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PloS one2016; 11(4); e0154376; doi: 10.1371/journal.pone.0154376

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.

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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Publication Date: 2016-04-27 PubMed ID: 27119730PubMed Central: PMC4847779DOI: 10.1371/journal.pone.0154376Google Scholar: Lookup
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Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This study analyzed how equine influenza viruses (EIVs) adapt to their hosts through changes in their codon usage, revealing that several factors, including mutation pressure and natural selection, play a role in this process.

Understanding Codon Usage in Equine Influenza Viruses

In this study, the researchers worked on understanding the codon usage patterns of equine influenza viruses. They focused on genome-wide codon usage patterns across 92 EIV strains from both H3N8 and H7N7 subtypes.

  • EIVs are responsible for severe respiratory infections in horses and can trigger significant outbreaks.
  • The codon usage of these viruses affects how they adapt to different hosts. Codons are sequences of three DNA or RNA nucleotides that correspond to a specific amino acid or signal during protein synthesis.

Study Methods and Data Analysis

Several methodologies were employed in analyzing the genome-wide codon usage patterns, including computing codon usage indices and utilizing multivariate statistical methods.

  • The researchers conducted a Relative Synonymous Codon Usage (RSCU) analysis, revealing that preferred synonymous codons are predominantly A/U-ended codons.
  • Through the application of RSCU and Effective Number of Codon(ENc) analyses, it was inferred that the overall codon usage bias in EIVs is mainly affected by nucleotide compositional constraints.

Findings and Significance

The study found that codon usage patterns in EIVs are governed by an interplay of factors, including mutation pressure, influences from natural hosts, and other undetermined factors.

  • Among the two studied EIV subtypes, H7N7 was found to be less adapted to its host (the horse), exhibiting a higher codon bias, lower mutation pressure, and less adaptation to the tRNA pool of equine cells.
  • These findings enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.
  • This research is significant as it is reportedly the first to describe the codon usage analysis of the complete genomes of EIVs.

Cite This Article

APA
Kumar N, Bera BC, Greenbaum BD, Bhatia S, Sood R, Selvaraj P, Anand T, Tripathi BN, Virmani N. (2016). Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses. PLoS One, 11(4), e0154376. https://doi.org/10.1371/journal.pone.0154376

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 11
Issue: 4
Pages: e0154376
PII: e0154376

Researcher Affiliations

Kumar, Naveen
  • Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Bera, Bidhan Chandra
  • Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Greenbaum, Benjamin D
  • Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Pathology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Bhatia, Sandeep
  • Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Sood, Richa
  • Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Selvaraj, Pavulraj
  • Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Anand, Taruna
  • Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Tripathi, Bhupendra Nath
  • Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Virmani, Nitin
  • Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.

MeSH Terms

  • Adaptation, Physiological / genetics
  • Animals
  • Biological Evolution
  • Codon
  • Gene Expression Regulation, Viral
  • Genetic Code
  • Genome, Viral
  • Horse Diseases / virology
  • Horses
  • Host-Pathogen Interactions
  • Influenza A Virus, H3N8 Subtype / genetics
  • Influenza A Virus, H3N8 Subtype / metabolism
  • Influenza A Virus, H7N7 Subtype / genetics
  • Influenza A Virus, H7N7 Subtype / metabolism
  • Models, Statistical
  • Mutation Rate
  • Orthomyxoviridae Infections / veterinary
  • Orthomyxoviridae Infections / virology
  • RNA, Transfer / genetics
  • RNA, Transfer / metabolism
  • Species Specificity
  • Virus Replication

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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