Establishment and application of a droplet digital PCR assay for sensitive detection of porcine deltacoronavirus

Porcine deltacoronavirus (PDCoV) is a newly emerging coronavirus that causes severe diarrhea and dehydration in newborn piglets, and can infect multiple animal species including humans, posing a substantial threat to global swine production and human health. To address these challenges, we developed a droplet digital PCR (ddPCR) method for detecting the N gene of PDCoV in clinical samples. Our ddPCR method exhibited good linearity, reproducibility, and repeatability. In comparison to conventional quantitative real-time PCR (qPCR), the ddPCR assay demonstrated exceptional sensitivity, with limits of detection (LoD) of 1.65 copies/reaction (95% CI: 1.39–2.14) for clinical sample and 1.62 copies/reaction (95% CI: 1.36–2.12) for standard plasmid, respectively. Besides, the ddPCR assay displayed no cross-reactivity with the other 6 common swine pathogens. The results of clinical sample testing showed that the positivity rate of ddPCR (29/182) was greater than that of qPCR (25/182), with a coincidence rate of 97.80%. The established ddPCR method exhibits good sensitivity, repeatability, and specificity, indicating that this method can be used as a promising tool for the sensitive detection and quantification of PDCoV.