Nanopore Sequencing in Veterinary Medicine: From Concepts to Clinical Applications

Maria Chaves^1*Amro Hashish^1,2*Iryna V. Goraichuk^3*Leonardo Cardia Caserta⁴Megan C. Mears³Eman Gadu^1,5Abhijeet Anil Bakre³Ellen Ruth Alexander Morris⁶Mostafa M. S. Shelkamy^1,7Swathi Nadendla¹Daniel Roberto Perez⁸Mohamed El-Gazzar¹

• ¹Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University of Science and Technology College of Veterinary Medicine, Ames, United States
• ²National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Gyza, Egypt
• ³Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratory, USDA-ARS National Poultry Research Center, Athens, United States
• ⁴Department of Population Medicine and Diagnostic Sciences, Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, United States
• ⁵Department of Avian and Rabbit Diseases, Mansoura University Faculty of Veterinary Medicine, Mansoura, Egypt
• ⁶Texas A&M Veterinary Medical Diagnostic Laboratory, College Station, United States
• ⁷Department of Avian and Rabbit Medicine, Suez Canal University Faculty of Veterinary Medicine, Ismailia, Egypt
• ⁸Department of Population Health, University of Georgia College of Veterinary Medicine, Athens, United States

Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.