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Principles of classification based on genotype
PVs genomes are fairly static: sequence changes by mutation or recombination are rare events and apparently occur at frequencies not very different from those of the DNA genomes of the infected host organisms. Maximum divergence occurs between viruses sampled from ethnic groups that evolved for a long time without interactions, for example Africans and American Indians. It leads to the conclusion that each HPV type was with the human species since our origin, and evolved and spread together with the infected cohort. There was never time or an ethnic group without common warts, genital warts, etc. The following taxonomic groups of PVs were developed:
- Genera Genera are designated by a Greek letter, for example Alphapapillomavirus. Presently there are 16 genera of papillomaviruses which are identified by Greek letters. The clinically most important genus is referred as alpha-papillomaviruses. It contains all HPV types associated with mucosal and genital lesions.
- Species Species are designated by a number, for example, Human papillomavirus - 10
- Types Types are designated by alphanumeric characters, for example, Human papillomavirus type 28. Currently more than 100 types of papillomaviruses were identified. First PV types were isolated in 1970’s. L1 ORF is most conserved gene within the PVs genome and has therefore been used for the identification of new PV types over the past decades. New type is defined when the L1 sequence differs more than 10% from the closest known PV type. The type is assigned after isolation and characterization of the complete genome.
- Subtypes Differences between 2% and 10% homology define a subtype.
- Variants Differences less than 2% define a variant.
