Sensitive detection of multiple rotavirus genotypes with a single reverse transcription-real-time quantitative PCR assay

J Clin Microbiol. 2008 Aug;46(8):2547-54. doi: 10.1128/JCM.02428-07. Epub 2008 Jun 4.

Abstract

Rotaviruses are one of the major causes of diarrhea in infants and children under 5 years old, especially affecting developing countries. In natural disasters, fecal matter and potable waters can mix, allowing low, yet infective, concentrations of rotavirus to be present in water supplies, constituting a risk for the population. Any of the most commonly detected rotavirus genotypes could originate an outbreak. The development of a fast and sensitive method that could detect the broadest possible range of rotavirus genotypes would help with efficient diagnosis and prevention. We have designed a reverse transcription (RT)-real-time quantitative PCR approach targeted to the rotaviral VP2 gene, based on a multiple-sequence alignment of different human rotaviral strains. To overcome the high nucleotide sequence diversity, multiple forward and reverse primers were used, in addition to a degenerate probe. The performance of the assay was tested on isolates representing the most prevalent human genotypes: G1P[8], G2P[4], G3P[8], G4P[8], G9P[8], and G12P[8]. The developed method improved classical rotavirus detection by enzyme-linked immunosorbent assay and nested RT-PCR by 5 and at least 1 order of magnitude, respectively. A survey of 159 stool samples indicated that the method can efficiently detect a broad range of rotavirus strains, including different G-P genotype combinations of human, porcine, and bovine origin. No cross-reactivity was observed with other enteric viruses, such as astrovirus, sapovirus, and norovirus.

Publication types

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

MeSH terms

  • Base Sequence
  • Capsid Proteins / genetics
  • Child, Preschool
  • Feces / virology
  • Humans
  • Infant
  • Infant, Newborn
  • Molecular Sequence Data
  • Oligonucleotide Probes / genetics
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Rotavirus / classification*
  • Rotavirus / isolation & purification*
  • Rotavirus Infections / diagnosis*
  • Rotavirus Infections / virology*
  • Sensitivity and Specificity
  • Sequence Alignment
  • Virology / methods*

Substances

  • Capsid Proteins
  • Oligonucleotide Probes
  • VP2 protein, Rotavirus