ArticleGenetics1999
Genealogical evidence for positive selection in the nef gene of HIV-1.
Article in Genetics, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 125 citations in OpenAlex.
- Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study.Retrovirology · 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
- Article
- Faster Adaptation in Smaller Populations: Counterintuitive Evolution of HIV during Childhood Infection.PLoS computational biology · 2016Article
- Dengue virus type 3 adaptive changes during epidemics in São Jose de Rio Preto, Brazil, 2006-2007.PloS one · 2013Article
- Genes in the terminal regions of orthopoxvirus genomes experience adaptive molecular evolution.BMC genomics · 2011Article
- Complex positive selection pressures drive the evolution of HIV-1 with different co-receptor tropisms.Science China. Life sciences · 2010Article
- JCoDA: a tool for detecting evolutionary selection.BMC bioinformatics · 2010Article
- Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.Molecular biology and evolution · 2010Article
- Coalescent simulation of intracodon recombination.Genetics · 2010Article
- Timing and evolution of the most recent common ancestor of the Korean clade HIV subtype B based on nef and vif sequences.Journal of microbiology (Seoul, Korea) · 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
- The population genetics of dN/dS.PLoS genetics · 2008Article
- Positive selection on HIV accessory proteins and the analysis of molecular adaptation after interspecies transmission.Journal of molecular evolution · 2008Article
- Positive selection in the N-terminal extramembrane domain of lung surfactant protein C (SP-C) in marine mammals.Journal of molecular evolution · 2007Article
- Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus.PLoS pathogens · 2007Article
- Adaptation to different human populations by HIV-1 revealed by codon-based analyses.PLoS computational biology · 2006Article
- A Dirichlet process model for detecting positive selection in protein-coding DNA sequences.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The pattern and process of evolution in the nef gene of HIV-1 was analyzed within and among patients. Using a maximum likelihood method that allows for variable intensity of selection pressure among codons, strong positive selection was detected in a hemophiliac patient over 30 mo of infection. By reconstructing the process of allele substitution in this patient using parsimony, the synapomorphic amino acid changes separating each time point were found to have high probabilities of being under positive selection, with selective coefficients of at least 3.6%. Positive selection was also detected among 39 nef sequences from HIV-1 subtype B. In contrast, multiple pairwise comparisons of nonsynonymous and synonymous substitution rates provided no good evidence for positive selection and sliding window analyses failed to detect most positively selected sites. These findings demonstrate that positive selection is an important determinant of nef gene evolution and that genealogy-based methods outperform pairwise methods in the detection of adaptive evolution. Mapping the locations of positively selected sites may also be of use in identifying targets of the immune response and hence aid vaccine design.
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