# Advances in CRISPR-Cas12a/13a-Based Nucleic Acid Detection for Porcine Viral Diseases: A Comprehensive Review

## TL;DR

CRISPR-based detection systems offer a fast and portable way to diagnose swine viral diseases, helping control outbreaks and protect the pig industry.

## Contribution

This paper reviews CRISPR-Cas12a/13a-based nucleic acid detection methods as a novel, rapid diagnostic solution for porcine viral diseases.

## Key findings

- CRISPR-Cas12a/13a systems can detect swine viruses like ASFV and PRRSV with high sensitivity and specificity in under an hour.
- These diagnostics work with simple readouts and do not require complex equipment, making them suitable for on-site testing.
- Challenges remain, including the need for nucleic acid extraction and fully integrated sample-to-result systems.

## Abstract

Swine viral diseases cause severe economic losses to the global pig industry. Traditional diagnostic methods often require complex equipment and take a long time, which limits their use for rapid on-site testing. This review discusses a new detection technology based on CRISPR-Cas systems, gene-editing tools that act like molecular scissors to precisely recognize viral genetic material. When combined with constant-temperature amplification methods, this approach can detect important swine viruses—such as African swine fever virus and porcine reproductive and respiratory syndrome virus—with high sensitivity and specificity within one hour. The test does not need expensive instruments and can be read using a simple test strip or a portable fluorescent device. Although sample processing steps are still required, this technology offers a breakthrough solution for fast, on-site diagnosis. It can help control outbreaks more quickly, protect animal health, and safeguard pork supply chains, thereby supporting the stability and sustainability of pig farming worldwide.

The global swine industry suffers persistent economic losses and health challenges due to major viral pathogens such as African swine fever virus (ASFV), porcine reproductive and respiratory syndrome virus (PRRSV), classical swine fever virus (CSFV), and porcine circovirus (PCV). Traditional diagnostic methods, including virus isolation, serology, and quantitative PCR (qPCR), are limited by time, equipment requirements, and field applicability. Recent advances in CRISPR-based diagnostics, particularly those leveraging the collateral cleavage activity of Cas12a and Cas13a, have enabled rapid, sensitive, and field-deployable nucleic acid detection. This review outlines the principles of CRISPR-Cas12a/13a systems, their integration with isothermal amplification techniques, and their application in detecting major swine viruses. Cas12a-based platforms (e.g., DETECTR) and Cas13a-based systems (e.g., SHERLOCK) achieve detection limits as low as single-copy/μL within 25–60 min at 37 °C, offering high specificity and compatibility with visual readouts. Applications include ASFV, PRRSV, CSFV, PCV, foot-and-mouth disease virus (FMDV), porcine rotavirus (PoRV), and porcine parvovirus 7 (PPV7). Despite significant advances, challenges remain, notably the reliance on nucleic acid extraction and the need for fully integrated “sample-in, result-out” systems. Ongoing innovations in extraction-free methods, lyophilized reagents, and multiplex detection will strengthen the role of CRISPR diagnostics in swine disease surveillance and control. From an application standpoint, the technology offers a low-capital, field-adaptable alternative to qPCR, with its value proposition rooted in early outbreak containment and loss prevention. Its adoption pathway is expected to vary across production systems—serving as a sentinel tool in intensive settings, a leapfrogging solution in rapidly intensifying regions, and through shared-service models in resource-limited contexts. However, translation to routine use still requires overcoming standardization hurdles, regulatory validation, and workflow integration.