الفهرس 
Studies on the epidemiology of respiratory diseases in chicken farms with relation to biosecurity and vaccination regimes adopted
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Abstract
Poultry production in Egypt is in jeopardy due to respiratory diseases outbreak. In this study, the prevalence of Avian Influenza Virus (AIV), Infectious Bronchitis Virus (IBV), Newcastle Diseases Virus (NDV) and Mycoplasma Gallisepticum (MG) was investigated in chickens suffering from respiratory manifestations. Trachea and lung tissues were collected under hygienic conditions from 70 chicken flocks (66 broiler flocks, 3-layer flocks, 1 breeder flock) (10 samples per flock),between November 2018 and April 2019. Collected samples were subjected to nucleic acid (RNA& DNA) Extraction, real-Time RT-PCR (rRT-PCR), virus isolation sequencing and phylogenetic analysis. Out of 66 commercial broiler flocks, 23 (34.8%) flocks weresuffered from single respiratory infection while the mixed infections were reported in 6 flocks (9.1%).The incidence of single infection with IBV, velogenic NDV (vNDV), AIV-H9N2 and MG was 10/66 (15.2%), 3/66 (4.5%), 4/66 (6.1%) and 6/66 (9.1%), respectively. Meanwhile, AIV-H9N2 and IBV mixed infections were the most observed cases [3/66 (4.5%)], other mixed infections reported including AIV-H5N8/MG, IBV/MG and vNDV/IBV/MG [1/66 (1.5%) each].Out of three commercial layer flocks, 1 (33.3%) was only infected with vNDV. AIV-H9N2 and vNDV were successfully isolated in embryonated chicken eggs (ECE).The phylogeny of molecularly characterized viruses revealed that the two AIV-H9N2 viruses were closely related to each other and also related to recent Egyptian and Middle East circulating strains that are belonging to G1- like lineage.The phylogeny of IBV revealed that (IBV/CK/EG/Sharkia/2018)and (IBV/CK/EG/Sharkia/2019) were clustered into Egyptian variant 1 and Egyptian variant 2 subgroups respectively that are belonging to GI-23 genotype. The phylogeny of vNDV showed that the two vNDV strains were classified as genotype VII1.1 with close relatedness to each other and with other recent Egyptian strains