The tracheal virome of broiler chickens with respiratory disease complex in Iran: the metagenomics study

Ali Hojabr Rajeoni; Arash Ghalyanchilangeroudi; Bahman Khalesi; Mohammad Sadegh Madadi; Hossein Hosseini

doi:10.18502/ijm.v13i3.6396

Ali Hojabr Rajeoni Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran
Arash Ghalyanchilangeroudi Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran
Bahman Khalesi Department of Poultry Diseases, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AEREO), Karaj, Iran
Mohammad Sadegh Madadi Department of Microbiology and Immunology, School of Veterinary Medicine, University of Tehran, Tehran, Iran
Hossein Hosseini Department of Clinical Sciences, School of Veterinary Medicine, Karaj Branch, Islamic Azad University, Alborz, Iran

DOI: https://doi.org/10.18502/ijm.v13i3.6396

Keywords: Metagenomics; Chickens; Iran; Virome; Trachea

Abstract

Background and Objectives: Avian respiratory disease complex (RDC) is one of the most detrimental economic diseases that affected different parts of the world. Various pathogens cause the disease, but the most significant viral pathogens include avian influenza virus (AIV), infectious bronchitis virus (IBV), and Newcastle disease virus (NDV) are the most prevalent. To detect these pathogens, various methods have been discovered in the last decades. Detection and characterization of viruses by metagenomics methods have improved our knowledge about the role of virome in the avian complex respiratory disease.

Materials and Methods: This research investigates the viral pathogen populations that mostly participate in emerging these diseases using the NGS method RNA-sequencing. In surveillance of ten broiler farms from different cities with respiratory symptoms, trachea samples were collected to determine the pathogenic virome causing the disease.

Results: In this metagenomics analysis, nine viral families were identified, comprising 72.82% of RNA viruses, 24.32% of RT viruses, and 2.86% of DNA viruses. RNA viruses had the highest contribution to the respiratory disease complex instead of disease, including paramyxoviridae, orthomyxoviridae, coronaviridae, and picornaviridae viruses. Other viruses from the RNA viruses and DNA virus families were also identified in addition to these results.

Conclusion: This research suggests that studies of pathogenic viromes in different diseases can help monitor different diseases and predict their future occurrence.