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Next-generation sequencing to be used to detect bovine diseases

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New study aims to mitigate transboundary and emerging diseases in livestock.
A newly funded project aims to mitigate the risks of cattle diseases.

Transboundary and emerging diseases are constant threats to the livestock industry. Even as biosafety measures have evolved, there is always the lingering threat of highly contagious or newly discovered diseases impacting animal health.

Through a newly funded project, researchers from Cornell University’s Animal Health Diagnostic Center, AHDC, and the Texas A&M Veterinary Medical Diagnostic Laboratory, TVMDL, aim to mitigate risks certain diseases pose to the cattle industry by developing technology to detect diseases before outbreaks occur or become widespread.

Diego Diel, DVM, associate professor at the Cornell University College of Veterinary Medicine, will serve as project director, and Kiril Dimitrov, DVM, TVMDL virology diagnostics section head, will co-lead this $1 million project. The project will be implemented in collaboration with the National Animal Health Laboratory Network, NAHLN, and the Plum Island Animal Disease Center. It is funded by the U.S. Department of Agriculture’s National Institute of Food and Agriculture, NIFA.

Using next-generation sequencing, NGS, the project’s goal is to develop new methods of early detection for transboundary and emerging diseases within the cattle industry. For this project, research will target the viruses responsible for foot-and-mouth-disease and those within the bovine respiratory disease complex – bovine viral diarrhea virus, bovine coronavirus, bovine respiratory syncytial virus and bovine parainfluenza virus Type 3.

One of the overarching goals of this project is to develop consistent procedures and protocols when using NGS technologies and train professionals from NAHLN laboratories. Once complete, the results of this project will be implemented across the NAHLN.

“The completion of this project will enhance the NAHLN’s diagnostic capabilities and emerging disease preparedness,” Dimitrov said. “The developed assays and staff training will facilitate the implementation of NGS diagnostic methods across the NAHLN.”

During the first two years of this project, the research team will develop and optimize targeted and random NGS diagnostics workflows for early detection and characterization of current, transboundary, and emerging pathogens in cattle. Also during the first two years, highly skilled bioinformaticians will develop rapid, semi-automated bioinformatics pipelines for data analyses. The third, and final, year of the project will involve training NAHLN laboratories on NGS procedures and processes the team develops.

What is next-generation sequencing?

Next-generation sequencing is a broad term to define the use of modern high-throughput methods of DNA sequencing. These methods allow for quicker and more cost-effective detection of DNA and RNA in biological samples and pathogen characterization.

Currently, real-time polymerase chain reaction, rtPCR, assays are most widely used in diagnostic laboratories for rapid pathogen detection. These assays are useful but are based on existing genomic information and may fail to detect emerging pathogens or variants of known pathogens. Additionally, rtPCR assays do not yield specific genomic information needed to track the source of disease outbreaks and differentiate strains — critical information necessary in developing corrective epidemiological action.

Although NGS technologies exist, widespread application across diagnostic laboratories is hindered. Currently, NGS use is bottlenecked by the lack of standardized protocols and procedures and the need for highly specialized methods to analyze biological data, known as bioinformatics, and the scarcity of NGS training scaled for diagnostic purposes.

The role of the National Animal Health Laboratory Network

In recent decades, diseases such as avian influenza, African swine fever, bovine spongiform encephalopathy, BSE, and swine influenza have spread across various animal industries. These instances severely impeded animal commerce and production and led to implications outside of their respective animal industries.

NAHLN, established in 2002, is a nationally coordinated effort to mitigate the effects that highly contagious disease outbreaks have on animal health, public health, and the nation’s food supply. The network is composed of 60 state and university veterinary diagnostic laboratories across the U.S. Each laboratory is capable of testing large numbers of samples for specific disease agents. These capabilities are imperative during animal disease outbreaks and support response methods.

Pathogens represent significant losses

Bovine diseases are costly across every segment of the cattle industry. Specifically, bovine respiratory disease is associated with over $800 million in economic losses annually.

“The U.S. is the largest producer of beef and cow milk in the world,” Dimitrov said. “Approximately 20% of the world’s beef is produced in the U.S. The exported beef and dairy products amount to over $8 billion and $6 billion annually, respectively. These enormous industries have vast socioeconomic significance and keeping them safe from transboundary and emerging pathogens is of utmost importance.”

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