Development of an RT-PCR-based RspCas13d system to detect porcine deltacoronavirus

Porcine deltacoronavirus (PDCoV) is an enteropathogen that causes diarrhea in piglets and may undergo cross-species transmission. The prevention and control of PDCoV are complicated, and a sensitive, specific, and accessible method of diagnosis would be advantageous. Whereas qPCR is a standard approach for detecting PDCoV, it is not effectively sensitive. In the present study, we report such a strategy using an RT-PCR-based RspCas13d detection system and its efficacy in clinical sample diagnosis. The detection limit of this method was 4 copies/μL and no cross-reaction with other viruses such as the porcine epidemic diarrhea virus, classical swine fever virus, pseudorabies virus, porcine reproductive and respiratory syndrome virus, transmissible gastroenteritis virus and porcine rotavirus. The method was also effective in clinical samples. In summary, we demonstrate that RT-PCR-based RspCas13d detection system is an extremely sensitive and specific nucleic acid-based approach for detecting PDCoV. KEY POINTS: • RspCas13d can be used as a candidate molecular diagnostic tool to diagnose viral genomes. • A novel method is proposed using an RT-PCR-based RspCas13d detection system and its effectiveness in the detection of PDCoV. • The RT-PCR-based RspCas13d detection system has excellent sensitivity and specificity.