ArticleRetrovirology2011
Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints.
Article in Retrovirology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 55 citations in OpenAlex.
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- Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.Viruses · 2023Article
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- HIV-1 and human genetic variation.Nature reviews. Genetics · 2021Review
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- A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.PLoS pathogens · 2020Article
- Many human RNA viruses show extraordinarily stringent selective constraints on protein evolution.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Divergence dating using mixed effects clock modelling: An application to HIV-1.Virus evolution · 2019Article
- Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak.Scientific reports · 2018Article
- The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies.Genome biology and evolution · 2018Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Increasing the CpG dinucleotide abundance in the HIV-1 genomic RNA inhibits viral replication.Retrovirology · 2017Article
- Adaptive HIV-1 evolutionary trajectories are constrained by protein stability.Virus evolution · 2017Article
- Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model.PLoS biology · 2017Article
- Article
- Arteriviruses, Pegiviruses, and Lentiviruses Are Common among Wild African Monkeys.Journal of virology · 2016Article
- 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
- Mapping the genomic diversity of HCV subtypes 1a and 1b: Implications of structural and immunological constraints for vaccine and drug development.Virus evolution · 2016Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe HIV-1 genome is subject to pressures that target the virus resulting in escape and adaptation. On the other hand, there is a requirement for sequence conservation because of functional and structural constraints. Mapping the sites of selective pressure and conservation on the viral genome generates a reference for understanding the limits to viral escape, and can serve as a template for the discovery of sites of genetic conflict with known or unknown host proteins.
resultsTo build a thorough evolutionary, functional and structural map of the HIV-1 genome, complete subtype B sequences were obtained from the Los Alamos database. We mapped sites under positive selective pressure, amino acid conservation, protein and RNA structure, overlapping coding frames, CD8 T cell, CD4 T cell and antibody epitopes, and sites enriched in AG and AA dinucleotide motives. Globally, 33% of amino acid positions were found to be variable and 12% of the genome was under positive selection. Because interrelated constraining and diversifying forces shape the viral genome, we included the variables from both classes of pressure in a multivariate model to predict conservation or positive selection: structured RNA and α-helix domains independently predicted conservation while CD4 T cell and antibody epitopes were associated with positive selection.
conclusionsThe global map of the viral genome contains positive selected sites that are not in canonical CD8 T cell, CD4 T cell or antibody epitopes; thus, it identifies a class of residues that may be targeted by other host selective pressures. Overall, RNA structure represents the strongest determinant of HIV-1 conservation. These data can inform the combined analysis of host and viral genetic information.
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