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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Exotic & Emerging Avian Viral Diseases Research » Research » Research Project #441272

Research Project: Next Generation Sequencing as a Diagnostic Tool for Poultry Pathogens

Location: Exotic & Emerging Avian Viral Diseases Research

Project Number: 6040-32000-082-001-T
Project Type: Trust Fund Cooperative Agreement

Start Date: Nov 1, 2021
End Date: Oct 31, 2026

Using next generation sequencing approaches, we will amplify and sequence potential pathogens from clinical poultry samples. Using advanced bioinformatic approaches, this sequence information will be used to identify pathogens in the samples, and when depth of coverage is high enough, additional analysis will be performed to identify the subtype, genotype, pathotype, and genetic lineage of the pathogens identified. This information will be used to help control disease outbreaks in the field by informing if and what type of vaccine or treatment is needed in the field.

Clinical samples including respiratory, enteric and tissue samples will be collected by Boehringer Ingleheim Animal Health USA Inc. from poultry flocks and will be provided to the Southeast Poultry Research Laboratory for testing. The samples will be provided on FTA cards according to the established sampling protocols. Boehringer Ingleheim Animal Health USA Inc. will provide as minimal metadata on each sample the country of origin, the sampling date, and the type of sample. Boehringer Ingleheim Animal Health USA Inc. Details on flock status, whether clinically healthy or experience clinical disease, age, and other metadata is encouraged to be provided, but it is not required. The ribonucleic acid (RNA) from the samples will be extracted and a random amplified sequencing approach using the MiSeq next generation sequencing instrument or similar sequencer will be used to identify any potential pathogens from the samples. Using a combination of commercial and in-house bioinformatics data analysis, a report will be prepared that identifies likely pathogens identified in the samples.