A universal heterologous internal control system for duplex real-time RT-PCR assays used in a detection system for pestiviruses

J Virol Methods. 2006 Sep;136(1-2):200-9. doi: 10.1016/j.jviromet.2006.05.020. Epub 2006 Jun 27.


A heterologous in vitro transcript based on a specific primer-probe HEX system was generated as a universal internal control (IC) to improve virus-specific real-time reverse-transcriptase PCR (RT-PCR) assays. By using a set of different primers, several PCR fragments of desired sizes of an in vitro transcript of the enhanced green fluorescent protein (EGFP) gene were generated, and the fragments were detected using a HEX-labelled probe. For long-term storage of the in vitro transcript a special RNA-safe buffer (RSB) was developed. Freezing and thawing of the IC diluted in RSB did not result in any substantial loss of detectable IC copy numbers. The new IC system was used for the first time in a duplex real-time RT-PCR assay for the detection of pestivirus-derived RNA, in particular from bovine viral diarrhea virus (BVDV). Primers and TaqMan probes for the 'panpesti' assay were selected by analysing the consensus sequence of the 5' non-translated region (5' NTR) of more than 600 different pestiviruses. Finally, the optimised primer probe combination showed an analytical sensitivity of less than 10 copies/reaction. In the duplex set-up, the analytical sensitivity of the validated real-time RT-PCR was identical to the sensitivity of the single assay without IC, and the diagnostic sensitivity of the duplex assay was equal or higher if compared to virus isolation.

Publication types

  • Comparative Study
  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Cattle
  • Green Fluorescent Proteins / genetics
  • Molecular Sequence Data
  • Pestivirus / isolation & purification*
  • RNA, Messenger / analysis
  • RNA, Messenger / genetics
  • RNA, Viral / analysis
  • RNA, Viral / genetics
  • Reference Standards
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Reverse Transcriptase Polymerase Chain Reaction / standards
  • Sensitivity and Specificity
  • Virus Cultivation


  • RNA, Messenger
  • RNA, Viral
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins