ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2018
The adaptation of codon usage of +ssRNA viruses to their hosts.
Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Synergistic effects of halo-plaque forming phage cocktails against polymicrobialMicrobiology spectrum · 2026Article
- Differences in codon usage between host-species-specific rabies virus clades are driven by non-GC3 nucleotide composition.Virus evolution · 2026Article
- tRNA Modifications: A Tale of Two Viruses-SARS-CoV-2 and ZIKV.International journal of molecular sciences · 2025Article
- Primary Sequence-Intrinsic Immune Evasion by Viral Proteins Guides CTL-Based Vaccine Strategies.Viruses · 2025Review
- Ciprofloxacin-driven purifying selection on viral genomes accelerates soil NProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Substitution-Mutation Rate Ratio (c/µ) As Molecular Adaptation Test Beyond Ka/Ks: A SARS-COV-2 Case Study.Journal of molecular evolution · 2025Article
- Metatranscriptomic identification of novel RNA viruses from raccoon dog (Nyctereutes procyonoides) feces in Japan.Scientific reports · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- Differentiation and validation of mild and severe strains of citrus tristeza virus through codon usage bias, host adaptation, and biochemical profiling.Frontiers in microbiology · 2025Article
- Bio-Chemoinformatics-Driven Analysis of nsp7 and nsp8 Mutations and Their Effects on Viral Replication Protein Complex Stability.Current issues in molecular biology · 2024Article
- Genealogical Diversity of Endogenous Retrovirus in the Jawless Fish Genome.Journal of microbiology and biotechnology · 2023Article
- Combination of genetically diverse Pseudomonas phages enhances the cocktail efficiency against bacteria.Scientific reports · 2023Article
- The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.International journal of molecular sciences · 2023Article
- Functional evolution of SARS-CoV-2 spike protein: Maintaining wide host spectrum and enhancing infectivity via surface charge of spike protein.Computational and structural biotechnology journal · 2023Article
- Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host.International journal of molecular sciences · 2022Article
- Synonymous Codon Pattern of Cowpea Mild Mottle Virus Sheds Light on Its Host Adaptation and Genome Evolution.Pathogens (Basel, Switzerland) · 2022Article
- SARS-CoV-2 host prediction based on virus-host genetic features.Scientific reports · 2022Article
- Bias at the third nucleotide of codon pairs in virus and host genomes.Scientific reports · 2022Article
- Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses.iScience · 2022Article
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Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).
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Registered trials
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