KP177R-based visual assay integrating RPA and CRISPR/Cas12a for the detection of African swine fever virus
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Haorui Luan, Shujuan Wang, Lin Ju, Tong Liu, Haoyue Shi, Shengqiang Ge, Shijin Jiang, Jiaqiang Wu, Jun Peng
African swine fever can devastate pig herds, yet the crucial first step is simply knowing where the virus is. This study turns that search into a visible signal that can be read outside a full laboratory.
Introduction: Early detection of the virus in the environment or in infected pigs is a critical step to stop African swine fever virus (ASFV) transmission. The p22 protein encoded by ASFV KP177R gene has been shown to have no effect on viral replication and virulence and can serve as a molecular marker for distinguishing field virus strains from future candidate KP177R deletion vaccine strains. Methods: This study established an ASFV detection assay specific for the highly conserved ASFV KP177R gene based on recombinase polymerase amplification (RPA) and the CRISPR/Cas12 reaction system. The KP177R gene served as the initial template for the RPA reaction to generate amplicons, which were recognized by guide RNA to activate the trans-cleavage activity of Cas12a protein, thereby leading to non-specific cleavage of single-stranded DNA as well as corresponding color reaction. The viral detection in this assay could be determined by visualizing the results of fluorescence or lateral flow dipstick (LFD) biotin blotting for color development, and was respectively referred to as fluorescein-labeled RPA-CRISPR/Cas12a and biotin-labeled LFD RPA-CRISPR/Cas12a. The clinical samples were simultaneously subjected to the aforementioned assay, while real-time quantitative PCR (RT-qPCR) was employed as a control for determining the diagnostic concordance rate between both assays. Results: The results showed that fluorescein- and biotin-labeled LFD KP177R RPA-CRISPR/Cas12a assays specifically detected ASFV, did not cross-react with other swine pathogens including PCV2, PEDV, PDCoV, and PRV. The detection assay established in this study had a limit of detection (LOD) of 6.8 copies/mL, and both assays were completed in 30 min. The KP177R RPA-CRISPR/Cas12a assay demonstrated a diagnostic coincidence rate of 100% and a kappa value of 1.000 (p < 0.001), with six out of ten clinical samples testing positive for ASFV using both KP177R RPA-CRISPR/Cas12a and RT-qPCR, while four samples tested negative in both assays.
Transcript
African swine fever can devastate pig herds, yet the crucial first step is simply knowing where the virus is. This study turns that search into a visible signal that can be read outside a full laboratory. African swine fever is a severe disease in pigs and wild boars, marked by high fever and bleeding, with a death rate that can reach every infected animal.
It can spread through certain soft ticks or direct contact with infected pigs, and since its arrival in China in 2018 it has dealt a fatal blow to the pig industry there. There is no credible commercial vaccine or effective treatment for infected pigs, so rapid, accurate detection and early action are critical for stopping outbreaks.
The test targets a highly conserved piece of the virus's genetic material, using recombinase polymerase amplification to generate many copies of that target. A CRISPR-based detector then recognizes that copied target and cuts nearby single-stranded genetic material, triggering a color reaction.
The result can appear as green fluorescence or as a colored mark on a dipstick, while clinical samples were also checked with a standard laboratory test for comparison. Some earlier CRISPR-based tests simplified detection, shortened the detection time, and greatly improved accuracy for viral nucleic-acid testing.
But the available joint methods relied on fluorescence or colorimetric analysis, without offering the simple test-strip staining used for field readout. The reported detection limits for those earlier methods varied widely, from three point five copies per microliter to five hundred and eighty copies per microliter.
The new test gave a green fluorescence signal only for the African swine fever virus material; the other swine-virus materials did not fluoresce. The dipstick gave a colored mark only for the African swine fever virus material, while the other groups showed no marks, indicating strong specificity.
The researchers diluted the positive KP177R plasmid step by step and still observed green fluorescence at the lowest tested concentration. The same lowest concentration produced a fluorescence signal in the microplate reader: six point eight three times ten to the zero copies per microliter.
That concentration also produced a red mark on the dipstick, establishing the assay's detection limit. When the new assay and the comparison test were used on clinical samples, their diagnostic coincidence rate was one hundred percent, with a kappa value of one point zero zero zero.
Six samples contained detectable virus material in both tests, while the remaining tested samples were negative in both, showing complete agreement across the set. The assay is described as suitable for field use on pig farms, especially for distinguishing field virus strains from possible future vaccines missing the targeted gene.
That makes it a potential screening tool for African swine fever eradication, with a rapid, sensitive, visual assay suitable for field application on swine farms. The assay can support rapid screening at clinical sample testing sites with poor experimental conditions, giving people there a way to check for the virus without relying on ideal laboratory surroundings.
The test found the virus specifically, detected very small amounts, and matched a standard laboratory test in the clinical samples examined. That could help farms screen animals and surroundings sooner, even where laboratory equipment is limited.
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