Introduction: Influenza A viruses possess a unique genomic structure which leads to genetic instability, especially in products of neuraminidase and hemagglutinin genes. These surface proteins play major roles in viral entry and release, and in the activation of the host immune system.
Methodology: This study involved an in silico sequence, phylogenetic and antigenic analyses of hemagglutinin and neuraminidase proteins of avian influenza A (H9N2) strains that circulated in Pakistan's poultry flocks from 1999 to 2008 and determined variations among these sequences at different levels.
Results: Sequence and phylogenetic analysis revealed a large number of similar substitution mutations and close evolutionary relation among sequences of both proteins. Changes were observed in the N-glycosylation sites of both surface proteins, along with the appearance of a new glycosylation site in the neuraminidase sequence isolated in 2007. Epitopes for hemagglutinin remained conserved, whereas for neuraminidase, epitopes from older strains reappeared in present sequences.
Conclusions: Because of the rapid mutating nature of avian influenza subtype H9N2, constant surveillance of annual sequence variations is important. Preventive measures and vaccine products can be evaluated by keeping track of changes that may lead to reassortment among different circulating strains in Pakistan's commercial poultry flocks or in humans.