ArticleMolecular biology and evolution2021
Biased Mutation and Selection in RNA Viruses.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 73 citations in OpenAlex.
- Systematic Review of Phylogenetic Analysis Techniques for RNA Viruses Using Bioinformatics.International journal of molecular sciences · 2025Pooled it
- Evolution of virulence of a plant RNA virus in developmental stage-structured host populations.Molecular biology and evolution · 2026Article
- Increased or decreased numbers of CpG dinucleotide motifs in the genome of influenza A virus do not affectJournal of virology · 2026Article
- Article
- Codon Usage Bias Analysis of Citrus Leaf Blotch Virus.Viruses · 2025Article
- Article
- Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity.Journal of molecular evolution · 2025Review
- Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.Viruses · 2025Review
- Impact of the Zinc Antiviral Protein on the Genomic Composition of RNA Viruses Infecting Vertebrates.Molecular biology and evolution · 2025Article
- Article
- Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction.Molecular biotechnology · 2025Article
- Selective Diversity in RNA Viruses: Do They Know How to Evolve? A Hypothesis.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- Regulation of innate immunity by liquid-liquid phase separation: a focus on veterinary viruses.Frontiers in microbiology · 2025Review
- Spillover: Mechanisms, Genetic Barriers, and the Role of Reservoirs in Emerging Pathogens.Microorganisms · 2024Review
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- RNAVirHost: a machine learning-based method for predicting hosts of RNA viruses through viral genomes.GigaScience · 2024Article
- Systematic analysis of the codon usage patterns of African swine fever virus genome coding sequences reveals its host adaptation phenotype.Microbial genomics · 2024Article
- Emerging perspectives on RNA virus-mediated infections: from pathogenesis to therapeutic interventions.World journal of virology · 2023Review
- Sensing nucleotide composition in virus RNA.Bioscience reports · 2023Review
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
RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.
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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.