ArticleJournal of molecular evolution2003
Widespread adaptive evolution in the human immunodeficiency virus type 1 genome.
Article in Journal of molecular evolution, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Integrated Genomic Analysis Uncovers the Evolutionary Landscape and Global Dissemination of Senecavirus A.Veterinary sciences · 2026Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 2022Article
- Divergent evolution and purifying selection of the Type 2 diabetes gene sequences in Drosophila: a phylogenomic study.Genetica · 2020Article
- Contrasting patterns of molecular evolution in metazoan germ line genes.BMC evolutionary biology · 2019Article
- Comparative Genomic Analysis ofBioMed research international · 2019Article
- Large Scale Analyses and Visualization of Adaptive Amino Acid Changes Projects.Interdisciplinary sciences, computational life sciences · 2018Article
- HIV Subtypes B and C gp120 and Methamphetamine Interaction: Dopaminergic System Implicates Differential Neuronal Toxicity.Scientific reports · 2015Article
- Synonymous site conservation in the HIV-1 genome.BMC evolutionary biology · 2013Article
- Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution.BMC genomics · 2011Article
- Selected amino acid mutations in HIV-1 B subtype gp41 are associated with specific gp120v₃ signatures in the regulation of co-receptor usage.Retrovirology · 2011Article
- Article
- Constraints on HIV-1 diversity from protein structure.Journal of virology · 2010Article
- HIV-1 subtype C envelope characteristics associated with divergent rates of chronic disease progression.Retrovirology · 2010Article
- Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms.Science China. Life sciences · 2010Article
- Analysis of the percentage of human immunodeficiency virus type 1 sequences that are hypermutated and markers of disease progression in a longitudinal cohort, including one individual with a partially defective Vif.Journal of virology · 2009Article
- HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.PLoS pathogens · 2009Article
- Differential stepwise evolution of SARS coronavirus functional proteins in different host species.BMC evolutionary biology · 2009Article
- Potent antibody-mediated neutralization and evolution of antigenic escape variants of simian immunodeficiency virus strain SIVmac239 in vivo.Journal of virology · 2008Article
- Identifying the important HIV-1 recombination breakpoints.PLoS computational biology · 2008Article
- The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.Retrovirology · 2008Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigated variable selective pressures among amino acid sites in HIV-1 genes. Selective pressure at the amino acid level was measured by using the nonsynonymous/synonymous substitution rate ratio (omega = dN/dS). To identify amino acid sites under positive selection with omega > 1, we applied maximum likelihood models that allow variable omega ratios among sites to analyze genomic sequences of 26 HIV-1 lineages including subtypes A, B, and C. Likelihood ratio tests detected sites under positive selection in each of the major genes in the genome: env, gag, pol, vif, and vpr. Positive selection was also detected in nef, tat, and vpu, although those genes are very small. The majority of positive selection sites is located in gp160. Positive selection was not detected if omega was estimated as an average across all sites, indicating the lack of power of the averaging approach. Candidate positive selection sites were mapped onto the available protein tertiary structures and immunogenic epitopes. We measured the physiochemical properties of amino acids and found that those at positive selection sites were more diverse than those at variable sites. Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1.
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