A catalog of human papillomavirus (HPV) type 16 (HPV-16) E6 and L1 signature nucleotides was used to develop PCR-based oligonucleotide probe systems capable of distinguishing HPV-16 class and subclass variants. Twenty-three E6-specific oligonucleotide probes targeting 13 variant nucleotide positions and 12 L1-specific oligonucleotide probes targeting 6 variant nucleotide positions were used to characterize HPV-16-containing cervicovaginal lavage specimens. Nucleotide positions that could be distinguished included E6 nucleotides 109, 131, 132, 143, 145, 178, 183, 286, 289, 335, 350, 403, and 532 and L1 nucleotides 6695, 6721, 6803, 6854, 6862, and 6994. Combined hybridization patterns were assigned on the basis of the predicted HPV-16 class, subclass, or minor class variants described previously (T. Yamada, C. M. Wheeler, A. L. Halpern, A.-C. M. Stewart, A. Hildesheim, and S.A. Jenison, J. Virol. 69:7743-7753, 1995). The major HPV-16 variant lineages detected included European prototype-like (E-P), Asian (As), Asian-American (AA), and African (Af1 and Af2) lineages. In addition, E-G131, an E-class variant, and AA-G183, an AA-class variant, were also identified. For each clinical specimen, DNA hybridization results were compared to nucleotide sequence determinations. Targeted L1 and E6 marker nucleotides covaried within all HPV-16 variant isolates examined. These hybridization-based methods result in minimal misclassification error, are amenable to targeting additional lineage-specific nucleotide positions, and should facilitate the large-scale, low-cost analysis of HPV-16 variants in epidemiologic investigations. Specifically, these methods will facilitate epidemiologic studies of HPV-16 transmission and natural history, as well as studies of associations between HPV variants, host immune responses, and cervical neoplasia.
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