A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples

Arch Virol. 2017 Feb;162(2):477-486. doi: 10.1007/s00705-016-3131-1. Epub 2016 Nov 3.

Abstract

Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.

MeSH terms

  • Base Sequence
  • Gene Expression
  • Genotype
  • Humans
  • Observer Variation
  • Phylogeny
  • RNA, Viral / genetics*
  • Real-Time Polymerase Chain Reaction / methods*
  • Real-Time Polymerase Chain Reaction / standards
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Reverse Transcriptase Polymerase Chain Reaction / standards
  • Rubella / diagnosis*
  • Rubella / virology
  • Rubella virus / classification
  • Rubella virus / genetics*
  • Rubella virus / isolation & purification
  • Sensitivity and Specificity
  • Sequence Alignment
  • Viral Proteins / genetics*

Substances

  • RNA, Viral
  • Viral Proteins