Dinucleotide analysis of C∶T and A∶G Transition mutations.

<p>The percent either of R (A or G) or Y (C or T) nucleotides occurring in either the −1 (5′) position or the +1 (3′) position to a mutation were calculated. Medians are represented for the control (n = 10; black bars), aviremic (n = 6; gray bars), and viremic HIV-1-infected groups (n = 15; white bars).</p

RGYW/WRCY motifs and targeted mutation frequencies in CDR and FR regions.

<p>Group medians are listed with the range of individual means in each group in parentheses. Overall p values are listed on the table.</p><p>^a Secondary analyses: control vs. viremic p<0.05; all other comparisons p>0.05.</p

Nucleotide mutation patterns and proportions in IgG V_H3 mRNA sequences.

<p>“% C nucleotides mutated” indicates the proportion of nucleotides in either the CDR1/2 or FR1/2/3 regions that were mutated relative to the total number of C nucleotides present in the unmutated reference sequence, expressed as a percent. “% of mutations that were C nts” indicates the proportion of mutations in either the CDR1/2 or FR1/2/3 regions that were C nucleotides in the unmutated reference sequence relative to the total number of mutations in the region expressed as a percent. The group medians are listed (individual patient mean ranges in parentheses). Overall p values are listed on the table.</p><p>^a Secondary analyses: all comparisons p>0.05.</p><p>^b Secondary analyses: control vs. viremic p<0.05; all other comparisons p>0.05.</p

Expression of V_H3, D, and J family genes.

<p>Data are shown as group medians among HIV-1-seronegative control subjects (n = 10; black bars or circles), aviremic patients (n = 6; gray bars or squares), and viremic HIV-1-infected patients with detectable plasma HIV-1 RNA (n = 15; white bars or triangles). Values were calculated from individual mean percent expression for each gene. A) V_H3 family gene expression. “Other” includes V_H3-13, -20, -43, -49, -64, -65, -66, -72, and unidentified genes which ranged from 0.4% to 12.6% expression. P values were calculated by Mann-Whitney test. Significant p values were found for V_H3-7 (p = 0.05), V_H3-9 (p = 0.05), V_H3-23 (p = 0.03), and V_H3-53 (p = 0.007). B) V_H3-23 expression. Each point represents the mean percentage of V_H3-23/total V_H3 genes for each patient. The solid bar indicates the group median. C) D gene expression was calculated as with V_H3 gene expression. “Other” includes D1-1, D1-7, D1-14, D1-20, D2-2, D2-8, D2-21, D3, D3-9, D3-16, D4, D4-b, D4-11, D4-23, D5-12, D6-6, and D6-25 which ranged from 0.4% to 4.3% expression. “No ID” (12.5–18.0% of sequences) indicates that gene identification could not be assigned. P values were calculated by Mann-Whitney test. Significant overall p values were found for D3-22 (p = 0.04), D5-24 (p = 0.05), and D6-19 (p = 0.04). D) J gene percent expression was calculated as described above. “Other” includes JH1, JH4a, JH4d, JH6a, and JH6c which ranged from 0.2% to 6.7% expression. Statistics were also calculated as above. A significant overall p value was found for JH6b (p = 0.01).</p

Amino acid mutation frequencies at each position do not differ significantly among groups.

<p>The percent of non-conservative (N; black bars) or conservative (C; gray bars) mutations relative to the total number of amino acids sampled at each position (Kabat numbering) are represented, the sums of which equal the total percent replaced amino acid mutation frequency at each position. The mean percent replacement amino acid mutation frequency was calculated for each individual at each amino acid position, and the median of the group mutation frequencies at each amino acid position was calculated from the individual means. Control subjects (A; n = 10), aviremic patients (B; n = 6), and viremic HIV-1-infected patients (C; n = 15).</p

Biochemical characteristics of amino acids in the CDR3 regions in HIV-1-infected and control subjects.

<p>CDR3 length and Hydrophobicity Index were calculated as described in the <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081913#s2" target="_blank">methods</a>. Residue characteristics were calculated with the number of each type of residue divided by the total number of residues in the CDR3 region of each sequence. Values are listed as the group median with the range of individual mean percents in parentheses. Overall p values are listed on the table.</p><p>^a Secondary analyses: aviremic vs. viremic p<0.05; all other comparisons p>0.05.</p

Frequencies of amino acid replacement mutations in specific V_H3 genes.

<p>The group median for CDR1/2 in each of the 5 most frequently expressed V_H3 genes (V_H3-74, -33, -07, -30.5, and -23) and for the V_H3 genes proposed to bind to HIV-1 gp120 outside of the antigen binding region (V_H3-30.5, -23, -15, -30, and -73) are calculated from the mean mutation frequencies for each individual subject in control (n = 10; black bars), aviremic (n = 6; gray bars), and viremic groups (n = 15; white bars). The table below shows the total number of sequences cloned (N) for each gene by group. P values were calculated for each gene. Only the overall p value for V_H3-33 was significant (p = 0.02). Secondary analyses: control vs. viremic p<0.05; all other comparisons p>0.05.</p

Mutation frequency is reduced in CDR1/2 regions of V_H3 genes from viremic HIV-1-infected patients.

<p>The mean percent of mutated nucleotides or the mean percent of replaced amino acids was calculated for each control subject (n = 10; black circles), aviremic patient (n = 6; gray squares), or viremic HIV-1-infected patient (n = 15; white triangles) based on the alignment of the cloned sequences with V_H3 sequences from the Vbase immunoglobulin database. The solid bar indicates the group median. A) The mean percent of mutated nucleotides in the CDR1/2 regions. The median (and range) of replacement to silent (R/S) ratios indicates the number of amino acids replaced as a result of nucleotide mutations relative to unchanged (silent) amino acids (overall p = 0.84). B) The mean percent of replaced amino acids in the CDR1/2 regions. The median (and range) percent non-conservative mutations was calculated relative to the total number of replaced amino acid mutations (overall p = 0.02, secondary analyses: control vs. aviremic p<0.05, all other comparisons p>0.05).</p

Main characteristics of subjects with inapparent dengue infections compared to symptomatic dengue-infected subjects.

<p>*Potential confounders with a P value of less than 0.20 in univariate analysis were retained for the final multivariable analyses. In this table: weight-based Z-score, platelets, neutrophils, lymphocytes, monocytes, ASAT, ALAT and NS1 antigen.</p>a<p>ASAT: Aspartate amino transferase.</p>b<p>ALAT: Alanine amino transferase.</p><p>Univariate and multivariable logistic regression were used for analyses.</p

Characteristics of dengue index cases (DIC, n = 215).

<p>*For 3 subjects infected by DENV-2, data related to IgG status were missing: 2 dengue fever cases and 1 severe dengue case.</p><p>Distribution of DIC is provided by region in relation to the presence of WHO criteria for severe dengue and IgG status during the acute phase.</p