IDENTIFICATION AND ASSESSMENT OF KNOWN AND NOVEL HUMAN PAPILLOMAVIRUSES BY POLYMERASE CHAIN-REACTION AMPLIFICATION, RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS, NUCLEOTIDE-SEQUENCE, AND PHYLOGENETIC ALGORITHMS

The identification and taxonomy of papillomaviruses has become increas ingly complex, as similar to 70 human papillomavirus (HPV) types have been described and novel HPV genomes continue to be identified. Method s and corresponding DNA sequence data bases were designed for the reli able identification of mucosal HPV genomes from clinical specimens. HP Vs are identified by the amplification of a fragment of the L1 region by consensus primer polymerase chain reaction (PCR) and subsequent hyb ridization or restriction fragment length polymorphism analysis. L1 PC R fragments may be further characterized by nucleotide sequencing. Con servation of 30 (of 151) predicted amino acids identifies HPV genomic fragments, and nucleotide sequence alignments allow calculation of the ir phylogenetic relatedness. Sequence differences >10% from any known HPV type suggest a novel HPV type. Phylogenetic relationships with kno wn HPV types may permit predictions of biology. With these criteria, 1 0 PCR fragments were identified that would qualify as new genital HPV types after complete genomic isolation.