ArticleJournal of virology2002
Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation.
Article in Journal of virology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
123 citing papers in PubMed, 248 citations in OpenAlex.
- Immunogenicity of ALVAC-HIV vCP1521 in infants of HIV-1-infected women in Uganda (HPTN 027): the first pediatric HIV vaccine trial in Africa.Journal of acquired immune deficiency syndromes (1999) · 2014Trial
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- Recovery of an 18bioRxiv : the preprint server for biology · 2026Article
- Large-Scale Plasma Proteome Epitome Profiling is an Efficient Tool for the Discovery of Cancer Biomarkers.Molecular & cellular proteomics : MCP · 2023Article
- Cohort-Specific Peptide Reagents Broaden Depth and Breadth Estimates of the CD8 T Cell Response to HIV-1 Gag Potential T Cell Epitopes.Vaccines · 2023Article
- Efficient targeting of NY-ESO-1 tumor antigen to human cDC1s by lymphotactin results in cross-presentation and antigen-specific T cell expansion.Journal for immunotherapy of cancer · 2022Article
- Computational Structural and Functional Analyses of ORF10 in Novel Coronavirus SARS-CoV-2 Variants to Understand Evolutionary Dynamics.Evolutionary bioinformatics online · 2022Article
- Common evolutionary features of the envelope glycoprotein of HIV-1 in patients belonging to a transmission chain.Scientific reports · 2020Article
- Immune escape mutations in HIV-1 controllers in the Brazilian Amazon region.BMC infectious diseases · 2020Article
- Predicted Structural Variability ofFrontiers in microbiology · 2020Article
- Hepacivirus A Infection in Horses Defines Distinct Envelope Hypervariable Regions and Elucidates Potential Roles of Viral Strain and Adaptive Immune Status in Determining Envelope Diversity and Infection Outcome.Journal of virology · 2018Article
- Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data.Immunology · 2018Article
- Treatment Intensification in HIV-Infected Patients Is Associated With Reduced Frequencies of Regulatory T Cells.Frontiers in immunology · 2018Article
- APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome.Frontiers in immunology · 2018Article
- Role of HIV-specific CD8The Journal of experimental medicine · 2017Article
- HIV-1 Tat and Viral Latency: What We Can Learn from Naturally Occurring Sequence Variations.Frontiers in microbiology · 2017Review
- Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture.PLoS pathogens · 2016Article
- Increased Valency of Conserved-mosaic Vaccines Enhances the Breadth and Depth of Epitope Recognition.Molecular therapy : the journal of the American Society of Gene Therapy · 2016Article
- Coevolutionary Analysis Identifies Protein-Protein Interaction Sites between HIV-1 Reverse Transcriptase and Integrase.Virus evolution · 2016Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors at 6 institutions in 3 countries.
Funding
Abstract
The human cytotoxic T-lymphocyte (CTL) response to human immunodeficiency virus type 1 (HIV-1) has been intensely studied, and hundreds of CTL epitopes have been experimentally defined, published, and compiled in the HIV Molecular Immunology Database. Maps of CTL epitopes on HIV-1 protein sequences reveal that defined epitopes tend to cluster. Here we integrate the global sequence and immunology databases to systematically explore the relationship between HIV-1 amino acid sequences and CTL epitope distributions. CTL responses to five HIV-1 proteins, Gag p17, Gag p24, reverse transcriptase (RT), Env, and Nef, have been particularly well characterized in the literature to date. Through comparing CTL epitope distributions in these five proteins to global protein sequence alignments, we identified distinct characteristics of HIV amino acid sequences that correlate with CTL epitope localization. First, experimentally defined HIV CTL epitopes are concentrated in relatively conserved regions. Second, the highly variable regions that lack epitopes bear cumulative evidence of past immune escape that may make them relatively refractive to CTLs: a paucity of predicted proteasome processing sites and an enrichment for amino acids that do not serve as C-terminal anchor residues. Finally, CTL epitopes are more highly concentrated in alpha-helical regions of proteins. Based on amino acid sequence characteristics, in a blinded fashion, we predicted regions in HIV regulatory and accessory proteins that would be likely to contain CTL epitopes; these predictions were then validated by comparison to new sets of experimentally defined epitopes in HIV-1 Rev, Tat, Vif, and Vpr.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.