HUMAN PAPILLOMAVIRUS TYPE-16 SEQUENCE VARIANTS - IDENTIFICATION BY E6AND L1 LINEAGE-SPECIFIC HYBRIDIZATION

A catalog of human papillomavirus (HPV) type 16 (HPV-16) E6 and L1 sig nature 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 targeti ng 6 variant nucleotide positions were used to characterize HPV-16-con taining cervicovaginal lavage specimens. Nucleotide positions that cou ld be distinguished included E6 nucleotides 109, 131, 132, 143, 145, 1 78, 183, 286, 289, 335, 350, 403, and 532 and L1 nucleotides 6695, 672 1, 6803, 6854, 6862, and 6994. Combined hybridization patterns were as signed on the basis of the predicted HPV-16 class, subclass, or minor class variants described previously (T. Yamada, C. M. Wheeler, A. L. H alpern, A.-C. M. Stewart, A. Hildesheim, and S. A. Jenison, J. Virol. 69:7743-7753, 1995). The major HPV-16 variant lineages detected includ ed European prototype-like (E-P), Asian (As), Asian-American (AA), and African (Af1 and Af2) lineages. In addition, E-G131, an E-class varia nt, and AA-G183, an AA-class variant, were also identified. For each c linical specimen, DNA hybridization results were compared to nucleotid e sequence determinations. Targeted L1 and E6 marker nucleotides covar ied within all HPV-16 variant isolates examined. These hybridization-b ased methods result in minimal misclassification error, are amenable t o targeting additional lineage-specific nucleotide positions, and shou ld facilitate the large-scale, low-cost analysis of HPV-16 variants in epidemiologic investigations. Specifically, these methods will facili tate epidemiologic studies of HPV-16 transmission and natural history, as well as studies of associations between HPV variants, host immune responses, and cervical neoplasia.