Emerging Technologies for Virus Detection in Livestock: From CRISPR-Based Diagnostics to Portable Genomic Sequencing

Abstract

Introduction: The emergence and re-emergence of viral pathogens in livestock pose a significant threat to global food security and public health. The use of some molecular diagnostic techniques, such as ELISA and PCR, in the detection of viral nucleic acid is limited due to lack of efficiency, adaptability, and scalability.

Methods: Recent technological advances in CRISPR-based diagnostics, particularly CRISPR-Cas12 and Cas13 systems, have proven to be rapid, sensitive, and portable techniques for the detection of viral pathogens, especially when integrated with lateral flow assays or fluorescent readouts. Furthermore, some other CRISPR-based diagnostic tools like SHERLOCK and DETECTR have been proven effective in the detection of various viruses like African swine fever virus (ASFV), foot-and-mouth disease virus (FMDV), and avian influenza viruses in livestock. The combined use of CRISPR-based diagnostic tools with portable genome sequencing approaches enables rapid detection and detailed genomic insight within a few hours in the field. Portable genomic sequencing technologies, such as Oxford Nanopore Technologies' MinION, have been effectively used in the surveillance of peste des petits ruminant virus (PPRV) and bovine viral diarrhea virus (BVDV) in the field without the need for a laboratory.

Results: Additionally, diagnostic approaches are shifting toward digital and decentralized diagnostics by integrating CRISPR with smartphone-based readers, AI-driven analysis tools, and cloud-linked biosurveillance platforms to enhance diagnostic throughput and usability.

Conclusions: Despite the intense revolution, the diagnosis of the virus is still challenged by ensuring regulatory validation, maintaining assay specificity in complex field samples, and reducing production costs for large-scale deployment. This review emphasizes the current trends of emerging diagnostic technologies for detecting viral diseases in livestock by analyzing their advantages, limitations, and integration potential in veterinary health systems.