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

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Title Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses
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Creator Naveen Kumar, B. C. Bera, Benjamin D. Greenbaum, Sandeep Bhatia, Richa Sood, Pavulraj Selvaraj, Taruna Anand, Bhupendra Nath Tripathi, Nitin Virmani
 
Subject Equine influenza virus, codon bias, codon usage, evolution
 
Description Not Available
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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Date 2019-12-06T07:40:29Z
2019-12-06T07:40:29Z
2016-04-27
 
Type Research Paper
 
Identifier Not Available
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http://krishi.icar.gov.in/jspui/handle/123456789/28423
 
Language English
 
Relation Not Available;
 
Publisher PLOS