ReviewRetrovirology2012
The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus.
Review in Retrovirology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 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.
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
58 citing papers in PubMed, 100 citations in OpenAlex.
- tRNA modifications in viral replication.The Journal of biological chemistry · 2026Review
- The biased adenosine-rich content of the HIV-1 genome serves as a molecular signature that facilitates efficient packaging.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Single-base mJournal of virology · 2025Article
- APOBEC3G Antagonism by Vif, or When Structure Meets Biological and Evolutionary Studies.Annual review of virology · 2025Review
- Computer aided design of inhibitor molecules against Vpr protein from different HIV-1 subtypes.In silico pharmacology · 2025Article
- Molecular mechanism for regulating APOBEC3G DNA editing function by the non-catalytic domain.Nature communications · 2024Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Article
- Mcl-1 Protein and Viral Infections: A Narrative Review.International journal of molecular sciences · 2024Review
- Sensing nucleotide composition in virus RNA.Bioscience reports · 2023Review
- Sub-stoichiometric Modulation of Viral Targets-Potent Antiviral Agents That Exploit Target Vulnerability.ACS medicinal chemistry letters · 2023Article
- Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.Viruses · 2023Article
- Evolution of the SARS-CoV-2 Mutational Spectrum.Molecular biology and evolution · 2023Article
- Article
- An endogenous lentivirus in the germline of a rodent.Retrovirology · 2022Article
- Analysis of evolutionary and genetic patterns in structural genes of primate lentiviruses.Genes & genomics · 2022Article
- Next-generation sequencing: A new avenue to understand viral RNA-protein interactions.The Journal of biological chemistry · 2022Review
- Compositional biases in RNA viruses: Causes, consequences and applications.Wiley interdisciplinary reviews. RNA · 2022Review
- Silent codon positions in the A-rich HIV RNA genome that do not easily become A: Restrictions imposed by the RNA sequence and structure.Virus evolution · 2022Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses often deviate from their hosts in the nucleotide composition of their genomes. The RNA genome of the lentivirus family of retroviruses, including human immunodeficiency virus (HIV), contains e.g. an above average percentage of adenine (A) nucleotides, while being extremely poor in cytosine (C). Such a deviant base composition has implications for the amino acids that are encoded by the open reading frames (ORFs), both in the requirement of specific tRNA species and in the preference for amino acids encoded by e.g. A-rich codons. Nucleotide composition does obviously affect the secondary and tertiary structure of the RNA genome and its biological functions, but it does also influence phylogenetic analysis of viral genome sequences, and possibly the activity of the integrated DNA provirus. Over time, the nucleotide composition of the HIV-1 genome is exceptionally conserved, varying by less than 1% per base position per isolate within either group M, N, or O during 1983-2009. This extreme stability of the nucleotide composition may possibly be achieved by negative selection, perhaps conserving semi-stable RNA secondary structure as reverse transcription would be significantly affected for a less A-rich genome where secondary structures are expected to be more stable and thus more difficult to unfold.This review will discuss all aspects of the lentiviral genome composition, both of the RNA and of its derived double-stranded DNA genome, with a focus on HIV-1, the nucleotide composition over time, the effects of artificially humanized codons as well as contributions of immune system pressure on HIV nucleotide bias.
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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.