Sequencing and phylogenetic analysis of nucleoprotein gene from an avian influenza virus subtype H9N2 isolated from Ahwaz

Avian influenza caused by H9N2 viruses is an important disease of industrial chickens inIran and many other parts of Asia. To understand the genetic features and phylogeneticrelationship of H9N2 viruses present in Ahwaz, the nucleotide sequence of nucleoproteingene (NP) was determined from an avian influenza virus (A/Chicken/Iran/Ahwaz-1/06)isolated from a broiler flock in Ahwaz suburb. Therefore, the coding region of the gene was amplified by RT-PCR and sequenced after cloning in to pMal-C2 vector. Nucleotide sequence analysis and phylogenetic studies were performed by comparing NP gene of this isolate with twenty four counterpart sequences retrieved from the GenBank. Based on the NP gene sequence, Ahwaz isolate had the highest percentage of homology (94.3%) with the representative virus of G1 sublineage and placed in a distinct branch of the sublineage, together with the recent isolates of Pakistan. In contrast, homology of the isolate A/Chicken/Iran/Ahwaz-1/06 with a 1999 Iranian isolate (A/Chicken/Iran/11T/99) was 86.4% and these two viruses assigned in two separate genetic sublineages. According to present study, it can be concluded that H9N2 viruses have been evolved genetically since entering to Iran or other possibility is different sublineages of the virus have entered to the country so far.