Comparative evaluation of single step real-time RT-PCR and gel based RT-PCR assay for detection of classical swine fever

To control classical swine fever (CSF), a highly contagious viral disease causing serious losses in the pig industry worldwide, rapid detection and identification of the causative agent is a crucial step. In the present study, real-time RT-PCR and-gel based RT-PCR techniques were compared for detection of CSF virus nucleic acid in both clinical as well as tissue samples. Clinical and tissue samples (325) were collected from CSF suspected outbreaks from different part of north eastern region of India. In gel based RT-PCR, % positivity was 44.61% while in real-time RT-PCR it was 57.23%. Highest per cent positivity was recorded in tonsil followed by mesenteric lymph node, blood, nasal swab, spleen, kidney and ileum. The study indicated that probe based RT-PCR could specifically detect CSF virus genome and detection limit was about one log higher than a gel based PCR assay targeting the non translated region. Total. time required to complete the gel based RT-PCR including extraction of viral RNA was about 6 h. On the other hand, real-time RT-PCR assay can be performed in 2 to 3 h, thus providing a rapid detection tool.