The United States’ poultry industry continues to be a critical part of the nation’s food supply. Although biosafety measures and surveillance testing have improved in recent decades, the multibillion-dollar industry is still facing a constant threat of infectious avian diseases.
Through a newly funded project, the Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL) is leading the effort to develop rapid next-generation sequencing procedures to assist in the detection and characterization of influenza A viruses (IAV) in avian species.
Kiril Dimitrov, DVM, PhD, virology section head, will serve as the principal investigator for this project with David Suarez, DVM, PhD, research leader at the USDA’s Southeast Poultry Research Laboratory (SEPRL), and Diego Diel, DVM, PhD, director of virology at Cornell University’s Animal Health Diagnostic Center (AHDC) serving as co-principal investigators, and Pam Ferro, MS, PhD, TVMDL molecular diagnostics section head, and Patrick Mitchell, MS, SCD, AHDC bioinformatics analyst, serving as co-investigators.
Funded by the Agricultural Improvement Act of 2018 (aka “2018 Farm Bill”) through the National Animal Health Laboratory Network (NAHLN), this $300,000 project aims to develop rapid and reliable Next-Generation Sequencing (NGS) testing protocols to identify influenza A viruses in birds and predict their pathogenicity. The project also plans to develop methods of analyzing biological data (bioinformatics).
“The $46.3 billion poultry industry is a thriving part of the U.S. economy, but infectious avian diseases continue to be a threat to its sustainability,” Dimitrov said. “Among these, avian influenza, caused by influenza A viruses, is of great economic and social importance.”
Benefits of NGS methods
NGS, is a broad-term to define the use of modern high-throughput methods of DNA sequencing. Once developed, NGS methods allow for accurate, rapid, and cost-effective detection of pathogen’s DNA or RNA in biological samples and characterization of the identified pathogens.
By establishing NGS methods, veterinary diagnostic laboratories, such as those in NAHLN, may be better prepared to detect influenza A viruses outbreaks in poultry an facilitate the control of disease outbreaks.
Impact of influenza A viruses in poultry
High pathogenicity avian influenza (HPAI) and low pathogenicity avian influenza (LPAI) are considered two of the most important poultry and wildlife diseases. Historically, HPAI has devastated entire poultry flocks, leading to severe economic losses to the poultry producer and potentially impacting the food supply. For example, the USDA estimates the 2014-2015 HPAI outbreak decimated over 50 million chickens and turkeys and totaled approximately $879 million in federal expenditures.
Looking toward the future of diagnostics
Currently, there are several well-established diagnostic tests and procedures for IAV detection. However, these tests are target-based, were developed using only the existing genetic information, and may not detect emerging, undiscovered pathogens. Rapid and accurate detection of new viral introductions are instrumental to containment measures and outbreak control.
“The existing routine assays do not provide pathogenicity, subtype (if other than H5 and H7) or other valuable epidemiological information,” Dimitrov said. “These challenges could be overcome with the use of NGS technologies, which provide the means for rapid and simultaneous detection, pathotype identification, and genetic characterization of pathogens.”
For more information on TVMDL, visit tvmdl.tamu.edu.