%0 Journal Article
%T Natural Selection Determines Synonymous Codon Usage Patterns of Neuraminidase (NA) Gene of the Different Subtypes of Influenza A Virus in Canada
%A Youhua Chen
%J Journal of Viruses
%D 2014
%R 10.1155/2014/329049
%X Synonymous codon usage patterns of neuraminidase (NA) gene of 64 subtypes (one is a mixed subtype) of influenza A virus found in Canada were analyzed. In total, 1422 NA sequences were analyzed. Among the subtypes, H1N1 is the prevailing one with 516 NCBI accession records, followed by H3N2, H3N8, and H4N6. The year of 2009 has the highest report records for the NA sequences in Canada, corresponding to the 2009 pandemic event. Correspondence analysis on the RSCU values of the four major subtypes showed that they had distinct clustering patterns in the two-dimensional scatter plot, indicating that different subtypes of IAV utilized different preferential codons. This subtype clustering pattern implied the important influence of natural selection, which could be further evidenced by an extremely flattened regression line in the neutrality plot (GC12 versus G3s plot) and a significant phylogenetic signal on the distribution of different subtypes in the clades of the phylogenetic tree ( statistic). In conclusion, different subtypes of IAV showed an evolutionary differentiation on choosing different optimal codons. Natural selection played a deterministic role to structure IAV codon usage patterns in Canada. 1. Introduction Codon usage is not a random event [1]. Codon usage bias has been broadly observed, and different mechanisms have been proposed to explain the bias patterns, for example, mutation pressure, translational efficiency, gene length [2], dinucleotide bias [3], tRNA abundance [4], organ specificity [5], and so on. Codon usage bias patterns have been broadly studied in recent years, especially for virus genomes [3, 6, 7]. In recent years, codon usage patterns have been widely explored for influenza viruses [6, 8¨C12]. Among the three influenza viruses, influenza A virus (IAV) is the major concern since it has a lot of subtypes. IAV is a genus of Orthomyxoviridae family of viruses, which caused influenza in birds and mammals [6, 13]. Among the eight RNA segments of IAV, hemagglutinin and neuraminidase (NA) genes are the principal concerns. Currently, most of modeling efforts on IAV are focused on Asian regions [6, 8]; little attention is paid on the evolutionary patterns of IAV in local areas of North America. To fill such a knowledge gap, in the present study, I analyzed all the available 1436 NA ORFs for IAV found in Canada to reveal the codon usage patterns of IAV different subtypes in Canada. 2. Materials and Methods 2.1. Sequence Data 1436 NA sequences found in IAV strains of Canada were extracted from NCBI GenBank database
%U http://www.hindawi.com/journals/jvi/2014/329049/