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 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.
Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Naveen
N
Kumar
Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Bidhan Chandra
BC
Bera
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.
Benjamin D
BD
Greenbaum
Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Sandeep
S
Bhatia
Immunology Lab, National Institute of High Security Animal Diseases (NIHSAD), Bhopal, Madhya Pradesh, India.
Richa
R
Sood
Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Pavulraj
P
Selvaraj
Biotechnology Lab, Veterinary Type Culture Collection, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Taruna
T
Anand
Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Bhupendra Nath
BN
Tripathi
Equine Pathology Lab, National Research Center on Equines (NRCE), Hisar, Haryana, India.
Nitin
0000-0001-5575-3307
N
Virmani
D000222:Adaptation, Physiological / Q000235:genetics; D000818:Animals; D005075:Biological Evolution; D003062:Codon; D015967:Gene Expression Regulation, Viral; D005815:Genetic Code; D016679:Genome, Viral; D006734:Horse Diseases / Q000821:virology*; D006736:Horses; D054884:Host-Pathogen Interactions; D053123:Influenza A Virus, H3N8 Subtype / Q000235:genetics* / Q000378:metabolism; D053126:Influenza A Virus, H7N7 Subtype / Q000235:genetics* / Q000378:metabolism; D015233:Models, Statistical; D059645:Mutation Rate; D009976:Orthomyxoviridae Infections / Q000662:veterinary* / Q000821:virology; D012343:RNA, Transfer / Q000235:genetics / Q000378:metabolism; D013045:Species Specificity; D014779:Virus Replication
D003062:Codon; D012343:RNA, Transfer