ArticlePloS one2016
Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed, 107 citations in OpenAlex.
- Dissecting the evolutionary forces shaping codon usage bias in SFTSV from eastern China: Insights from a previously underrepresented region.Virulence · 2026Article
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- Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events.BMC genomics · 2025Article
- Decoding codon usage in human papillomavirus type 59.Virus genes · 2025Article
- Analysis of synonymous codon usage bias of Lassa virus.Virus research · 2025Article
- Equine Influenza: Epidemiology, Pathogenesis, and Strategies for Prevention and Control.Viruses · 2025Review
- 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
- Comprehensive Analysis of Codon Usage Bias in Human Papillomavirus Type 51.Polish journal of microbiology · 2024Article
- Dengue virus preferentially uses human and mosquito non-optimal codons.Molecular systems biology · 2024Article
- Comprehensive Genomics Investigation of Neboviruses Reveals Distinct Codon Usage Patterns and Host Specificity.Microorganisms · 2024Article
- Comparative analysis of the complete mitogenomes ofFrontiers in plant science · 2024Article
- Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein.Journal of virology · 2023Article
- Discovery and comparative genomic analysis of a novel equine anellovirus, representing the first complete Mutorquevirus genome.Scientific reports · 2023Article
- Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses.Frontiers in immunology · 2023Article
- Insights into the Epidemiology, Phylodynamics, and Evolutionary Changes of Lineage GI-7 Infectious Bronchitis Virus.Transboundary and emerging diseases · 2023Article
- Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host.International journal of molecular sciences · 2022Article
- Article
- Compositional biases in RNA viruses: Causes, consequences and applications.Wiley interdisciplinary reviews. RNA · 2022Review
- Equine Influenza.Cold Spring Harbor perspectives in medicine · 2022Review
- Evolution of codon usage inFrontiers in veterinary science · 2022Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.
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