Molecular characterization and phylogenetic analysis of hemagglutinin and neuraminidase genes of H9N2 avian influenza viruses isolated in Iran in 1999 and 2009

Influenza virus type A is raised as a unique genomic structure due to genetic instability, especially in products of Neuraminidase and Haemagglutinin genes. These two surface proteins play a significant role to let the viruses bind with and release from host cells and immune system. In this study, we characterized Haemagglutinin and Neuraminidase genes of 6 Iranian isolates which have been isolated from commercial broiler chickens in Iran in 1999 and 2009. Nucleotide sequence analysis of six representative isolates confirmed that amino acid motif at cleavage site of Haemagglutinin is R-S-SR/GLF and K-S-S-R/GLF. Deduced amino acid sequences showed the presence of Lucine at position 226 (position 234 in H9 numbering) in all isolates indicated the preference of α 2-6 sialic acid at the binding site of the receptors. The neuraminidase stalk region in these viruses had no deletion or insertion or shortening. The hemadsorbing site of neuraminidase had amino acid substitutions and showed some differences between them and also with earlier Iranian isolates. A/Ck/Ir/95/2009 isolate had one deletion in the glycosylation site as compared to another isolates. Phylogenetic analysis of Haemagglutinin and Neuraminidase genes showed that they shared a common ancestor Qa/HK/G1/97 isolate which had contributed internal genes of H5N1 virus. Because of the nature of rapid mutation in H9N2 type of Avian influenza, it is important to have constant monitoring in sequence differences. Preventive measures and vaccine products can be evaluated by examining the changes which may lead to reassortment among different circulating strains of Avian influenza virus in Iran’s commercial poultry flocks or in humans.