The identification and taxonomy of papillomaviruses has become increasingly complex, as approximately 70 human papillomavirus (HPV) types have been described and novel HPV genomes continue to be identified. Methods and corresponding DNA sequence data bases were designed for the reliable identification of mucosal HPV genomes from clinical specimens. HPVs are identified by the amplification of a fragment of the L1 region by consensus primer polymerase chain reaction (PCR) and subsequent hybridization or restriction fragment length polymorphism analysis. L1 PCR fragments may be further characterized by nucleotide sequencing. Conservation of 30 (of 151) predicted amino acids identifies HPV genomic fragments, and nucleotide sequence alignments allow calculation of their phylogenetic relatedness. Sequence differences > 10% from any known HPV type suggest a novel HPV type. Phylogenetic relationships with known HPV types may permit predictions of biology. With these criteria, 10 PCR fragments were identified that would qualify as new genital HPV types after complete genomic isolation.

Human papillomaviruses (HPVs) are described as ''types'' based on their genome sequences and identified by a number. For example, HPV-6 is associated with genital warts, and HPV-16 with anogenital cancers. The genomes of many HPV types have been reisolated, sequenced and compared to reference ''prototypes'' countless times by laboratories throughout the world. It was found that each HPV type occurs in the form of ''variants'', identified by about 2% nucleotide differences in most genes and 5% in less conserved regions. Less than 100 variants of any HPV type have been detected, a scenario that is very different from the quasi-species formed by many RNA viruses. The variants of each HPV type form phylogenetic trees, and variants from specific branches are often unique to specific ethnic groups. Immigrant populations contain, depending on their respective ethnic origins, mixtures of variants. The absence of HPV genomes intermediate to specific types show that all HPV types existed already when humans became a species. Consequently, humans had always suffered from lesions like anogenital cancer, genital warts and common warts. A growing number of epidemiological, etiological and molecular data suggest that variants of the same HPV type are biologically distinct and may confer differential pathogenic risks. Since the distribution of some variants of HPV-16 and 18 correlates with the distribution of human populations that have an increased risk to develop anogenital cancer, the study of HPV type variation may point to one of the reasons for the higher incidence rates of these lesions in specific cohorts. ' 2005 Wiley-Liss, Inc.Key words: papillomavirus; evolution; epidemiology; etiology Papillomavirus (PV) genomes comprise 8 kb of doublestranded, circular DNA with 8 protein-coding genes (L1 and L2 that encode capsid proteins and E1, E2, E4, E5, E6 and E7 that encode proteins involved in replication, transcription and transformation) and a noncoding, regulatory long control region (LCR). The genomes of PVs change by point mutations, deletions and insertions just like those of their hosts. Mutations occur fortuitously but can become established in a population if there is some mechanism that positively selects for the mutant, or, if they are functionally neutral, by selective expansion of the host population infected with the mutant (genetic drift). DNA genomes change much slower than RNA genomes, because of the proofreading abilities of DNA polymerases. As an example, the most remotely related PV genomes have a nucleotide diversity of about 50%, established during coevolution with their mammalian hosts over millions of years. By contrast, the RNA-based HIV-1 genomes within a single AIDS patient can diverge to a similar extent during a 10-year-infection. PV genomes are further stabilized by the apparent absence of inter-and intra-type recombination. Diversification of PV genomes is also limited by the slow replication of the virus in synchrony with division of the host epithelial cells. Since the replication rate of ep...

The upstream regulatory region of the human papilloma virus‐16 (HPV‐16) genomic DNA contains a sequence element with a large degree of homology to the partially palindromic sequence GGTACANNNTGTTCT, which is the consensus sequence of the glucocorticoid responsive elements of known genes regulated by this steroid hormone. DNase I and dimethylsulfate protection experiments reveal the binding of this sequence by rat glucocorticoid receptor protein. A 400‐bp DNA segment centrally containing this sequence confers strong inducibility by dexamethasone to the promoter p97 of HPV‐16 and to the Herpes simplex virus thymidine kinase promoter, as judged by chloramphenicol acetyltransferase activity and RNase protection assays. The same DNA segment, that does not contain the consensus sequences of all papilloma viruses relevant for E2 protein‐mediated transcription enhancement, functions in an enhancer‐like fashion in addition to its glucocorticoid responsive action. This hormone‐independent transcription enhancement is absent in human MCF7 cells, but is strong in human HeLa cells where the combined activity of the constitutive and the steroid hormone‐dependent enhancer elements stimulate transcription by a factor of 500. This cell type specificity of the HPV‐16 enhancer may be responsible for the tissue tropism of the virus. These observations and the presence of numerous homologies to known enhancers of cellular and viral genes suggest a complex pattern of activation of the human papilloma virus‐16 promoters.