Detection and quantitation of group A rotaviruses by competitive and real-time reverse transcription-polymerase chain reaction

J Virol Methods. 2002 Sep;105(2):277-85. doi: 10.1016/s0166-0934(02)00118-0.

Abstract

A competitive reverse transcription-polymerase chain reaction (RT-PCR) was developed to detect and to quantitate the RNA of group A rotaviruses. In the assay, a 433 bp fragment is amplified by a one-tube RT-PCR protocol using primers with binding sites located in a highly conserved region of segment 6 of the rotavirus genome. An in vitro synthesized RNA with a 43-base deletion with respect to the wild-type sequence of this fragment was used as an internal control. Using these transcripts as templates, 10 RNA molecules were amplified reproducibly and detected in ethidium bromide-stained agarose gels or by fluorimetry using the SYBR Green I dye in a real-time RT-PCR assay. The efficiency of the protocol was confirmed by the detection of small amounts of viral RNA of group A rotaviruses in clinical samples obtained from various animal species and man.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line
  • DNA Primers
  • Humans
  • Polymerase Chain Reaction / methods*
  • RNA, Viral / genetics
  • RNA, Viral / isolation & purification
  • Reverse Transcriptase Polymerase Chain Reaction*
  • Rotavirus / classification
  • Rotavirus / genetics*
  • Rotavirus / isolation & purification*
  • Sensitivity and Specificity
  • Sequence Deletion

Substances

  • DNA Primers
  • RNA, Viral