Evolutionary relationships among seventeen human papillomavirus genotypes.

The DNA and the protein sequences of the six major open reading frames (ORFs) of 17 human papillomavirus (HPV) genotypes have been carefully aligned. Conserved primary and probable secondary structural features of the proteins have been identified. From the analysis of variations in the aligned positions, the most consistent evolutionary relationships have been reconstructed for each gene and for the genomes as a whole. The L1 gene encoding the major capsid protein and the E1 gene encoding a replication protein are the most conserved. The hinge region in E2 is the most divergent. With varying degrees of sequence relatedness, the major groups and subgroups of HPV genotypes can be recognized, these clusters: the mucosotrophic virus types (33, 58), (16, (31, 35)), (18, 39), (51), (6b, 11); mucosal/cutaneous transitional virus types (2a, 57); and the cutaneous virus types (47, (5, 8)), (1a), (41), closely reflect epithelial tissue-type predilections and clinical pathogenicities.