ArticleBMC genomics2017
Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 54 citations in OpenAlex.
- Codon Usage Bias Analysis of Citrus Leaf Blotch Virus.Viruses · 2025Article
- Codon Usage Bias of the Polyphenol Oxidase Genes inPlants (Basel, Switzerland) · 2025Article
- Analysis of synonymous codon usage bias of Lassa virus.Virus research · 2025Article
- Genetic and codon usage analyses reveal the evolution of the seoul virus.Frontiers in genetics · 2025Article
- Codon usage bias analysis of the gene encoding NADArchives of microbiology · 2023Article
- Equine Influenza.Cold Spring Harbor perspectives in medicine · 2022Review
- Reconstruction of the Evolutionary Origin, Phylodynamics, and Phylogeography of the Porcine Circovirus Type 3.Frontiers in microbiology · 2022Article
- Evolutionary dynamics of codon usages for peste des petits ruminants virus.Frontiers in veterinary science · 2022Article
- Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis.Frontiers in microbiology · 2022Article
- Phylogenetic and codon usage analysis for replicase and capsid genes of porcine circovirus 3.Veterinary research communications · 2021Article
- Equine Influenza Virus and Vaccines.Viruses · 2021Review
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- Comprehensive analysis of synonymous codon usage patterns and influencing factors of porcine epidemic diarrhea virus.Archives of virology · 2021Article
- Analysis of codon usage of severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) and its adaptability in dog.Virus research · 2020Article
- Analysis of the Codon Usage Pattern of HA and NA Genes of H7N9 Influenza A Virus.International journal of molecular sciences · 2020Article
- Origin and Evolution of H1N1/pdm2009: A Codon Usage Perspective.Frontiers in microbiology · 2020Article
- Article
- Genome-Wide Variation in Potyviruses.Frontiers in plant science · 2019Article
- Evolution of Codon Usage Bias in Henipaviruses Is Governed by Natural Selection and Is Host-Specific.Viruses · 2018Article
- Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses.International journal of molecular sciences · 2018Article
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEquine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective.
resultsThe group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2.
conclusionsVarious lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the codon usage patterns and evolution of polymerase genes of EIVs.
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