Analysis of the genetic diversity and phylogenetic relationships of putative human papillomavirus types

J Gen Virol. 2013 Nov;94(Pt 11):2480-2488. doi: 10.1099/vir.0.055137-0. Epub 2013 Aug 30.


More than 170 human papillomavirus (HPV) types have been completely sequenced, curated and divided into five genera: Alphapapillomavirus, Betapapillomavirus, Gammapapillomavirus, Mupapillomavirus and Nupapillomavirus. With the application of PCR methods, hundreds of putative novel HPV types have been identified as PCR amplicons in mucosa and skin. However, at present there are no studies reporting a systematic search of the currently known L1 amplicons and their phylogenetic relationships. This survey revealed the existence of at least 202 different putative HPV types that are pending for full-genome characterization: five alphapapillomaviruses, 37 betapapillomaviruses, 159 gammapapillomaviruses and one mupapillomavirus. All potential viruses of the genera Alphapapillomavirus and Betapapillomavirus were grouped in the defined species, while 59 putative gammapapillomaviruses types were segregated in 21 unidentified putative species. These data highlight the need for progress in the identification of additional taxa of the family Papillomaviridae in order to elucidate the diversity, evolution and medical implications of these viruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphapapillomavirus / classification
  • Alphapapillomavirus / genetics
  • Betapapillomavirus / classification
  • Betapapillomavirus / genetics
  • Capsid Proteins / genetics
  • DNA Primers
  • DNA, Viral / analysis
  • DNA, Viral / genetics
  • Gammapapillomavirus / classification
  • Gammapapillomavirus / genetics
  • Genetic Variation*
  • Genome, Viral
  • Humans
  • Mupapillomavirus / classification
  • Mupapillomavirus / genetics
  • Oncogene Proteins, Viral / genetics
  • Papillomaviridae / classification*
  • Papillomaviridae / genetics*
  • Papillomavirus Infections / diagnosis
  • Papillomavirus Infections / epidemiology
  • Papillomavirus Infections / virology*
  • Phylogeny*
  • Polymerase Chain Reaction
  • Sequence Analysis, DNA


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