ArticleGenetics2004
Mapping sites of positive selection and amino acid diversification in the HIV genome: an alternative approach to vaccine design?
Article in Genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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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
26 citing papers in PubMed, 56 citations in OpenAlex.
- HIV-1 Nef sequence and functional compartmentalization in the gut is not due to differential cytotoxic T lymphocyte selective pressure.PloS one · 2013Trial
- Changes in selective pressures associated with human population expansion may explain metabolic and immune related pathways enriched for signatures of positive selection.BMC genomics · 2016Article
- Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry.BMC evolutionary biology · 2015Article
- Natural polymorphisms and unusual mutations in HIV-1 protease with potential antiretroviral resistance: a bioinformatic analysis.BMC bioinformatics · 2014Article
- High genetic diversity and adaptive potential of two simian hemorrhagic fever viruses in a wild primate population.PloS one · 2014Article
- Molecular characterization of HTLV-1 gp46 glycoprotein from health carriers and HAM/TSP infected individuals.Virology journal · 2013Article
- The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.Bioinformation · 2013Article
- Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms.Science China. Life sciences · 2010Article
- Coalescent simulation of intracodon recombination.Genetics · 2010Article
- HLA footprints on human immunodeficiency virus type 1 are associated with interclade polymorphisms and intraclade phylogenetic clustering.Journal of virology · 2009Article
- Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects.Retrovirology · 2009Article
- Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.Virology journal · 2008Review
- Frequent toggling between alternative amino acids is driven by selection in HIV-1.PLoS pathogens · 2008Article
- Investigating selection on viruses: a statistical alignment approach.BMC bioinformatics · 2008Article
- Positive selection on HIV accessory proteins and the analysis of molecular adaptation after interspecies transmission.Journal of molecular evolution · 2008Article
- Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei.PloS one · 2008Article
- Reducing the false positive rate in the non-parametric analysis of molecular coevolution.BMC evolutionary biology · 2008Article
- Protein structure and oligomerization are important for the formation of export-competent HIV-1 Rev-RRE complexes.Protein science : a publication of the Protein Society · 2008Article
- Tat protein vaccination of cynomolgus macaques influences SHIV-89.6P cy243 epitope variability.Virus genes · 2008Article
- Modification of chicken avian beta-defensin-8 at positively selected amino acid sites enhances specific antimicrobial activity.Immunogenetics · 2007Article
Corrections and comments
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Authors and funding
8 authors at 6 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A safe and effective HIV-1 vaccine is urgently needed to control the worldwide AIDS epidemic. Traditional methods of vaccine development have been frustratingly slow, and it is becoming increasingly apparent that radical new approaches may be required. Computational and mathematical approaches, combined with evolutionary reasoning, may provide new insights for the design of an efficacious AIDS vaccine. Here, we used codon-based substitution models and maximum-likelihood (ML) methods to identify positively selected sites that are likely to be involved in the immune control of HIV-1. Analysis of subtypes B and C revealed widespread adaptive evolution. Positively selected amino acids were detected in all nine HIV-1 proteins, including Env. Of particular interest was the high level of positive selection within the C-terminal regions of the immediate-early regulatory proteins, Tat and Rev. Many of the amino acid replacements were associated with the emergence of novel (or alternative) myristylation and casein kinase II (CKII) phosphorylation sites. The impact of these changes on the conformation and antigenicity of Tat and Rev remains to be established. In rhesus macaques, a single CTL-associated amino substitution in Tat has been linked to escape from acute SIV infection. Understanding the relationship between host-driven positive selection and antigenic variation may lead to the development of novel vaccine strategies that preempt the escape process.
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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.