Isolation and full genome characterization of avian influenza subtype H9N2 from poultry respiratory disease outbreak in Egypt.

Low pathogenic avian influenza virus of subtype H9N2 is panzootic in multiple avian species causing respiratory manifestations and severe economic losses. H9N2 co-circulate simultaneously with high pathogenic avian influenza virus subtype H5N1 in Egyptian chicken farms suggesting the possibility of reassortment. The aim of the present study was to isolate and characterize H9N2 from the recent outbreaks in chicken farms. Also the diversity of amantadine-resistant mutants among these isolates was tested by in situ ELISA and sequence analysis. Three influenza H9N2 viruses, designated A/chicken/Egypt/SCU8/2014, A/chicken/Egypt/SCU9/2014 and A/chicken/Egypt/SCU20/2014 were isolated from commercial broiler and broiler breeder chickens in specific pathogen free embryonated chicken eggs. The eight gene segments were amplified by RT-PCR, cloned, and subjected to full length sequencing. Phylogenetic analysis of these viruses revealed a close relationship between Egyptian, Middle Eastern and Israel isolates with an average of 96-99 % nucleotide homology and identified an ancestor relationship to low pathogenic H9N2 Quail/HK/G1/1997 prototype. The internal segments of the currently isolated viruses were derived from the same sub-lineage with no new evidence of reassortment. The three isolates were sensitive to amantadine as suggested by absence of mutations of M2 and confirmed by a phenotypic assay. In conclusion, avian influenza H9N2 virus is circulating in Egyptian chicken farms causing respiratory manifestations. Continuous monitoring of the molecular epidemiology and its impact on the virulence as well as emergence of new strains are necessary.