Serological Survey, Molecular Identification and Phylogenetic Analysis of Avian Influenza Virus H9N2 in Backyard Chickens in Rural Areas of Fars Province, Iran

Avian influenza virus belongs to genus A of Orthomyxoviridae family and only this genus is pathogenic in birds. Backyard chickens all over the world, especially in the Middle East, play an important role in feeding people. These birds can also play a significant role in the epidemiology of AI and the spread of the virus to commercial poultry flocks. Therefore, the aim of this study was to investigate H9N2 influenza virus in backyard chickens of rural areas of 30 counties of Fars province, Iran using serological and molecular methods.

In this study, from July 2019 to January 2020, tracheal and cloacal swabs and blood samples were taken from backyard chickens of rural areas of Fars province, Iran for virus isolation and HI test in order to detect H9N2 infection and identification of possible isolates.

54% of the serum samples were HI test positive also 14 out of the 30 surveyed counties showed positive results in terms of H9N2 influenza virus serum antibodies and also average HI titer of 5.18 and 74% as the rate of seroprevalance detected in these cities, respectively. In RT-PCR test with H9 specific primer, only one isolate was positive demonstrating the band of 488bp which confirmed by sequencing. According to comparative alignment and phylogenetic analysis this strain was closely related to the strain D1 in the gene bank.

Due to the positive serum titer in a large number of backyard chickens in the rural areas, constant monitoring of these birds in terms of avian influenza infection and implementing more effective control programs seem necessary.