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

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...

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Vydáno v:	PloS one Ročník 11; číslo 4; s. e0154376
Hlavní autoři:	Kumar, Naveen, Bera, Bidhan Chandra, Greenbaum, Benjamin D., Bhatia, Sandeep, Sood, Richa, Selvaraj, Pavulraj, Anand, Taruna, Tripathi, Bhupendra Nath, Virmani, Nitin
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	United States Public Library of Science 27.04.2016 Public Library of Science (PLoS)
Témata:	Adaptability Adaptation Adaptation, Physiological - genetics Analysis Animals Avian influenza viruses Bias Biological Evolution Biology and Life Sciences Codon Codon bias Codons Data processing Fitness Gene amplification Gene Expression Regulation, Viral Genetic Code Genome, Viral Genomes Health aspects Horse Diseases - virology Horses Host-Pathogen Interactions Influenza Influenza A Virus, H3N8 Subtype - genetics Influenza A Virus, H3N8 Subtype - metabolism Influenza A Virus, H7N7 Subtype - genetics Influenza A Virus, H7N7 Subtype - metabolism Interferon Machinery Machinery and equipment Medicine and Health Sciences Models, Statistical Mutation Mutation Rate Natural selection Orthomyxoviridae Orthomyxoviridae Infections - veterinary Orthomyxoviridae Infections - virology Outbreaks Pandemics Pressure Reproductive fitness RNA, Transfer - genetics RNA, Transfer - metabolism Species Specificity Statistical methods Transfer RNA tRNA Vaccines Virus Replication Viruses New York United States > US India
ISSN:	1932-6203, 1932-6203
On-line přístup:	Získat plný text
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Shrnutí:	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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: NV BCB NK. Performed the experiments: NV BDG NK. Analyzed the data: NK BDG BCB. Contributed reagents/materials/analysis tools: TA BNT BDG RS PS NK. Wrote the paper: NK NV BCB BDG SB. Competing Interests: The authors have declared that no competing interests exist. These authors also contributed equally to this work.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0154376