IDENTIFICATION AND ASSESSMENT OF KNOWN AND NOVEL HUMAN PAPILLOMAVIRUSES BY POLYMERASE CHAIN-REACTION AMPLIFICATION, RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS, NUCLEOTIDE-SEQUENCE, AND PHYLOGENETIC ALGORITHMS
Hu. Bernard et al., IDENTIFICATION AND ASSESSMENT OF KNOWN AND NOVEL HUMAN PAPILLOMAVIRUSES BY POLYMERASE CHAIN-REACTION AMPLIFICATION, RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISMS, NUCLEOTIDE-SEQUENCE, AND PHYLOGENETIC ALGORITHMS, The Journal of infectious diseases, 170(5), 1994, pp. 1077-1085
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.