full length characterization of pa gene of h9n2 isolated from broilers during 1998 to 2009

background and aims: avian influenza (ai) h9n2 subtype was first reported to infect turkeys in the united states in 1966 and has been panzootic in europe and asia. the impact of avian influenza caused by h9n2 viruses in iran is now significantly more severe than in previous years. methods: sequence analysis and phylogenetic study of the complete coding region polymerase a (pa) gene of h9n2 subtype of avian influenza virus isolates (outbreaks of 1999-2009) in iran were studied. results: sequence and phylogenetic analysis revealed a large number of similar substitution mutations and close evolutionary relation among sequences of pa. based on analysis of aminoacid sequences iranian h9n2 isolates have some substitution that found in human and mouse adapted isolates. it is raised concern that h9n2 isolates has trend to infect mammalian host. in phylogenetic analysis iranian isolates cluster in unknown indian-middle east cluster. however, the early isolate of h9n2 (11t strain) in iran classified in dk-1 lineage. conclusion: the results show, iranian avian influenza h9n2 isolates have undergone extensive genetic reassortment which led to emergence of a new genotype. interestingly, continuous monitoring of viral genetic changes throughout the years is warranted to monitor variations of influenza viruses in the field.