b>A–F</b>. Children in whom anellovirus DNA was detected were older than children in whom anellovirus DNAS was not detected. Patients were broken down by age into 6 month age groups and analyzed for the presence of DNA from TTV (<b>A–B</b>), TTMDV (<b>C–D</b>), or TTMV (<b>E–F</b>) in patient plasma (<b>A, C, E</b>) or NP (<b>B, D, F</b>) specimens. <b>G</b>. Other demographic analysis showed that anellovirus species TTV and TTMDV were more prevalent in patient specimens from African-Americans than Caucasians, but using multivariate logistic models the race effect was not significant after adjusting for the febrile status. <b>H</b>. There was no correlation between anellovirus positivity and patient gender.</p

    PCR analysis showed that DNA from human anellovirus species TTV and TTMDV, but not TTMV, were more prevalent in febrile patient specimens compared to afebrile controls.

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    <p><b>A–C</b>. PCR identified TTV (<b>A</b>) and TTMDV (<b>B</b>) in a higher percentage of febrile patients compared to afebrile controls while TTMV (<b>C</b>) was present in equivalent percentages (plasma TTV, p = 0.0567; NP TTV, p = 0.0182; patient TTV, p = 0.0026). <b>D</b>. The majority of patients were either positive or negative for TTV, TTMDV, and TTMV DNA in both their plasma and NP specimens. P-values determined by chi-squared test.</p

    Analysis of stool samples for 24 subjects sequenced at variable regions V1–V3 and V3–V5, mapped to the RDP database.

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    <p>In Figure (a), a pairwise distance matrix was generated using Euclidean distance, and multidimensional scaling was used to display the distribution of these 48 trees showing V1–V3 (red) and V3–V5 (blue) samples are overlapping; In Figure (b), the MLE tree for the 48 trees is illustrated; and in Figures (c) and (d), the MLE tree for trees corresponding to V1–V3 and V3–V5 regions are shown, respectively.</p

    MDS plot showing the distribution of the taxonomic trees corresponding to stool samples sequenced at region V3–V5.

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    <p>The MLE tree of all samples is denoted by MLE (dot in black) in the MDS plot. Individual taxonomic trees are denoted by with  = {2, 3, 5, 7, 16, 18} and these are shown around the MDS plot to illustrate how the tree structure varies. The tree branches are color-coded to represent their weight values (sum of confidence) according to the reference table at the bottom left side of the plot. Blue denote the branches with the highest confidence among all while red denote the branches with lowest confidence. Note here that the tip of each branch represents a genus, and the location of each genus is the same on all trees.</p

    Illustration of the MLE tree for stool samples, region V3–V5.

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    <p>Sample individual taxonomic trees shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0048996#pone-0048996-g002" target="_blank">Figure 2</a> ( with  = {2, 3, 5, 7, 16, 18}) are displayed around the MLE tree to illustrate some of tree structures represented by the MLE tree.</p

    P-values of the two sample test comparison, using LRT statistics and 1000 bootstraps, to test for similarities across samples from variable regions V1–V3 and V3–V5 of the 16S rRNA gene, within a body site.

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    <p>P-values of the two sample test comparison, using LRT statistics and 1000 bootstraps, to test for similarities across samples from variable regions V1–V3 and V3–V5 of the 16S rRNA gene, within a body site.</p
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