Nucleotide and amino acid sequence variation in the L1 and E7 open reading frames of human papillomavirus type 6 and type 16

Nucleotide sequences and further characterization of human papillomavirus DNA present in the CaSki, SiHa and HeLa cervical carcinoma cell lines.

“…It is clear from these results that most, if not all, of the 60-600 distinct HPV-16 variant copies in CaSki cells (Baker et al, 1987 ;Callahan et al, 1992) are derived from the same HPV DNA. No heterogeneity was observed at any nucleotide position in any of the amplicons, and no conflicts were found with previous PCR-based partial CaSki HPV-16 sequence determinations (Chan et al, 1992 ;Icenogle et al, 1991 ;Xi et al, 1997 ;D. Galutira, personal communication), further supporting the genetic homogeneity of the CaSki HPV-16 variant.…”

“…1 lists the 30 point mutations and the single 1 nt deletion in CaSki HPV-16 relative the to HPV-16R reference sequence. Seven of these point mutations have been previously noted in CaSki HPV-16 partial sequence determinations using PCR-based methods (Chan et al, 1992 ;Icenogle et al, 1991 ;Xi et al, 1997 ;D. Galutira, personal communication).…”

Diversifying Selection in Human Papillomavirus Type 16 Lineages Based on Complete Genome Analyses

“…Of the high-risk HPV types associated with cervical cancer, HPV16 is the most prevalent and is found in approximately half of all cancers (7, 49). Numerous variants of HPV16 have been identified in different geographic locations and ethnic groups (35,42,53,68). Although all HPV16 isolates are closely related, previous studies inferred five distinct phylogenetic branches among HPV16 variants: European (E), Asian (As), Asian-American (As-Am), African-1 (Af-1), and African-2 (Af-2), corresponding to the geographic locations from which the samples were obtained (12,34).…”

High Level of Correlation of Human Papillomavirus-16 DNA Viral Load Estimates Generated by Three Real-time PCR Assays Applied on Genital Specimens

“…However, L1 sequence data are available from a limited number of isolates and four sites of polymorphism have been described in the probe sequence (nucleotides 6862, 6864, 6865, and 6868) in European, Asian American, and African variants (46,48,(55)(56)(57)(58). Three sites of polymorphism have been described in the area hybridizing with the upper primer (nucleotides 6567, 6582, and 6576) and could impede amplification with the HPV-16 L1 assay (57,59). When devising quantitative real-time PCR assays, great care should be taken to first characterize the genomic polymorphism of the HPV type targeted by the assay to ensure that differences in HPV DNA quantity or viral load are not due to impaired binding of probe or primers to HPV DNA rather than due to a truly lower HPV viral load.…”