Host Specific Codon Usage Pattern of H1N1 Influenza A Viruses

Codon usage preference and the highly expressed genes have strong correlations occur in many organisms. Codon usage preference of viruses may evolve much similar with its infected host to increase the fitness. In this study we investigated differences in codon usage preferences among influenza A H1N1 viruses which infected avian, swine and human, and may cause major pandemic around world. The relative synonymous codon usage (RSCU) indices of HA gene in H1N1 viruses were calculated and we further incorporate the principal component analysis (PCA) to characterizing different host infected viruses. Host-specific codon usage pattern of H1N1 viruses were reported in this study. In 2009 influenza A H1N1 virus was a major epidemic challenge of disease control department. We propose to use the codon based method to gain a better understanding of the features of virus genome and evolutionary processes.