Molecular Detection of Respiratory Virus Infection and Co-infection in Chicken Farms

In recent years, with the rapid expansion of poultry production and international poultry trade, the incidence of respiratory viral infections in commercial chickens in Egypt has also increased. The frequency of the most economically significant respiratory viruses circulating in chicken flocks was the primary focus of this investigation. Between 2023 and 2024, 50 flocks of chickens with respiratory, neurological, digestive tract, and kidney infections were investigated for respiratory viral pathogens using specific primers for Newcastle virus (NDV), infectious bronchitis virus (IBV), and Avian influenza virus (AIV) using real-time PCR (rtRT-PCR). Five IBV strains were selected for sequencing and identification. The rtRT-PCR test results showed that the detection rate of IBV was the highest (52%), followed by NDV (16%), and the detection rates of AIV H5 and H9 were 6% and 8%, respectively. Only two samples in this study had documented co-infection with IBV, one with AIV H9 and the other with AIV H5. The mortality rate ranged from 1.5- 40%, with a mortality rate of 16% in the case of IBV and AI-H9N2 co-infection, even with IBV vaccination, although the highest mortality rate was 40% in single NDV infection. IBV and NDV infections were detected in both vaccinated and unvaccinated flocks, whereas AIV H5 and H9 infections were detected only in unvaccinated flocks. The phylogenetic tree of the selected five IBV field strains and other reference strains showed that the five IBVs were divided into two different branches and were far away from the IB vaccine strains. Despite different vaccination programs, IBV and NDV continue to circulate and cause morbidity and mortality in chicken farms; strict hygiene measures and up-to-date vaccination regimens must be implemented to protect the chicken industry.