title: Insights into the Usage of Nucleobase Triplets and Codon Context Pattern in Five Influenza A Virus Subtypes.
abstract: Influenza A virus is a single-stranded RNA virus with a genome of negative polarity. Owing to the antigenic diversity and cross concrete shift, an immense number of novel strains have developed astronomically over the years. The present work deals with the codon utilization partialness among five different influenza A viruses isolated from human hosts. All the subtypes showed the homogeneous pattern of nucleotide utilization with a little variation in their utilization frequencies. A lower bias in codon utilization was observed in all the subtypes as reflected by higher magnitudes of an efficacious number of codons. Dinucleotide analysis showed very low CpG utilization and a high predilection of A/T-ending codons. The H5N1 subtype showed noticeable deviation from the rest. Codon pair context analysis showed remarkable depletion of NNC-GNN and NNT-ANN contexts. The findings alluded towards GC-compositional partialness playing a vital role, which is reflected in the consequential positive correlation between the GC contents at different codon positions. Untangling the codon utilization profile would significantly contribute to identifying novel drug targets that will pacify the search for antivirals against this virus.
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Himangshu
authors.initials: H
authors.lastname: Deka
authors.affiliation: Department of Biotechnology, Assam University, Silchar-788011, Assam, India.
authors.forename: Supriyo
authors.initials: S
authors.lastname: Chakraborty
mesh_terms: D001482:Base Composition; D003062:Codon; D015967:Gene Expression Regulation, Viral; D009980:Influenza A virus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D014764:Viral Proteins / Q000235:genetics
chemical_list: D003062:Codon; D014764:Viral Proteins
keywords: Codon usage bias; codon pair context; dinucleotide; influenza A virus; preferred codon