Biased amplification of human papillomavirus DNA in specimens containing multiple human papillomavirus types by PCR with consensus primers

Cancer Sci. 2011 Jun;102(6):1223-7. doi: 10.1111/j.1349-7006.2011.01922.x. Epub 2011 Mar 30.


Genotyping human papillomavirus (HPV) in clinical specimens is important because each HPV type has different oncogenic potential. Amplification of HPV DNA by PCR with the consensus primers that are derived from the consensus sequences of the L1 gene has been used widely for the genotyping. As recent studies have shown that the cervical specimens often contain HPV of multiple types, it is necessary to confirm whether the PCR with the consensus primers amplifies multiple types of HPV DNA without bias. We amplified HPV DNA in the test samples by PCR with three commonly used consensus primer pairs (L1C1/L1C2+C2M, MY09/11, and GP5+/6+), and the resultant amplicons were identified by hybridization with type-specific probes on a nylon membrane. L1C1/L1C2+C2M showed a higher sensitivity than the other primers, as defined by the ability to detect HPV DNA, on test samples containing serially diluted one of HPV16, 18, 51, 52, and 58 plasmids. L1C1/L1C2+C2M failed to amplify HPV16 in the mixed test samples containing HPV16, and either 18 or 51. The three consensus primers frequently caused incorrect genotyping in the selected clinical specimens containing HPV16 and one or two of HPV18, 31, 51, 52, and 58. The data indicate that PCR with consensus primers is not suitable for genotyping HPV in specimens containing multiple HPV types, and suggest that the genotyping data obtained by such a method should be carefully interpreted.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphapapillomavirus / classification
  • Alphapapillomavirus / genetics*
  • Alphapapillomavirus / isolation & purification*
  • Base Sequence
  • Capsid Proteins / genetics
  • Cervix Uteri / virology*
  • Consensus Sequence
  • DNA Primers
  • DNA, Viral / analysis
  • DNA, Viral / genetics*
  • Female
  • Gene Amplification
  • Genotype
  • Humans
  • Oncogene Proteins, Viral / genetics
  • Papillomavirus Infections / virology*
  • Polymerase Chain Reaction*
  • Uterine Cervical Diseases / virology


  • Capsid Proteins
  • DNA Primers
  • DNA, Viral
  • Oncogene Proteins, Viral