Classification of papillomavirus types is based on the DNA sequence of the L1 gene. See de Villiers et al., 2004 and Bernard et al., 2010 for details.

New types: Must have a completely cloned genome and the DNA sequence of the L1 region must differ by >10% of the closest known type. The PaVE L1 Taxonomy Tool is available to assist you in gauging the probability that your sequence is a novel PV type.

Variants: < 2% sequence difference from a known type

Genera: Members of the same genus share >60% nucleotide sequence identity in the L1 ORF.

Species: The PV types within a species share between 71% and 89% nucleotide identity within the complete L1 ORF.

New Genomes can be compared against existing papillomaviridae members using
NCBI PASC tool(currently for complete genomes only)

Non-reference genomes: To be recognized as a novel papillomavirus type, a viral genome has to fulfill a strict set of requirements (For details See de Villiers et al., 2004 and Bernard et al., 2010). These requirements are:

  1. The entire viral genome must be cloned (overlapping fragments is OK).
  2. The L1 sequence cannot share more than 90% nucleotide sequence identity with its closest neighbor.
  3. The cloned genome must be submitted to, and reviewed by, the International Human Papillomavirus Reference Center or the Animal Papillomavirus Reference Center.
Because of recent advances in Next-Gen sequencing, several putative novel genomes have been described (for a review see de Villiers, 2013) that do not meet all these requirements, and will therefore not be recognized as novel viral types by the International Human Papillomavirus Reference Center. However, in order to reflect the known papillomavirus diversity PaVE has chosen to include viruses that meet the "90% sequence identity" rule, even if they do not meet the other criteria. Throughout the PaVE database these viruses will be identified by the appendix "nr" (e.g. HPV-XXXXnr). PaVE tools contain a filter to enable inclusion or exclusion of these "non-reference" viruses.