One-pot platform for rapid detecting virus utilizing recombinase polymerase amplification and CRISPR/Cas12a

The livestock industry has been deeply affected by African swine fever virus (ASFV) and Capripoxvirus (CaPV), which caused an enormous economic damage. It is emergent to develop a reliable detection method. Here, we developed a rapid, ultra-sensitive, and one-pot DNA detection method combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a for ASFV and CaPV, named one-pot-RPA-Cas12a (OpRCas) platform. It had the virtue of both RPA and CRISPR/Cas12a, such as high amplification efficiency, constant temperature reaction, and strict target selectivity, which made diagnosis simplified, accurate and easy to be operated without expensive equipment. Meanwhile, the reagents of RPA and CRISPR/Cas12a were added to the lid and bottom of tube in one go, which overcame the incompatibility of two reactions and aerosol contamination. To save cost, we only need a quarter of the amount of regular RPA per reaction which is enough to achieve clinical diagnosis. The OpRCas platform was 10 to 100 times more sensitive than qPCR; the limit of detection (LOD) was as low as 1.2 x 10(-6) ng/mu L (3.07 copies/mu L by ddPCR) of ASFV and 7.7 x 10(-5) ng/mu L (1.02 copies/mu L by ddPCR) of CaPV with the portable fluorometer in 40 min. In addition, the OpRCas platform combined with the lateral flow assay (LFA) strip to suit for point-of-care (POC) testing. It showed 93.3% consistency with qPCR for clinical sample analysis. Results prove that OpRCas platform is an easy-handling, ultra-sensitive, and rapid to achieve ASFV and CaPV POC testing.

Automated summary

The livestock industry has suffered significant economic damage from African swine fever virus (ASFV) and Capripoxvirus (CaPV), highlighting the urgent need for a reliable detection method. In this study, a rapid and ultra-sensitive DNA detection method, combining recombinase polymerase amplification (RPA) and CRISPR/Cas12a, was developed for ASFV and CaPV. The method, called one-pot-RPA-Cas12a (OpRCas) platform, exhibited high amplification efficiency, constant temperature reaction, and strict target selectivity, providing simplified, accurate, and affordable diagnosis for these viruses.