Nucleic acid extraction and molecular detection of classical swine fever virus, porcine reproductive and respiratory syndrome virus, porcine epidemic diarrhoea virus, and porcine circovirus type 2 in faecal samples

The goal of this study was to compare the efficiency of three co-extraction methods, namely the QIAamp cador Pathogen Mini Kit (Q), the Viral Gene-spinTM Viral DNA/RNA Extraction Kit (G), and the E.Z.N.A. Universal Pathogen Kit (E), for isolating DNA and RNA from 92 pooled faecal samples. TaqMan tests, which were to detect classical swine fever (CSF), porcine reproductive and respiratory syndrome (PRRS), porcine epidemic diarrhoea (PED), and porcine circovirus type 2 (PCV2) viruses were used to evaluate the extraction efficiency of the three kits. The Q kit performed the best extraction, which indicated the highest average yield, elution volume, and purity in both DNA and RNA. No PCR inhibitors were detected. The Q and G kits were able to yield detectable PEDV RNA products and PCV2 DNA products in four dilutions. The number of the positive samples of the Q and G kits was higher than those of the E kit. No significant differences in the Cq values were detected between the extraction kits. In addition, the TaqMan assays successfully detected these four viruses in field samples and seemed suitable for the use of epidemiological surveillance. Further studies on a large number of positive samples, more available kits for extraction, and other types of samples should be performed.