Phylogeny and Taxonomy of Papillomaviruses.
from: Papillomavirus Research: From Natural History To Vaccines and Beyond (Edited by: M. Saveria Campo). Caister Academic Press, U.K. (2006)
Papillomaviruses (PVs) have similar genomic organizations, and any pair of two PVs contains at least five homologous genes, although the nucleotide sequence may diverge by more than 50%. Phylogenetic algorithms that permit to compare homologies led to phylogenetic trees that have a similar topology independently of the gene analyzed. Phylogenetic studies strongly suggest that PVs normally evolve together with their mammalian and bird host species, do not change host species, do not recombine, and have maintained their basic genomic organization for a period exceeding 100 million years. These sequence comparisons have laid the foundation for a PV taxonomy, which is now officially recognized by the International Committee on Taxonomy of Viruses. All PVs form the family "Papillomaviridae", which is distinct from the "Polyomaviridae" thus eliminating the term "Papovaviridae". Major branches of the phylogenetic tree of all PVs are considered as "genera", which are identified by Greek letters. Minor branches are considered "species" and unite PV types that are genomically distinct without exhibiting known biological differences. This new taxonomic system does not affect the traditional identification and characterization of PV "types" and their independent isolates with minor genomic differences, referred to as "subtypes" and "variants", all of which are taxa below the level of "species". Understanding the tremendous diversity of PV types, the worldwide distribution of variants of individual human PV (HPV) types, and their potential pathogenic distinctions, continue to be challenges for phylogenetic research and etiological considerations read more ...