Genotyping efficiency and nucleotide sequence identities of 26 DBS specimens with a VL ≥1000 copies/mL and collected on W-903, A-226, and M-TFN filter papers.

<p>*:Fisher's exact test; ^#SD: Standard deviation.</p><p>Genotyping efficiency and nucleotide sequence identities of 26 DBS specimens with a VL ≥1000 copies/mL and collected on W-903, A-226, and M-TFN filter papers.</p

HIV drug resistance mutation Profiles of DBS specimens collected on W-903, A-226, and M-TFN filter papers.

<p>HIV-1 drug resistance genotyping analyses of the <i>pol</i> region were performed for all the DBS specimens with a viral load ≥1,000 copies/mL and with all three types of the filter papers using a broadly sensitive genotyping assay (N = 26). Drug resistance mutations against nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) were identified using the HIVdb program, and HIV-1 drug resistance profiles were determined by the HIValg program at the Stanford HIV Drug Resistance Database website. Discordant mutations that were identified in only one type of filter paper are shown in boldface type. Specimens that had a difference in drug susceptibility ratings with one of the filter paper types are indicated by asterisk (*). Eight specimens with no mutations detected in any of the filter paper types were excluded from the table.</p><p>HIV drug resistance mutation Profiles of DBS specimens collected on W-903, A-226, and M-TFN filter papers.</p

Descriptive statistics of ambiguous mutation in various sequence datasets.

<p>Plot of ambiguous mutations with descriptive statistics was performed using online statistical tool (<u><a href="http://www.physics.csbsju.edu/stats/" target="_blank">http://www.physics.csbsju.edu/stats/</a></u>). Individual country dataset was described for minimal and maximal ranges (short horizontal line at the bottom and top of the box), interquartile range (IQR, at 1^st to 3^rd quartile, box), median (line inside box), suspected outlier (open dot), and outlier (solid dot). Number in the bracket is the number of sequences from the country, Angola (AO), Botswana (BW), China (CN), Kenya (KE), Malawi (MW), Tanzania (TZ), Vietnam (VN), Nigeria (NG), and Canada (CA) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077649#B24" target="_blank">24</a>]. Numbers with asterisk were calculated without the outlier in dash square box. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077649#pone-0077649-g001" target="_blank">Figure 1</a>-insert shows the descriptive statistics of ambiguous mutation index in the dataset based on subtype (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077649#pone-0077649-t003" target="_blank">Table 3</a>).</p

Proportional distribution of mutated and ambiguous mutated amino acids at HIVDR sites.

<p>The mutation score at each of the drug resistance sites [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077649#B9" target="_blank">9</a>] was proportionally calculated with the mutated and ambiguous mutated amino acids for all the sequences in the datasets. A mutated or ambiguous mutated amino acid was defined as an amino acid had mutated from a wild type to a pure non-synonymous mutation or an ambiguous mutation in the mixture allele. The scores were summed by 1 for a pure amino acid mutation and 0.5 for an ambiguous amino acid mutation, and then converted to percentages against the total number of wild-type amino acids at the site. The distribution of drug resistance mutation scores was plot by the dataset of Threshold (bottom panel), Vietnam (VN, central panel) and Baseline (top panel). The <i>x</i>-axis is the wild-type amino acids at drug resistance sites; the <i>y</i>-axis is the drug resistance mutation score (%). The sites with obvious score changes across the 3 datasets from bottom to top panel were labeled by up-triangle (increased), rhombus (remained), and down- triangle (decreased). Amino acids of protease gene (Prt) were top-dash lined, and of reverse transcriptase gene (RT) were top-solid lined.</p