Results

All 505 women contributed four study visits each over the 1st year; however, there were missing samples for eight women (1.6%) at the 4-month visit and for twelve women (2.4%) at the 8-month visit, for a final total of 2000 study visits with samples. All available samples were valid (positive for either β-globin or HPV). Baseline characteristics of the subcohort have previously been reported;19 the mean age was 33.5 years (range: 18–57) and most women were married (49%) or living as married (33%). There were 281/2000 (14%) samples positive for any betapapillomavirus across all study visits. The prevalence and incidence of individual betapapillomaviruses are presented in Table 1. The most prevalent and incident types were HPV38, HPV21, HPV5, HPV22, and HPV8, respectively; these were the only types with a time-averaged prevalence above 1%.
We observed significant clustering within HPV genera (Table 2). Over the four visits, we observed 44 samples positive for two or more alphapapillomavirus types, and 56 samples positive for two or more betapapillomavirus types. This represents respectively 1.74 (95%CI 1.26-2.44) times more alphapapillomavirus type co-detections than expected and 2.24 (95%CI 1.65-3.29) times more betapapillomavirus type co-detections than expected when assuming independence of types. The betapapillomavirus types most often found in co-detection with others were also the most commonly detected types (HPV 38, HPV21, HPV5, HPV22, and HPV8).
Conversely, there were fewer than expected co-detections of alphapapillomaviruses and betapapillomaviruses (Table 2). Over the four visits, we observed 33 samples positive for both an alphapapillomavirus and a betapapillomavirus type together. This represents 0.64 (95%CI 0.51-0.83) times fewer cross-genus co-detections than expected when assuming independence of all types. After accounting for the within-genus expected clustering of both genera, this represented 0.80 (95%CI 0.62-1.06) times fewer cross-genus detections than expected when assuming cross-genus independence.
Cross-sectional and prospective associations between betapapillomavirus positivity, alphapapillomavirus positivity, and sexual risk factors are presented in Table 3 and Table 4. Samples were somewhat less likely to be positive for alphapapillomavirus types if a betapapillomavirus type was present (OR 0.73, 95%CI 0.50-1.07). They were also somewhat less likely to be positive for betapapillomavirus types if an alphapapillomavirus type was present (OR 0.79, 95%CI 0.56-1.12), but neither of these associations were significant. Women were also less likely to become newly positive for alphapapillomavirus types if a betapapillomavirus type was present at the previous visit (HR 0.84, 95%CI 0.49-1.43), and were less likely to become newly positive for betapapillomavirus types if an alphapapillomavirus type was present at the previous visit (HR 0.72, 95%CI 0.45-1.15), but these associations were also not significant. Alphapapillomavirus prevalence and incidence were strongly associated with age, increasing lifetime number of sex partners, and having new sex partners in the previous interval. Conversely, betapapillomavirus prevalence and incidence were not associated with age, and were inversely correlated with the number of lifetime sex partners. While having a new sex partner in the previous interval was not associated with prevalence or incidence, having sex with any partner in the previous interval was associated with a higher incidence of betapapillomavirus (HR 1.56, 95%CI 1.00-2.46). Multivariable adjustment did not change these associations.