ArticleJournal of virology2009
Quantifying differences in the tempo of human immunodeficiency virus type 1 subtype evolution.
Article in Journal of virology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 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
63 citing papers in PubMed, 92 citations in OpenAlex.
- Integrating haplotype-enhanced HIV surveillance with national databases improves the resolution of transmission networks, drug resistance, and risk assessment.Emerging microbes & infections · 2026Article
- Phylodynamics analysis of HIV epidemic history in Belarus in 1987-2022.Frontiers in epidemiology · 2025Article
- Expectation-Maximization enables Phylogenetic Dating under a Categorical Rate Model.Systematic biology · 2024Article
- Phylodynamics of HIV in the Mexico City Metropolitan Region.Journal of virology · 2022Article
- HIV Capsid Protein Genetic Diversity Across HIV-1 Variants and Impact on New Capsid-Inhibitor Lenacapavir.Frontiers in microbiology · 2022Article
- Genetic Diversity and Low Therapeutic Impact of Variant-Specific Markers in HIV-1 Pol Proteins.Frontiers in microbiology · 2022Article
- Article
- Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods.Genes · 2021Review
- Computational Design of gRNAs Targeting Genetic Variants Across HIV-1 Subtypes for CRISPR-Mediated Antiviral Therapy.Frontiers in cellular and infection microbiology · 2021Article
- Comparative Circulation Dynamics of the Five Main HIV Types in China.Journal of virology · 2020Article
- Article
- Characterisation of HIV-1 Molecular Epidemiology in Nigeria: Origin, Diversity, Demography and Geographic Spread.Scientific reports · 2020Article
- Distinct rates and patterns of spread of the major HIV-1 subtypes in Central and East Africa.PLoS pathogens · 2019Article
- Article
- 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
- Geographically-stratified HIV-1 group M pol subtype and circulating recombinant form sequences.Scientific data · 2018Article
- Maintenance and reappearance of extremely divergent intra-host HIV-1 variants.Virus evolution · 2018Article
- Evolution of HIV-1 within untreated individuals and at the population scale in Uganda.PLoS pathogens · 2018Article
- Molecular evolution methods to study HIV-1 epidemics.Future virology · 2018Review
- The Effect of RNA Substitution Models on Viroid and RNA Virus Phylogenies.Genome biology and evolution · 2018Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human immunodeficiency virus type 1 (HIV-1) genetic diversity, due to its high evolutionary rate, has long been identified as a main cause of problems in the development of an efficient HIV-1 vaccine. However, little is known about differences in evolutionary rate between different subtypes. In this study, we collected representative samples of the main epidemic subtypes and circulating recombinant forms (CRFs), namely, sub-subtype A1, subtypes B, C, D, and G, and CRFs 01_AE and 02_AG. We analyzed separate data sets for pol and env. We performed a Bayesian Markov chain Monte Carlo relaxed-clock phylogenetic analysis and applied a codon model to the resulting phylogenetic trees to estimate nonsynonymous (dN) and synonymous (dS) rates along each and every branch. We found important differences in the evolutionary rates of the different subtypes. These are due to differences not only in the dN rate but also in the dS rate, varying in roughly similar ways, indicating that these differences are caused by both different selective pressures (for dN rate) and the replication dynamics (for dS rate) (i.e., mutation rate or generation time) of the strains. CRF02_AG and subtype G had higher rates, while subtype D had lower dN and dS rates than the other subtypes. The dN/dS ratio estimates were also different, especially for the env gene, with subtype G showing the lowest dN/dS ratio of all subtypes.
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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.