Detection and differentiation of human papillomavirus genotypes HPV-6 and HPV-11 by FRET-based real-time PCR

J Virol Methods. 2008 Nov;153(2):245-9. doi: 10.1016/j.jviromet.2008.07.014. Epub 2008 Sep 4.


A real-time PCR (RT-PCR) assay was developed based on fluorescence resonance energy transfer (FRET) hybridization probe technology, allowing very sensitive and specific detection of HPV-6 and HPV-11, reliable differentiation of HPV-6 and HPV-11, as well as prototypic and non-prototypic HPV-6 genomic variants, in a single PCR reaction. The primers and probe were designed on the basis of multiple alignments of 74 HPV-6 E2 gene sequences and 20 HPV-11 E2 gene sequences. Testing on defined plasmid standards showed that the RT-PCR allowed simple and reliable identification of HPV-6 and HPV-11 using type specific amplification followed by probe-specific post-amplification dissociation analysis. Sensitivity, assessed by probit analysis at a 95% detection level, was 42.9, 43.4, and 25.3 DNA copies per assay for prototypic and non-prototypic HPV-6 variants and HPV-11, respectively. The results obtained by the developed assay on 51 HPV DNA-negative samples and 149 HPV DNA-positive samples, including 81 HPV-6 positive samples (19 prototypic and 62 non-prototypic HPV-6 variants), 28 HPV-11 positive samples, 10 samples of HPV-44 and HPV-74 (the closest relatives of HPV-6 and HPV-11) and 30 samples of 15 other important alpha HPV, showed complete agreement with those obtained with the INNO-LiPA human papillomavirus (HPV) Genotyping Assay and HPV-6 E2 and E6 gene sequencing.

Publication types

  • Evaluation Study

MeSH terms

  • DNA Primers
  • Female
  • Fluorescence Resonance Energy Transfer / methods*
  • Genotype
  • Human papillomavirus 11* / classification
  • Human papillomavirus 11* / genetics
  • Human papillomavirus 11* / isolation & purification
  • Human papillomavirus 6* / classification
  • Human papillomavirus 6* / genetics
  • Human papillomavirus 6* / isolation & purification
  • Humans
  • Papillomavirus Infections / virology
  • Polymerase Chain Reaction / methods*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Viral Proteins / genetics


  • DNA Primers
  • E2 protein, Human papillomavirus type 11
  • Viral Proteins