Detailed reactivity maps for HCV structural proteins.

<p>Data represent individual RFscores for antibody, CD4⁺ and CD8⁺ T cell responses plotted for each antigen translated from the HCV H77 reference polyprotein: A–C = core; D–F = E1; G–I = E2. The red line denotes average frequency for all antibody, CD4 and CD8 T cell responses. Note: Data displayed for antibody reactivity only include linear epitopes. Note: decimal values for RF scores on the Y-axis are converted to percent in the text.</p

Epitope distribution among host species.

<p>Data represent the number of epitopes identified (in parentheses) for each host species reported to date.</p

Analysis of immune responsiveness versus physical properties of HCV polyprotein.

<p>A) Antibody response (RF) scores plotted along the length of the HCV H77 polyprotein, B) T cell response frequency (RF) scores plotted along the length of the HCV H77 polyprotein, C) Hydrophilicty data calculated for the HCV H77 polyprotein using the Parker method, and D) Entropy scores calculated for all HCV sequence data available from the Los Alamos Lab HCV database and plotted along the entire ployprotein. Black arrows indicate regions of high imunoreactivity and low entropy.</p

A list of HCV strains used for mapping peptides to polyproteins.

<p>A list of HCV strains used for mapping peptides to polyproteins.</p

Response frequency data for immunodominant CD4⁺ T cell epitope NS3 (1248–1261)

<p>A larger region was chosen in order to allow for visualization of reactivity upstream and downstream of the known epitope.</p

HCV epitope distribution by genotype

<p>The total number of epitopes reported for each genotype is presented. These data are then broken down by response phenotype: all T cell, CD4/class II, CD8/Class I and antibody. All reported genotypes are shown here; not all HCV genotypes have been studied. In some cases, genotypes were reported in the literature as simply ‘genotype 1’ or ‘genotype 2’ with no further specification provided. In other cases, no specific genotype was given and the authors simply referred to the epitope's source as HCV; it is these records that are presented with the qualifier ‘unspecified.’ For genotypes 3, 4, 5 and 6, data were bulked together (all subtypes), due to the small number of epitopes reported for each. The assignment of epitope genotype is made based on the assayed immunogen or antigen when these are indicated in the reference.</p

Summary of immune epitope data for HCV.

<p>The data represent all antibody and T cell epitopes reported for all HCV genotypes in all hosts. MHC binding data has been excluded. Non-peptidic epitopes and MHC ligand elution structures have not been described for HCV to date. ‘References’ denotes the number of individual peer-reviewed papers reporting HCV epitope data. ‘Total structures’ include positive and negative peptides. ‘Epitopes’ represents all positive structures. Clustering was performed using default 80% sequence homology of positive epitopes using IEDB Search interface. Note: total numbers for individual T cell and antibody responses may be more than the number of total reported epitopes because many structures are reported as both T and antibody.</p

Response frequency score data for NS3 (1248–1261) mapped onto reference genome.

<p>Data represent epitope immunoreactivity for a region on the NS3 protein (aa1230–1275) containing the immunodominant epitope has been mapped onto the reference genome HCV strain H77. A larger region was chosen in order to allow for visualization of reactivity upstream and downstream of the known epitope. RFscores (frequency values in the 0–1 range) are shown on the Y-axis and the location on the HCV polyprotein in amino acid is presented on the X-axis. User inputs include the ‘start’ and ‘end’ position of the region of interest, the minimum and maximum axis value and the RFscore cutoff point to adjust stringency of data returned.</p

Detailed reactivity maps for HCV non-structural proteins.

<p>Data represent individual RFscores for antibody, CD4⁺ and CD8⁺ T cell responses plotted for each antigen translated from the HCV H77 reference polyprotein: A–C = NS2; D–F = NS3; G–I = NS4a; J–L = NS4b; M–O = NS5a; P–R = NS5b. The red line denotes average frequency for all antibody, CD4 and CD8 T cell responses. Note: decimal values for RF scores on the Y-axis are converted to percent in the text.</p

Characterization of Humoral Response by Antigen

<p>Antibody immunoreactivity was analyzed by <i>assay type</i> for each HCV antigen. Two categories are presented: neutralizing assays (standard neutralization assays or any inhibition of antigen activity assay) and other antibody response assays (ELISA, FIA, ELISPOT, immunoblot, RIA, SPR, Immunopanning, mass spec, challenge assay, etc.). Data shown are the total number of assays, not epitopes.</p