Estimates of the proportion of the sampled genomic regions for which the most closely related haplotype comes from each study population, for chimpanzees and humans.

<p>Parentheses show the empirical central 95% region of the distribution of values for the 100 re-samples of the human data.</p

Map of the geographic distribution of four populations of common chimpanzee.

<p><i>After </i><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002504#pgen.1002504-Gonder2" target="_blank">[<i>3</i>]</a><i>, Figure 6b</i>. Colours show the ranges of each population (yellow - <i>P. t. troglodytes</i>, red - <i>P. t. ellioti</i>, blue - <i>P. t. verus</i>, green - <i>P. t. schweinfurthii</i>) with major rivers indicated. The Sanaga River in Cameroon has been proposed to form the boundary between the ranges of <i>P. t. ellioti</i> and <i>P. t. troglodytes</i>.</p

Pairwise F_ST values for human samples.

<p>Parentheses show the empirical central 95% region of the distribution of values for the 100 re-samples of the human data.</p

Structure estimates of ancestry in three populations.

<p>For each sampled individual the figure shows the estimated proportion of ancestry from Structure's three putative ancestral populations, with <i>P. t. troglodytes</i> in yellow, <i>P. t. ellioti</i> in red and <i>P. t. verus</i> in blue. Structure reveals the same pattern of group memberships as PCA, and additionally suggests that <i>P. t. troglodytes</i> and <i>P. t. ellioti</i> individuals may share more DNA from the other group than either shares with <i>P. t. verus</i> (blue). The two known hybrid individuals (C024, C025, with ancestry estimated at close to 50% in each of <i>P. t. troglodytes</i> and <i>P. t. verus</i>) and two <i>P. t. ellioti</i> chimpanzees with <i>P. t. troglodytes</i>-like mtDNA (C127, C541) are labelled.</p

Number of NS3-peptides that induce IFNγ production by CD4 T-cells or IL-2/IFNγ dual cytokine production by CD8 T-cells.

<p>PRE, pre challenge. POST, post challenge.</p

Cytolytic killing of CFSE-loaded target cells.

<p>(A) Specific lysis of NS3_1258–1272-pulsed Patr-A*03∶01 target cells (red peak) in comparison with unpulsed Patr-A*03∶01 target cells (yellow peak) by NS3-peptide-pool expanded PBMC from Vac1 isolated 10 weeks after HCV 1bJ4 challenge (blue peak). (B) No specific lysis of NS3_1258–1272-pulsed Patr-B*02∶01 target cells. (C) and (D) Control experiments showing no killing of unpulsed Patr-A*03∶01 or Patr-B*02∶01 target cells. (E,F,G) Percentage of lysis for all MHC class-I-peptide-combinations tested in Vac1, Vac2, Vac3 respectively.</p

Dose-inhibition curves for selected NS3-peptides to Patr-A*03∶01.

<p>Binding affinity of selected NS3-peptides to Patr-A*03∶01, established by peptide binding competition assay. Patr-A*0301 cells were incubated with increasing concentrations of NS3 p59 (top left), LGFGAYMSK (LGF, top right), AATLGFGAY (AAT, bottom left), or KGGLRPRAG (control, bottom right) in the presence of biotin-labeled indicator peptide. Binding of indicator peptide was quantified by incubation with europium labeled streptavidin. Indicated is reduction in percentage of europium positive cells relative to cells incubated with indicator-peptide only. The indicated IC₅₀ values (µM) are derived from the regression curves of three independent experiments in the case of p59, LGF and AAT, and of two individual experiments in the case of KGG. The IC₅₀ values were estimated using non-linear least-squares regression with the “R” platform for statistical computing.</p

MHC class I genotypes of the chimpanzees.

A<p>Vac3 is likely to be homozygous A*0901.</p

Evaluation of peptide-specific IL-2, IFNγ and TNFα expression in CD4 and CD8 T-cells.

<p>A representative example of the analysis performed in Vac1 (left panel) and Vac2 (right panel), two weeks after the final vaccine boost, is shown. PBMC were first expanded for a 12 day period using a pool of all NS3 peptides, restimulated with individual peptides (medium alone, p59 or p64) and analyzed for induction of IFNγ, IL-2 and TNFα cytokine expression by expanded CD4 and expanded CD8 cells, using the gating strategy described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095103#pone.0095103.s001" target="_blank">Figure S1</a>. The numbers in the quadrants, represent the percentage of positive cells calculated from the parent-population.</p

Heat map of NS3-peptide-specific T-cell responses in four immunized chimpanzees at different study time points.

<p>(A) Percentage of expanded CD4 T-cells producing IFNγ upon restimulation with individual peptides, subdivided into three categories; i.e. low response (light green; 0.001%–0.1% specific IFNγ production), intermediate (green; 0.1–1% specific response), high (dark green;>1% specific response). (B) Percentage of expanded CD8 T-cells showing IL-2/IFNγ double cytokine production upon restimulation with individual peptide, subdivided into three categories; i.e. low response (light blue; 0.01%–0.1% specific IFNγproduction), intermediate (blue; 0.1–1% specific response), high (dark blue; > 1% specific response). White areas indicate where no responses were detected. The red boxes highlight areas within NS3 that are broadly recognized. Per animal 6 time points of analysis are shown lined up beneath each other; -12) Two weeks following the 1st MVA boost, cells stimulated with NS3_vaccine, -4) Four weeks following 2^nd MVA boost, cells stimulated with NS3_vaccine, 0) Day of HCV infection, stimulation with NS3_vaccine, 0) Day of HCV infection, stimulation with NS3_challenge, and 4 and 36 weeks after challenge, stimulation with NS3_challenge. The individual peptides tested are indicated at the top of the map by the numbers 1 to 156. The red boxes represent broadly recognized regions within NS3. Total frequency (all peptide responses combined) of (C) IFNγ production by expanded CD4 T-cells and (D) IFNγ/IL2 dual cytokine production by expanded CD8 T-cells per animal. (E) Frequency of p59 specific triple positive IL2/TNFα/IFNγ producing CD8 T-cells. The numbers on the X-axis represent the study week, relative to time of challenge. * Despite several attempts, frozen cells from Vac1 from 4 weeks following HCV infection did not respond to either NS3_vaccine or NS3_challenge peptide stimulation and no expansion could be achieved. @ Due to a high IFNγ background, peptide specific CD8 responses could not be detected</p