Novel light-upon-extension real-time PCR assay for simultaneous detection, quantification, and genogrouping of group A rotavirus

J Clin Microbiol. 2010 May;48(5):1859-65. doi: 10.1128/JCM.02288-09. Epub 2010 Mar 10.

Abstract

We have developed a light-upon-extension (LUX) real-time PCR assay for detection, quantification, and genogrouping of group A rotavirus (RV), the most common cause of acute gastroenteritis in children. The LUX system uses a fluorophore attached to one primer and having a self-quenching hairpin structure, making it cost-effective and specific. We designed genogroup-specific primers having different fluorophores, making it possible to differentiate between the two main genogroups of human group A RVs. The assay was applied on clinical stool specimens from Sweden and Central America (n=196) and compared to immunological and conventional PCR assays. The genogrouping ability was further validated against a subset of clinical specimens, which had been genogrouped using monoclonal antibodies. Our real-time PCR assay detected and quantified all positive specimens (n=145) and exhibited higher sensitivity than immunological assays and conventional PCR. The assay exhibited a wide dynamic range, detecting from 5 to >10(7) genes per PCR, resulting in a theoretical lower detection limit of <10,000 viruses per gram of stool. No cross-reaction was observed with specimens containing norovirus, sapovirus, astrovirus, or adenovirus. In total, 22 (15%) of the positive clinical specimens were identified as genogroup I, 122 (84%) were identified as genogroup II, and 1 specimen was found to contain a mix of both genogroups. All genogroup I-positive specimens were associated with capsid glycoprotein 2 (G2). No significant difference in viral load was found between genogroups or geographic region. The detection and quantification, combined with the genogrouping ability, make this assay a valuable tool both for diagnostics and for molecular epidemiological investigations.

Publication types

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

MeSH terms

  • Central America
  • DNA Primers / chemistry
  • DNA Primers / genetics
  • Feces / virology
  • Fluorescence
  • Fluorometry / methods
  • Genotype
  • Humans
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Rotavirus / classification*
  • Rotavirus / genetics
  • Rotavirus / isolation & purification*
  • Rotavirus Infections / diagnosis*
  • Rotavirus Infections / virology
  • Sensitivity and Specificity
  • Sweden
  • Viral Load / methods*

Substances

  • DNA Primers