Molecular characterization of avian respiratory pathogens by next generation sequencing (NGS)

Abstract

Industrial poultry production has a critical role in the national economy. Brazil is currently the main exporter and the third major producer of chicken meat. Respiratory diseases are responsible for major losses in the poultry industry, interfering directly in the agribusiness. The major respiratory diseases are avian influenza (AI) and Newcastle disease (ND), which are reportable diseases to the animal health authorities. However, other respiratory pathogens are endemic, such as infectious bronchitis virus (IB) and infectious coryza (IC), which are controlled by vaccination and biosecurity measures. Respiratory diseases in poultry production could be multifactorial and complex, caused by many concomitant pathogens. Clinical signs induced by respiratory pathogens are very similar. Therefore, differential diagnoses are necessary to determine the etiologic agents involved. In Brazil, the National Poultry Health Program from the Ministry of Agriculture, Livestock and Supply (MAPA) regulates the AI and ND control and surveillance to reduce the risk of introduction and spread of these agents. The Advanced Center of Poultry Research from Instituto Biológico is an official laboratory for molecular diagnostics of AI and ND. This lab belongs to the laboratorial network of MAPA; it also provides diagnostic services to many private companies. The objective of this project is to perform the molecular characterization of important respiratory diseases in poultry by next generation sequencing (NGS), amplifying the molecular and epidemiological knowledge of agents such as avian influenza virus (AIV), Newcastle diseases virus (NDV), infectious bronchitis virus (IBV) and Avibacterium paragallinarum, the causative agent of IC. With these analyses, it will also be possible to differentiate between vaccine and field strains. For this, we are requesting a scholarship for traineeship under the supervision of Dr. Rodrigo A. Gallardo (Department of Population Health and Reproduction - School of Veterinary Medicine - University of California - Davis - USA), who is the professor responsible for many projects related with molecular characterization of avian pathogens. Dr. Gallardo is the principal investigator at the Poultry Medicine Lab and co-responsable for the Feed the Future Innovation Lab for Genomics in Poultry (USAID). He is also the principal investigator in the projects: "Infectious Coryza: Typing and vaccine protection studies" (Merck Animal Health and Elanco Animal Health), "Discovering innate responses to infectious bronchitis virus" (CFAH/USDA/NIFA) and "False layer syndrome caused by IBV in layers: Characterization and pathobiology" (Merck Animal Health). During this traineeship, we will research genomics and bioinformatics analyses and determine the complete genome sequences of important etiological agents responsible for respiratory poultry diseases. These results will allow a better understanding of the molecular tools available for diagnostics and genotyping, as well as the epidemiological aspects of pathogens, contributing to the improvement of prevention and control methods of these diseases in poultry farms. (AU)