Genomic Analysis of Influenza A Viruses, including Avian Flu (H5N1) Strains

Abstract

This study was designed to conduct genomic analysis in two steps, such as the overall relative synonymous codon usage (RSCU) analysis of the five virus species in the orthomyxoviridae family, and more intensive pattern analysis of the four subtypes of influenza A virus (H1N1, H2N2, H3N2, and H5N1) which were isolated from human population. All the subtypes were categorized by their isolated regions, including Asia, Europe, and Africa, and most of the synonymous codon usage patterns were analyzed by correspondence analysis (CA). As a result, influenza A virus showed the lowest synonymous codon usage bias among the virus species of the orthomyxoviridae family, and influenza B and influenza C virus were followed, while suggesting that influenza A virus might have an advantage in transmitting across the species barrier due to their low codon usage bias. The ENC values of the host-specific HA and NA genes represented their different HA and NA types very well ...