Design and Pre-Clinical Evaluation of a Universal HIV-1 Vaccine

BACKGROUND: One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test. METHODOLOGY AND FINDINGS: To address the HIV-1 variation, we designed a novel T cell immunogen, designated HIV(CONSV), by assembling the 14 most conserved regions of the HIV-1 proteome into one chimaeric protein. Each segment is a consensus sequence from one of the four major HIV-1 clades A, B, C and D, which alternate to ensure equal clade coverage. The gene coding for the HIV(CONSV) protein was inserted into the three most studied vaccine vectors, plasmid DNA, human adenovirus serotype 5 and modified vaccine virus Ankara (MVA), and induced HIV-1-specific T cell responses in mice. We also demonstrated that these conserved regions prime CD8(+) and CD4(+) T cell to highly conserved epitopes in humans and that these epitopes, although usually subdominant, generate memory T cells in patients during natural HIV-1 infection. SIGNIFICANCE: Therefore, this vaccine approach provides an attractive and testable alternative for overcoming the HIV-1 variability, while focusing T cell responses on regions of the virus that are less likely to mutate and escape. Furthermore, this approach has merit in the simplicity of design and delivery, requiring only a single immunogen to provide extensive coverage of global HIV-1 population diversity

Functional characterisation of HIV-1 specific CD8+ T lymphocytes

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Characterisation of nef from HIV-1 subtype c-infected individuals

A dissertation submitted to the Faculty of Health Sciences, Umversity of the Witwatersrand, Johannesburg, for the degree of Masters of Science in Medicine (Virology). Johannesburg, 2001This dissertation examines HIV-1 subtype C nucleotide and amino acid Nef sequences from South African recently-infected (n=12) and chronically-infected individuals (n=9) and from AIDS patients (n=ll). The overall aim is to determine which regions of subtype C Nef are variable and which are conserved and to associate these regions with targeting by the immune system. Phylogenetic analysis and sequence alignments showed that there was no association of Nef variations with stage of disease. Nef amino acid alignments of 32 sequences showed a high degree of conservation in areas of functional and structural importance. The mean intrasubtype variation from these isolates was 15.8%, with sequences from the AIDS cohort being significantly (p<0.05) more variable than those from recent or chronic infectionIT201

Human immunodeficiency virus-specific gamma interferon enzyme-linked immunospot assay responses targeting specific regions of the proteome during primary subtype C infection are poor predictors of the course of viremia and set point.

It is unknown whether patterns of human immunodeficiency virus (HIV)-specific T-cell responses during acute infection may influence the viral set point and the course of disease. We wished to establish whether the magnitude and breadth of HIV type 1 (HIV-1)-specific T-cell responses at 3 months postinfection were correlated with the viral-load set point at 12 months and hypothesized that the magnitude and breadth of HIV-specific T-cell responses during primary infection would predict the set point. Gamma interferon (IFN-gamma) enzyme-linked immunospot (ELISPOT) assay responses across the complete proteome were measured in 47 subtype C HIV-1-infected participants at a median of 12 weeks postinfection. When corrected for amino acid length and individuals responding to each region, the order of recognition was as follows: Nef > Gag > Pol > Rev > Vpr > Env > Vpu > Vif > Tat. Nef responses were significantly (P < 0.05) dominant, targeted six epitopic regions, and were unrelated to the course of viremia. There was no significant difference in the magnitude and breadth of responses for each protein region with disease progression, although there was a trend of increased breadth (mean, four to seven pools) in rapid progressors. Correlation of the magnitude and breadth of IFN-gamma responses with the viral set point at 12 months revealed almost zero association for each protein region. Taken together, these data demonstrate that the magnitude and breadth of IFN-gamma ELISPOT assay responses at 3 months postinfection are unrelated to the course of disease in the first year of infection and are not associated with, and have low predictive power for, the viral set point at 12 months

Tissue types and infecting viruses of human blood donors

a<p>HIV-1/2-uninfected subjects</p>b<p>UK HIV-1-infected patients vaccinated with HIVA vaccines</p>c<p>Patients infected with HIV-1 in Africa <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000984#pone.0000984-Hanke1" target="_blank">[4]</a></p><p>n.a. – not applicable; n.d. not done</p

HIV_CONSV-induced T cell responses in HLA-A*0201-transgenic mice, strain HHD.

<p>(A) Mice were immunized using the DAM regimen and the vaccine-induced responses were detected in an <i>ex vivo</i> ELISPOT assay. Results are shown as a mean±SD (n = 4). For doses and timing, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000984#s2" target="_blank">Methods</a>. (B) Identified epitope peptides and their origin. (C) Killing of murine EL4 A2-K^d (top) and human JK A2-K^d (bottom) target cells sensitized with the shown peptides in a ⁵¹Cr-release assay after a 5-day <i>in vitro</i> peptide re-stimulation. Black, grey and white bars indicated effector to target ratios of 100, 50 and 25 to 1, respectively.</p

The HIV_CONSV immunogen.

<p>(A) Localization of the 14 most highly conserved regions of the HIV-1 proteome. The numbers written vertically under each fragment boundary indicate the first and last aa positions using the HXB2 reference strain numbering (<a href="http://www.hiv.lanl.gov/content/hiv-db/LOCATE/locate.html" target="_blank">http://www.hiv.lanl.gov/content/hiv-db/LOCATE/locate.html</a>). (B) Predicted aa sequence of the the HIV_CONSV immunogen with indicated fragment numbers. (C) Summary of the fragments including: the fragment number; the protein in which it was embedded; the clade of the consensus sequence selected for inclusion in the immunogen, alternating between clades A–D; additional clades that have identical HIV_CONSV; and position numbers in the chimeric vaccine. The number of additional clades with identical consensus sequences to selected clade reflects the high level of conservation in these regions, and is encouraging in terms of the global potential of the vaccine. The consensus sequences compared were to the M group consensus, clades A–K, and three very common recombinant circulating forms CRF01 (common in Asia and Africa), CRF02 (common Africa), CRF08 (common in China) retrieved from the Los Alamos database 2004 consensus alignment (<a href="http://www.hiv.lanl.gov/content/hiv-db/CONSENSUS/M_GROUP/Consensus.html" target="_blank">http://www.hiv.lanl.gov/content/hiv-db/CONSENSUS/M_GROUP/Consensus.html</a>). (D) Schematic representation of the HIV_CONSV immunogen (not drawn to scale) indicating clade anternation (above), overlapping peptide pool derivation and protein origin by colour coding. (E) Hamming distances between the HIV_CONSV antigen fragments and the global circulating viral sequences. The full M group alignment, including recombinant sequences, was used for the comparison. The Los Alamos database alignment contains only one sequence person, and contains sequences from between 600 and 1000 individuals in these proteins. The Hamming distance range for 95% of the sequences relative to the vaccine immunogen is given by the vertical lines. The distances between the full length natural proteins were then calculated relative to HXB2 reference strain Env, Vif, Gag and Pol sequences for comparison. Distance measures are minimal estimates, as gaps inserted in regions where insertions and deletions occur were not counted. (F) Numbers of known CD8⁺ T cell epitopes (defined to within 12 aa or less in the Los Alamos HIV-1 database) in each of the 14 conserved protein fragments included in the HIV_CONSV immunogen are shown. When more than one HLA class I presenting molecules can present the same HIV-1 epitope, then each is counted as a distinct epitope; if more than one sequence variant has been described as an epitope presented by the same class I molecule, then these are counted as a distinct epitopes; however, if an HLA serotype and genotype that are potentially the same are each described as presenting the same epitope (like <i>A2</i> and <i>A*0201</i>) they are scored as a single epitope.</p