Sequence variation in the extreme 5' end of the human papillomavirus type 6a long control region

A sequence analysis of human papillomavirus (HPV) type 6a isolates from 15 exophytic condylomata acuminata lesions was done to determine the prototype sequence for this region of HPV 6a, which sequences are conserved and which vary, and whether the variability might be useful in epidemiologic studies. The long control region (LCR) was amplified by the polymerase chain reaction and approximately 242 bp were directly sequenced. The data indicate that all isolates contain a 94-bp insertion relative to prototype HPV 6b and confirm that this insertion should be considered a part of the HPV 6 LCR. Seven of the 15 isolates were in 1 group, and the rest were distributed among 4 groups. There was no strong correlation between DNA group and location of lesion, sex of patient, or pregnancy status. In addition, although there was variation among isolates, a region implicated by deletional analysis to have transcriptional silencing activity was conserved.