CD4+ T cells remaining in the chronic phase (as % of baseline) and their recovery as functions of the CD4+ T cells remaining at nadir.

<p>Full line represents the relationship expected for constant level of immune control. Grey area is the level of CD4+ T cells at nadir lower than the acute survival threshold of 3.3% of baseline. (A) Survival threshold of 24.1% of baseline based on chronic phase CD4 T cell level (dashed line bordering the red area) almost exactly corresponds to the acute threshold, based on the assumption of constant immune response. The animals with data points below the full line have less CD4+ T cells remaining in the chronic phase than expected from the nadir. (B) CD4+ recovery is defined as the difference between the nadir and the chronic level. The points above the curve represent better than expected recovery. All animals with the level of remaining CD4+ T cells lower than the survival threshold recover considerably less than expected.</p

Differential recovery in progressors and controllers.

<p>We defined the “differential recovery” as the difference between the actual recovery and the amount of recovery expected if the immune response were constant. The differential recovery in progressors was significantly lower than in controllers (Mann-Whitney <i>p</i><0.0001).</p

Measures of accuracy of the survival tests based on CD4 preservation and viral load in the chronic and acute phases of SHIV infection.

<p>(A–C) Chronic phase tests: (A) sensitivity and specificity of the test based on chronic level of CD4+ T cells; (B) sensitivity and specificity of the test based on set point viral load, vertical dashed line represents the best choice of threshold; (C) ROC areas of the chronic phase tests; (D–E) Acute phase tests: (D) sensitivity and specificity of the test based on acute level of CD4+ T cells; (E) sensitivity and specificity of the test based on peak viral load, (F) ROC areas of the acute phase tests.</p

Evidence for and against Cytolytic Control of HIV.

<p>Evidence for and against Cytolytic Control of HIV.</p

Summary of measures of accuracy of survival tests based on depletion of CD4+ T cells.

<p>Summary of measures of accuracy of survival tests based on depletion of CD4+ T cells.</p

Summary of measures of accuracy of survival tests based on viral load.

<p>Summary of measures of accuracy of survival tests based on viral load.</p

Conserved polypurine tracts shown in a representative alignment of 54 hypermutated HIV-1 sequences used in this study.

<p>Each line is a full genome hypermutated sequence within which the positions of GGGG motifs are shown by small triangles.</p

Percentage change of motifs within which G-to-A change(s) in the context of GG has occurred.

<p>The number of available GGs (i.e. mutability) has been used to normalize the results. a) Analysis of whole HIV genome; b) Analysis of the HIV genome without polypurine tracts. Hypermutated sequences (see reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087679#pone.0087679-Armitage1" target="_blank">[5]</a> for details) are shown on the horizontal axes.</p

Principal component analysis of the motif representation data of HIV-1 sequences from subtypes/recombinant B, C, A1 and 01_AE.

<p>a) Scores plot (PC11 vs. PC13). Each point is an HIV-1 full genome sequence. The accession numbers of the two sequences that extend in the direction of mutation by APOBEC3F and/or other similar APOBEC3 members are shown near their points. b) Loadings plot (PC11 vs. PC13). Each point is a motif. The arrow shows the direction of GA→AA mutation by APOBEC3F and/or other similar APOBEC3 enzymes.</p

A schematic of principal component analysis applied to the motif representation data of HIV sequences.

<p>A schematic of principal component analysis applied to the motif representation data of HIV sequences.</p