ArticleJournal of virology2017
Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species.
Article in Journal of virology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Article
- Comprehensive Codon Usage Analysis Across Diverse Plant Lineages.Biochemical genetics · 2026Article
- Characterization of Z-DNA dynamics across the tree of life.bioRxiv : the preprint server for biology · 2025Article
- RNA editing signatures and codon adaptation reveal potential translational compatibility between Hendra virus and its natural host Pteropus Alecto.Archives of microbiology · 2025Article
- Effect of increased CpG and UpA dinucleotides in the West Nile virus genome on virus transmission byJournal of virology · 2025Article
- Evolutionary paradigm of distinct viral coding regions of BVDV associated with different nucleotide usage patterns.BMC veterinary research · 2025Article
- Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.Viruses · 2025Review
- The effect of taxonomic, host-dependent features and sample bias on virus host prediction using machine learning and short sequence k-mers.Scientific reports · 2025Article
- Ciprofloxacin-driven purifying selection on viral genomes accelerates soil NProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Deciphering the Code of Viral-Host Adaptation Through Maximum-Entropy Nucleotide Bias Models.Molecular biology and evolution · 2025Article
- Uncovering the hidden RNA virus diversity in Lake Nam Co: Evolutionary insights from an extreme high-altitude environment.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Human Riboviruses: A Comprehensive Study.Journal of molecular evolution · 2025Review
- Article
- Machine learning methods for predicting human-adaptive influenza A virus reassortment based on intersegment constraint.Frontiers in microbiology · 2025Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Predicting novel mosquito-associated viruses from metatranscriptomic dark matter.NAR genomics and bioinformatics · 2024Article
- Depletion of CpG dinucleotides in bacterial genomes may represent an adaptation to high temperatures.NAR genomics and bioinformatics · 2024Article
- Xinyang flavivirus, fromThe Journal of general virology · 2024Article
- Article
- A novel tamanavirus (The Journal of general virology · 2023Article
16 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses use the cellular machinery of their hosts for replication. It has therefore been proposed that the nucleotide and dinucleotide compositions of viruses should match those of their host species. If this is upheld, it may then be possible to use dinucleotide composition to predict the true host species of viruses sampled in metagenomic surveys. However, it is also clear that different taxonomic groups of viruses tend to have distinctive patterns of dinucleotide composition that may be independent of host species. To determine the relative strength of the effect of host versus virus family in shaping dinucleotide composition, we performed a comparative analysis of 20 RNA virus families from 15 host groupings, spanning two animal phyla and more than 900 virus species. In particular, we determined the odds ratios for the 16 possible dinucleotides and performed a discriminant analysis to evaluate the capability of virus dinucleotide composition to predict the correct virus family or host taxon from which it was isolated. Notably, while 81% of the data analyzed here were predicted to the correct virus family, only 62% of these data were predicted to their correct subphylum/class host and a mere 32% to their correct mammalian order. Similarly, dinucleotide composition has a weak predictive power for different hosts within individual virus families. We therefore conclude that dinucleotide composition is generally uniform within a virus family but less well reflects that of its host species. This has obvious implications for attempts to accurately predict host species from virus genome sequences alone.
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