Genetic and phylogenetic analysis of the ribonucleoprotein complex genes of H9N2 avian influenza viruses isolated from commercial poultry in Iran

The H9N2 subtype of avian influenza viruses (AIVs) has been isolated in multiple avian species in many European, Asian, African and American countries. Since the first outbreak of H9N2 virus in Iran in 1998, this virus has widely circulated throughout the country, resulting in major economic losses in chicken flocks. Several amino acids in the virus ribonucleoprotein (RNP) complex including the nucleoprotein (NP) and polymerase (PB2, PB1 and PA) proteins are associated with host range and virulence. Our aim was to understand the molecular characterization of RNP complex proteins of Iranian H9N2 subtype isolates. The full length nucleotide sequences of RNP complex genes of two strains designated as Ck/IR/ZMT-101/98 and Ck/IR/EBGV- 88/10 were amplified and sequenced. The phylogenetic analysis revealed that both strains were located in different sub-lineages. However, based on the genetic similarities, PB1, PAand NP genes of Ck/IR/EBGV-88/10 strain had a close relationship with a H7N3 subtype strain, isolated from Pakistan. Most positions of RNP proteins contained amino acids typical of avian determinants of host range. The results showed that the Iranian RNP complex genes have undergone genetic reassortment. Continuous AIV monitoring in poultry industry would help to obtain more information about genetic variation of H9N2 viruses and possible emergence of virulent and/or pandemic viruses.