ArticlePLoS computational biology2012
Modeling HIV-1 drug resistance as episodic directional selection.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 43 citations in OpenAlex.
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Characterizing Physicochemical Selection in Protein Evolution with Property-Informed Models (PRIME).bioRxiv : the preprint server for biology · 2026Article
- Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.Genome biology and evolution · 2024Article
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- The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus.Virus evolution · 2023Article
- FHbp variants among meningococci of serogroup B in Italy: Evolution and selective pressure, 2014-2017.PloS one · 2023Article
- Impact of viral features, host jumps and phylogeography on the rapid evolution of Aleutian mink disease virus (AMDV).Scientific reports · 2021Article
- Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches.Molecular biology and evolution · 2021Article
- Article
- Bovine Coronavirus: Variability, Evolution, and Dispersal Patterns of a No Longer Neglected Betacoronavirus.Viruses · 2020Article
- Avian Metapneumovirus subtype B around Europe: a phylodynamic reconstruction.Veterinary research · 2020Article
- Evolution of infectious bronchitis virus in the field after homologous vaccination introduction.Veterinary research · 2019Article
- Genome-scale analysis of evolutionary rate and selection in a fast-expanding Spanish cluster of HIV-1 subtype F1.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2018Article
- Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy.Scientific data · 2018Article
- Article
- Evolution of gag and gp41 in Patients Receiving Ritonavir-Boosted Protease Inhibitors.Scientific reports · 2017Article
- The Influence of HIV on the Evolution of Mycobacterium tuberculosis.Molecular biology and evolution · 2017Article
- Plant Actin-Depolymerizing Factors Possess Opposing Biochemical Properties Arising from Key Amino Acid Changes throughout Evolution.The Plant cell · 2017Article
- Finding Direction in the Search for Selection.Journal of molecular evolution · 2017Article
- Porcine circovirus type 2 (PCV2) evolution before and after the vaccination introduction: A large scale epidemiological study.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
Abstract
The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance.
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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.