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
PaVE BLAST
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: