In the current release, PAVE contains only sequences from reference or prototype genomes. PAVE will host variant sequences in the future, when a robust and uniform nomenclature has been adopted.

Variant Nomenclature

Papillomavirus genomes with < 10% nucleotide sequence difference from the L1 ORF in the reference genome have been named subtypes or variants. The ICTV Papillomavirus Study Group recently proposed classification and nomenclature criteria for papillomavirus variants.

  • Sequence difference between variants is calculated using the entire genomic sequence.
  • Distinct variant lineages have approximately 1.0% nucleotide sequence difference.
  • Sub-lineages have 0.5% - 1.0% nucleotide sequence difference.
  • Each variant lineage is named with an alphanumeric value. The prototype or reference genome is always in variant lineage A and sublineage A1.

For more information, see Chen et al., 2011

Variant Nomenclature tree from Chen et al., 2009

Reproduced with permission from the American Society for Microbiology from Chen et al., 2009