Prospective studies of the persistence of human papillomavirus (HPV) variants are rare and typically small. We sequenced HPV-16 variants in longitudinal pairs of specimens from 86 women enrolled in the ASCUS-LSIL Triage Study.A change of variants was identified in 4 women (4.7% [95% confidence interval, 1.3%-11.5%]). Among women with intervening HPV results ( ), a variant switch occurred n p 60 in 2 of 11 who had evidence of intervening negativity for HPV-16, compared with 1 of 49 who consistently tested positive ( ). These results suggest the possibility that rare P p .11 misclassification of transient infections as persistent infections occurs in natural history studies of type-specific HPV infections.Studies of the natural history of human papillomavirus (HPV) infection define viral persistence at a type-specific level-that is, as the same genotype of HPV DNA detected during a certain time period. Intervening negativity is usually assumed to be the result of fluctuation in viral DNA load to below a detectable threshold [1]. In practice, it is difficult to distinguish typespecific persistence from recurrent infection.In light of the intratypic diversity of the HPV genome [2], the persistence of type-specific HPV infection may be better defined by analyses of nucleotide alterations in viral isolates [3]. For any given type of HPV, isolates that differ by !2% in the DNA sequence of the L1 (conserved major capsid) gene are designated as variants. Because HPV evolution is slow (genetic drift occurs at approximately the same rate as in the human genome) [4], spontaneous mutations in HPV variants during the life span of infected hosts occur extremely rarely. Accordingly, different variants in consecutive samples from an individual most likely represent separate infections.In the present study, we compared sequence variations in HPV-16 variants in pairs of specimens collected prospectively from a subset of women who were enrolled in a nested casecontrol study investigating the clinical relevance of HPV-16 variants.Methods. Cervical samples examined were from the casecontrol study of women enrolled in the ASCUS-LSIL Triage Study (ALTS), a randomized, multicenter, clinical trial designed to evaluate strategies for the management of equivocal and mildly abnormal cervical cytology. These women were followed semiannually over 2 years for HPV typing and detection of cervical lesions. A detailed description of the ALTS design and study population has been presented elsewhere [5].Case patients were women who had (1) cervical intraepithelial neoplasia grade 2 or 3 (CIN2-3) initially diagnosed during follow-up and (2) HPV-16 DNA detected by polymerase chain reaction (PCR)-based reverse line blot [6] at follow-up visits concurrent with or before the diagnosis of CIN2-3. Control patients were selected from those who did not have a diagnosis of CIN2-3 during the entire study period and had HPV-16 DNA detected at 1 or more follow-up visits. The study protocol was approved by the institutional human subject review board of the Unive...