VESPA analysis of R5 and CXCR4-using B-HIV Envs.

<p>Amino acid positions are relative to the HXB2 Env. Values represent the percentage of all R5 or CXCR4-using Envs with the indicated amino acid. 43 CXCR4-using (23 R5X4 and 20 X4) and 223 R5 B-HIV Envs were analyzed. ns, not significant. -, deleted sequence.</p><p>VESPA analysis of R5 and CXCR4-using B-HIV Envs.</p

Performance of genotypic algorithms modified to include the “440 rule”.

<p>The “440 rule” involves rescreening sequences predicted to be R5 by the indicated genotypic algorithm for the presence of Asp or Glu at position 440, the presence of which results in a “CXCR4-using” prediction. % Sens, sensitivity was calculated by dividing the number of correctly predicted CXCR4-using sequences by the total number of phenotypically characterised CXCR4-using sequences. % Spec, specificity was calculated by dividing the number of correctly predicted R5 sequences by the number of phenotypically characterised R5 sequences. Values in parentheses represent percentage differences between modified and unmodified algorithms. Differences in area under the receiver operating characteristic curve (AUROC) considered significant (p≤0.05) are highlighted in bold and italicized. 43 CXCR4-using (23 R5X4 and 20 X4) and 223 R5 B-HIV design sequences and 32 CXCR4-using (23 R5X4 and 9 X4) and 70 R5 B-HIV test sequences were analysed. FPR, false positive rate.</p><p>Performance of genotypic algorithms modified to include the “440 rule”.</p

Three-dimensional model of the CD4-bound gp120 containing V3 and C4 docked to a CCR5 N-terminus peptide.

<p>(A) The gp120 molecule is shown in ribbon representation, the V3 is shown in grey and the C4 region is shown in blue. The CCR5 N-terminus peptide is shown in ribbon representation (red) with wire mesh van der Waals surface representation, and the amino acids are shown in stick representation. Asp11 in the CCR5 N-terminus and Glu322 and Arg440 in gp120 are shown in stick representation and colored according to charge; positively charged residues are colored blue and negatively charged residues colored red. (B, C) Close up of gp120 and the CCR5 N-terminus peptide interface is represented as described above. Notably, CCR5 N-terminus mesh surface representation and amino acid stick representation was removed, and mesh surface van der Waals surface representation was added to Asp11 in the CCR5 N-terminus, Arg440 (B) and Lys 440 (C). (D) Three-dimensional model of CD4-bound gp120 containing V3 and C4 docked to the CCR5 N-terminus (to aid visual distinction between gp120 and the CCR5 N-terminus peptide) with (E) original Glu322/Arg440 genotype or (F) mutated Arg322/Glu440 genotype, shown in surface charge representation colored according to charge. The number of hydrogen bonds (N_HB) and salt bridges (N_SB) predicted to form at the interface between gp120 and the CCR5 N-terminus was calculated using PISA software.</p

Analysis of covariance of charged amino acids at Env positions 322/440 in non-B subtype HIV-1 strains.

<p>Values represent the percentage of Envs within each subtype that have the indicated type of amino acid (+, positively charged; -, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109771#pone-0109771-g001" target="_blank">Figure 1</a>. P-values were calculated by chi-square analysis (ns, not significant; N/A, not applicable).</p

Correlation between charged amino acids at Env positions 322/440 and coreceptor usage for phenotypically characterized C-HIV, D-HIV and AE-HIV strains.

<p>Values represent the percentage of R5 or CXCR4-using Envs within C-HIV (A), D-HIV (B) and AE-HIV (C) subtypes that have the indicated type of amino acid (+, positively charged; −, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs within each subtype that have the indicated combination of amino acid types at positions 322/440. Amino acids are colored according to charge, as described in the legend for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109771#pone-0109771-g001" target="_blank">Figure 1</a>.</p

Nucleotide codon usage of R5 and CXCR4-using B-HIV Envs at position 440.

<p>The size of each node indicates the relative frequency of the indicated nucleotide codon. A black line connects codons separated by one nucleotide substitution. Codons encoding positively charged amino acids at colored blue, codons encoding negatively charged amino acids are colored red and codons encoding neutral amino acids are colored white. Nucleotide codons at position 440 were aligned and analysed using CLC Main Workbench version 6.5. 75 CXCR4-using (46 R5X4 and 29 X4) and 293 R5 sequences were analyzed.</p

Correlation between charged amino acids at Env positions 322/440 in phenotypically characterized B-HIV strains.

<p>(A) Values represent the percentage of Envs that have the indicated type of amino acid (+, positively charged; -, negatively charged; o, neutral) at position 440 out of all Envs with the indicated type of amino acid at position 322. Subscript values represent the percentage of R5 or CXCR4-using Envs that have the indicated combination of amino acid types at positions 322/440. (B) Values represent the percentage of R5 or CXCR4-using Envs that have the combination of indicated amino acids at Env positions 322/440. Amino acids are colored according to charge; positively charged (+, Arg and Lys) in blue, negatively charged (-, Asp and Glu) in red and neutral (o) in white. 322/440 amino acid combinations are colored according to charge; +322/+440 in dark blue, −322/−440 in dark red, +322/−440 or −322/+440 in purple, +322/o440 or o322/+440 in light blue, −322/o440 or o322/−440 in light red and o322/o440 in white. P-values were calculated by chi-square analysis.</p

Phenotype and envelope gene diversity of -deleted HIV-1 isolated from long-term survivors infected from a single source-0

<p><b>Copyright information:</b></p><p>Taken from "Phenotype and envelope gene diversity of -deleted HIV-1 isolated from long-term survivors infected from a single source"</p><p>http://www.virologyj.com/content/4/1/75</p><p>Virology Journal 2007;4():75-75.</p><p>Published online 16 Jul 2007</p><p>PMCID:PMC1939844.</p><p></p>roduction in culture supernatants was measured by RT assays. Values shown are means from duplicate infections. Error bars represent standard deviations. Results are representative of two independent experiments using cells obtained from different donors

Phenotype and envelope gene diversity of -deleted HIV-1 isolated from long-term survivors infected from a single source-4

<p><b>Copyright information:</b></p><p>Taken from "Phenotype and envelope gene diversity of -deleted HIV-1 isolated from long-term survivors infected from a single source"</p><p>http://www.virologyj.com/content/4/1/75</p><p>Virology Journal 2007;4():75-75.</p><p>Published online 16 Jul 2007</p><p>PMCID:PMC1939844.</p><p></p>-1 infected PBMC and subjected to GeneScan analysis, as described in the Methods and elsewhere [41, 56]. (A) GeneScan sample files generated from amplified products. (B) Fraction of sequences with a given V1V2 nucleotide length, which was calculated from GeneScan sample files. Peaks and bars shown in red represent V1V2 amplimers from early viruses, and peaks and bars shown in blue represent V1V2 amplimers from late viruses. Similar results were obtained in two independent experiments

Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS-0

<p><b>Copyright information:</b></p><p>Taken from "Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS"</p><p>http://www.retrovirology.com/content/4/1/89</p><p>Retrovirology 2007;4():89-89.</p><p>Published online 12 Dec 2007</p><p>PMCID:PMC2225424.</p><p></p>nal Envs cloned from the cross sectional (PA-R5 viruses NB23, NB24, NB25, NB27 and A-R5 viruses NB2, NB6, NB7, NB8) (B) or longitudinal (PA- and A-R5 viruses from subject IK1) (C) primary R5 HIV-1 isolates and 2 μg pSVL-Tat, as described in the Methods. Env expression at 72 h post-transfection was measured by Western blot analysis of cell lysates using rabbit anti-gp120 polyclonal antisera. Positions of gp160 and gp120 are shown on the right. C1, C2, C3 and C4 refer to independent Envs cloned from each virus