ArticlePLoS computational biology2007
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Variation in Intra-individual Lentiviral Evolution Rates: a Systematic Review of Human, Nonhuman Primate, and Felid Species.Journal of virology · 2019Pooled it
- Association of HIV diversity and virologic outcomes in early antiretroviral treatment: HPTN 052.PloS one · 2017Trial
- Association of pol diversity with antiretroviral treatment outcomes among HIV-infected African children.PloS one · 2013Trial
- Slowdown of synonymous substitution rate preceding the emergence of multiple SARS-CoV-2 variants.Virus evolution · 2026Article
- Single genome amplification and molecular cloning of HIV-1 populations in acute HIV-1 infection: implications for studies on HIV-1 diversity and evolutionary rate.Virus evolution · 2026Article
- wavess: An R package for simulation of adaptive within-host virus sequence evolution.PLoS computational biology · 2025Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Higher HIV-1 evolutionary rate is associated with cytotoxic T lymphocyte escape mutations in infants.Journal of virology · 2024Article
- The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus.Nature communications · 2024Article
- Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.Virus evolution · 2024Article
- PCR-Based Detection and Genetic Characterization of Parainfluenza Virus 5 Detected in Pigs in Korea from 2016 to 2018.Veterinary sciences · 2023Article
- Molecular Basis of the Toxigenic Vibrio cholerae O1 Serotype Switch from Ogawa to Inaba in Haiti.Microbiology spectrum · 2023Article
- Deep-sequencing of viral genomes from a large and diverse cohort of treatment-naive HIV-infected persons shows associations between intrahost genetic diversity and viral load.PLoS computational biology · 2023Article
- Emergence and Evolutionary Response of Vibrio cholerae to Novel Bacteriophage, Democratic Republic of the CongoEmerging infectious diseases · 2022Article
- Plasma-Derived HIV-1 Virions Contain Considerable Levels of Defective Genomes.Journal of virology · 2022Article
- Intrahost evolution of the HIV-2 capsid correlates with progression to AIDS.Virus evolution · 2022Article
- HIV/AIDS: Current Updates on the Disease, Treatment and Prevention.Proceedings of the National Academy of Sciences, India. Section B · 2021Review
- Review
- Purifying Selection in Human Immunodeficiency Virus-1Journal of clinical medicine research · 2020Article
- ToxigenicProceedings of the National Academy of Sciences of the United States of America · 2020Article
60 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
8 authors.
Funding
Abstract
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new "relaxed-clock" phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the detrimental effects of immune activation. Humoral immune responses, on the other hand, are the major determinant of nonsynonymous rate changes through time in the envelope gene, and our relaxed-clock estimates support a decrease in selective pressure as a consequence of immune system collapse.
Indexed as
Identifiers
What OpenQuestion holds
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.