Papillomavirus classification system

Overview:

Taxonomic level	Criteria	Number
Genera	Less than 60% nt identity in entire L1 ORF	18 genera (alpha to sigma)
		2 additional new genera, yet unnamed (containing TtPV2 and RaPV1 respectively)
Species	Between 60% and 70% nt identity in L1	From 1 species (in most genera) up to 15 species (in genus alpha)
Genotypes	Between 71 and 89 % nt identity in L1	Currently 120 papillomavirus genotypes completely genomically characterized and available in Genbank (98 human: HPV; 32 non-human)
Subtypes	Between 90 and 98 % identity in L1	Very rare
Variants	More than 98 % identity in L1

Remarks:

- For a novel papillomavirus sequence to be classified as a new genotype, the complete genome has to be cloned and the L1 ORF has to differ by more than 10% from the closest known PV type.

 

Genetic regions suitable for classification:

Current classification is based on sequence identity in the L1 ORF because:

- The L1 ORF is the most conserved gene within the genome, and has been used for identification of new PV genotypes over past decades.

- Almost all subgenomic PCR amplicons that are generated with the currently available consensus or degenerate primer sets are located within the L1 ORF.

 

Reasons why other genomic regions are not used for classification:

- Some ORFs are not present in all papillomaviruses: E4, E5, E6 and E7 are lacking in some PVs.

- The E1, E2, E4, E4, E5, E6, E7 and L2 ORFs are all less conserved than L1, making reliable alignment of these ORFs difficult for PVs belonging to different genera, and only short conserved parts of these ORFs can be reliably aligned.

 

Reference:

de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H. Classification of papillomaviruses. Virology. 2004 Jun 20;324(1):17-27.