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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Cancer Epidemiol Biomarkers Prev. Author manuscript; available in PMC 2011 August 19.
Published in final edited form as:
PMCID: PMC3158656

Determinants of incidence and clearance of high-risk HPV infections in rural Rakai, Uganda



We used self-administered vaginal swabs to assess the incidence and clearance of carcinogenic HPV infections in rural Rakai, Uganda.


Women provided self-administered vaginal swab at annual, home-based visits. Type-specific carcinogenic HPV incidence and clearance, and risk-factors were assessed.


Carcinogenic HPV incidence was 17.3/100 person-years (PY) among HIV-positive, compared with 7.0/100 PY among HIV-negative women (p<0.001). HPV-51 had the highest incidence followed by HPV-16 (1.8/100 PY, and 1.5/100 PY, respectively). In multivariate model, HIV-positive women were twice as likely to have incident infection compared to HIV-negatives. Younger women were at higher risk for incident infection, as were women with higher lifetime and recent sexual partners, and high perception of AIDS. Married women were less likely to have incident infection. Approximately half of all carcinogenic HPV infections cleared over the study follow-up of three years. HPV-31, 35, and 16 had the lowest clearance (16.7%, 27.9%, and 38.3%, respectively). In multivariate model, HIV-positives, women over 30, higher HPV viral burden, and more lifetime sex partners were less likely to clear infections.


Self-collected vaginal swabs provide accurate HPV exposure assessment for studying the HPV exposure and epidemiology, and can be an important tool for research in populations unwilling to undergo pelvic exam.

Keywords: HIV, incident, clearance, risk factors, carcinogenic HPV


Human papillomavirus (HPV) is the etiologic agent for cervical cancer and the most common viral sexually transmitted infection (STI). HPV infections represent a major public health problem worldwide as a cause of cervical cancer in women, genital warts in men and women, other anogenital cancers, and some nasopharyngeal cancers. Acquisition of HPV is especially common among young sexually active adolescents with 3 year cumulative incidence estimated at more than 40% 19;42;43. While HPV point prevalence is very high, most clear spontaneously, especially among young women 16;23, however, persistent infection with high-risk HPV types is considered the crucial step in the development of cervical cancer 34.

As a consequence of cervical cytology screening, cervical cancer incidence and mortality has been drastically reduced in developed counties, while such a decline has not occurred in less developed countries where 80% of cervical cancers occur. Beyond lack of, or inadequate coverage of screening programs 33,11 in developing countries, women rarely present for a routine pelvic exam if they are asymptomatic for disease. Hence, to increase screening coverage in settings with low compliance for pelvic-exam based screening, use of self-collected vaginal swabs has been widely advocated and evaluated in the literature 4;5;8;10;12;15;18;20-22;26;27;32;35;44 showing good agreement between self-collected vaginal swabs and clinician-collected cervical swabs for HPV DNA detection. This allows self-collection of vaginal samples to be used as a screening tool for HPV. Furthermore, the possibility of primary prevention of HPV infection and thus cervical cancer via HPV vaccination has been realized. Information on the epidemiology of HPV in understudied regions is fundamental to planning and evaluating future vaccine implementation programs. Finally, the prevention of HPV and cervical cancer is of particular urgency in Africa where there are an estimated 17 million women living with HIV 2.

We previously showed comparable HPV DNA detection from self-collected vaginal and physician-collected cervical swabs in this population 29. To investigate the utility of self-collected vaginal swabs beyond screening, in this analysis our objective was to investigate the epidemiology (incidence and clearance) of HPV using self-collected vaginal swabs from a general rural African population. If our findings, based on self-collected vaginal samples, are similar to findings from other studies of the natural history of HPV which relied on clinician obtained cervical samples, self-sampling could represent an acceptable and valid alternative for epidemiologic studies in the developing world where low compliance with pelvic exams may lead to self-selection of participants and a reluctance to provide repeat samples for research studies. Further, self-sampling may provide an efficient way to monitor vaccine effectiveness in these high-risk populations.

Materials and Methods

Study Population

Participants were from the ongoing Rakai Community Cohort Study (RCCS), described in detail elsewhere 41. Briefly, the RCCS conducts annual home-based surveys, with comprehensive interviewer-administered questionnaires on sociodemographic, behavioral and health characteristics, on an average population of 12,000 adults aged 15-49 years. Biological samples are collected following the interview. Venous blood is collected for HIV-1, syphilis, and herpes simplex type 2 (HSV-2) serology. Starting in 1998, self-collected vaginal swabs were obtained during routine follow-up visits. Consenting women were asked to provide a self-collected vaginal sample at home, using the Digene sampler kit, with a Dacron swab. Women were asked to squat and insert a sterile 20-cm Dacron swab into the vagina up to the vault, and to rotate the swab 3 times in the vaginal vault. The swab was then placed in 1 ml standard transport media (STM); (Digene Corporation, Gaithersburg, MD), and kept on ice until transported back to the field laboratories and frozen at -80 °C. All samples were periodically shipped to Johns Hopkins University and stored at -80°C until the time of assay.

While majority (over 85%) of women provided self-collected vaginal swabs at each Rakai follow-up visit, for this longitudinal study, our analytic sample was comprised of women who provided 3-4 self-collected swabs at consecutive follow-up visits.

The study was approved by Institutional review Boards in Uganda and at Johns Hopkins and Columbia universities.

Laboratory Analyses

HIV serology

The HIV status of each participant was determined using two enzyme immunoassays (EIAs) (Vironostika HIV-1, Organon Teknika, Charlotte, NC and Cambridge Biotech, Worcester, MA), and discordant EIA results or new seroconversions were confirmed by Western blot (HIV-1 Western Blot, Bio-Merieux-Vitek, St.Louis, MO).

HPV detection and genotyping

HPV status was determined using a two-stage approach. First, using hybrid capture-2 (HC2); (Digene Corporation, Gaithersburg, MD), all samples were screened for the presence of 13 carcinogenic HPV genotypes most clinically relevant to cervical pre-malignant and malignant lesions. Subsequently, all HC2 HPV-positive samples, and 10% random sample of HC2 HPV-negatives were genotyped using the PGMY09/11 L1 consensus-primer PCR to amplify HPV DNA, and reverse hybridization technique (Roche Molecular Systems, Pleasanton, CA) to detect 37 HPV genotypes 13;14.

HPV-DNA testing by HC2

HC2 is a FDA approved, commercially available HPV test which collectively detects 13 carcinogenic HPV types (HPV 16,18,31,33,35,39,45,51,52,56,58,59, and 68) without distinguishing the HPV genotype. HC2 is a signal amplification assay that uses antibody capture of HPV DNA and RNA probe hybrids and chemiluminescent signal detection. The HC2 assay was performed according to manufacturer's instructions on a 100 μl aliquot of each specimen, a strategy which preserved sufficient sample volume for the additional PCR-based analyses.

HPV-DNA testing by Roche-PCR line blot assay

DNA extraction

HPV genotyping was performed using the reverse line blot assay as previously described 14. Briefly 50μl of STM sample was denatured with 10× digestion buffer for 1 hour at 65°C followed by heat denaturation at 95°C for 10 minutes. DNA was precipitated with ethanol and ammonium acetate at -20°C overnight. After centrifugation at 21,000 g for 30 minutes at 4°C, DNA pellet was dried and re-suspended in 25 μl Tris-EDTA and stored at −20°C 12.

Five μl of DNA was amplified using the PGMY 09/11 system which co-amplifies HPV genotypes, and human β-globin internal control target in a single reaction 12-14. Genotypes were discriminated by hybridizing the biotinylated PCR products to a probe array (RMS Linear Array) developed by Roche Molecular Systems, Inc. (Alameda, CA) as described earlier which can differentiate between 37 HPV types 13.

Appropriate quality control samples were imbedded during the DNA purification, PCR, and genotype discrimination steps.

Statistical Analyses

Incidence of HR-HPV infection

Genotype-specific HPV incident infection was defined as a positive test result for that genotype not present at study baseline. Subsequently, the 13 HR-HPV (16,18,31,33,35,39,45,51,52,56,58,59, and 68) genotypes most associated with cervical cancer were combined into one outcome variable of ‘incidence of new carcinogenic HPV’ infection. Person-time methods were used to calculate the type-specific incidence density 1.

Univariate and multivariate Poisson regression was used to evaluate the effect of exposure variables on the risk of new HR-HPV infection. Incidence of any of the 13 HR-HPV, was measured as the number of new infections in a given time interval divided by the population at risk during the interval. The log of the HPV incidence rate is assumed to be linearly associated with the risk factors, and the model parameters, after exponentiation, can be interpreted as relative incidence, which is similar to the relative risk. Behavioral and demographic factors measured at every visit were entered into the models as time-dependent covariates. When subjects missed study visits, the exposures were treated as missing. The independent contribution of each exposure variable, after adjustment for the effects of the other covariates, was expressed as the adjusted relative incidence rate, or rate ratio.

Clearance of HR-HPV infection

Subjects included in the clearance analysis had to have been positive at least once for any of the 13 HR-HPV genotypes during their follow-up visits.

Methods for multiple failure-time data were used to evaluate the effect of covariates on the risk of type specific HR-HPV clearance. The unit of analysis for the carcinogenic HPV clearance is the HPV infection. Hence, individuals infected with multiple HPV genotypes could clear one but not another type and one or more clearance events could occur for the same individual. We first assigned clearance for each HPV genotype and then constructed an overall variable for combined clearance. We assumed clearance events to be unordered, which means that clearing one HPV type was independent on clearing another HPV type. We then used survival analysis methods to evaluate factors associated with type-specific HPV clearance. Time was measured from the first time a woman tested positive for a specific HPV type, and the event, type-specific HPV clearance, was defined as the first time a woman tested negative following a positive measurement. Those who never cleared the specific HPV type infection were administratively censored at the end of the study follow-up. Since it is not reasonable to assume that clearance of each HPV type should have the same baseline hazard, the Cox model was stratified by each HPV type. Relative hazards below one indicate lower clearance.


Incidence of carcinogenic HPV infection

One thousand seventy nine women contributed 2954 visits for the incidence analysis. The median number of visits per person was 3, with an interquartile range (IQR) of 2-4 visits. There were 24 women with only one visit who were excluded from this analysis leaving 1055 women in the analytic sample.

When we compared the analytic sample to all women in the Rakai cohort (n=6520) at the HPV study baseline visit, we observed significant differences in certain characteristics suggesting that the analytic sample had a lower risk profile for HPV infection. Women in the analytic sample were slightly younger (median age 28, IQR: 23-36) compared to those not in the analytic sample (median age 29: IQR 22-40) (p=0.005), less likely to be HIV+ compared to others (14% vs. 21%, p=<0.0001), more likely to be currently married (75% vs. 63%, p=<0.0001) and with fewer numbers of lifetime sexual partners (p=<0.0001) (data not shown). Thus the analytic sample had a lower risk profile than the general population.

Table 1 shows the univariate associations with new HR-HPV infections. Incidence was constatnt over time of observation, indicating that there were no temporal trends over the study duration. HR-HPV incidence was highest among younger women, and decreased with age. There were no associations with education. Married women had a lower incidence of HR-HPV infection compared to single women. Incidence was lower among gravid women, and decreased among multigravid (6 or more pregnancies) compared to nulligravid women. Incidence was higher among never pregnant women; however, this was due to confounding by single marital status.

Table 1
Factors associated with HR-HPV incidence: Crude and Adjusted Rates

HIV-positive women were at a significantly elevated risk of new HR-HPV infection compared to HIV-negative women (RR=2.48, CI: 1.79-3.43). Self-reported numbers of current STD symptoms, or self-reported general health symptoms were not associated with new HR-HPV infection (table 1).

Age at first sex was not associated with new HR-HPV infection (table 1), while HR-HPV incidence was significantly elevated among women who reported 2, and 3 or more lifetime sexual partners (RR=1.86 CI: 1.19-2.91 and 2.06, CI 1.36-3.13, respectively), compared to women with none or 1 lifetime partners. Incidence was marginally elevated among women with 2 or more sex partners in the past year. Women who perceived themselves or their partner to be at high risk for HIV/AIDS infection were more likely to have new HR-HPV infection. Drinking alcohol was not associated with incident HR-HPV.

Risk factors associated with new HR-HPV infections in the univariate analyses were evaluated in multivariate models (Table 1). After adjustment, risk of incident HR-HPV was significantly increased with younger age, HIV-infection, unmarried women, 2 and 3 or more lifetime sex partners, and two or more partners in the past year. Women who perceived their recent partner to be at high risk for HIV/AIDS infection were more likely to have new HR-HPV infection.

Table 2 shows incidence rates for the 13 HR-HPVs individually and combined. HPV51 had the highest incidence rate, followed by HPV16, while HPV 31 and 35 had the lowest incidence rates. A total of 178 new HR-HPV infections were observed during 2054 person years of observation, reflecting an incidence rate of 8.7 per 100 person years. Stratifying by HIV serostatus, among 8 of the 13 HR-HPV types, the risk of a new infection was significantly greater among HIV-positive compared to HIV-negative women (types 16, 18, 35, 45, 51, 58, 59 and 68). The highest incidence rate ratio comparing HIV-positive to HIV-negative women was observed for HPV58. The risk of a new HPV infection was significantly higher among HIV-positives (17.3/100 PY) compared to HIV-negative (7.0/100 PY) women (p<0.0001).

Table 2
Type-specific HR-HPV incidence - overall and HIV-stratified

Clearance of HPV infections

One hundred and ninety five HPV positive women contributed 389 observations (the unit of analysis is type-specific HPV infections), and 465 person times for analysis of viral clearance. Two hundred and forty nine of the infections cleared over the follow-up period (53.55%).

Table 3 presents findings of univariate findings of factors associated with HPV clearance. Women over 30 were less likely to clear infections compared to women 15-29 years. Women with higher education were more likely to clear infection compared to those with no education, as were currently married women. Ever pregnancy and gravidity were not associated with clearance in univariate analyses.

Table 3
Factors associated with HR-HPV clearance - Crude and Adjusted Rates

HIV-positive women were significantly less likely to clear infection compared to HIV-negative women (RR 0.70, CI: 0.56-0.87). Clearance was not associated with symptoms suggestive of STDs, AIDS, opportunistic infections, or infection with multiple HPV types (Table 4). Women with greater HPV shedding as indicated by the higher RLU (based on HC2 assays) were less likely to clear their infection compared to those in the lowest RLU.

Table 4
Clearance rate for the 13 HR-HPV types (unit of analysis is infections)

Clearance rates were lower in women who reported 2, or more than 3 lifetime partners compared to women with 1 lifetime sex partner (RR=0.77 and 0.79, respectively). There were no associations with age at first sex, recent sex partners, AIDS perception or drinking.

In multivariate analysis (Table 3), HIV-positive women were less likely to clear their infection (ARR: 0.75, CI: 0.59-0.96) compared to HIV-negatives, as were women over 30 years compared to women 29 years or younger (ARR=0.84, CI: 0.68-1.02). Clearance was also reduced in women reporting 2 or more lifetime partners, and among women with higher HPV viral burden. Women with secondary or higher education were more likely to clear their infection. Stratified analysis by HIV-status showed that among HIV-positives, higher HPV viral burden and higher number of lifetime sexual partners and age (marginal effect) were associated with lower clearance. However, among HIV-negatives, age was associated with a marginal decrease in clearance, but having education was associated with higher clearance (data not shown).

Table 4 presents clearance rates for the 13 different HR-HPV types. Highest clearance rates were observed for HPV18, HPV68, followed by HPV39. Lowest clearance occurred for HPV31 and HPV35, followed by HPV16. Stratifying by HIV status, for almost all viral types (with the exception of HPV56), we observed lower clearance rate among HIV-positive compared to HIV-negative women, HPV33 achieved statistical significance after adjusting for age and lifetime number of sexual partners.


Data on the epidemiology of HPV from resource poor countries are sparse, mainly due to lack of longitudinal studies. A constraint on performing these studies has been recruiting and retaining participants to studies which require pelvic examination for collection of cervical specimens. This analysis based on self-collected vaginal swabs demonstrated that HR-HPV incidence and clearance from a rural community in Uganda mirrors studies of the epidemiology of HPV based on cervical samples. These findings have important implications for future longitudinal studies in settings where resource constraints limit pelvic exams, and most importantly, where women are reluctant to participate in studies that rely on pelvic exams for data collection 6;7;25;30.

We were comfortable using self-collected vaginal swab to determine the epidemiology of HPV, because in an earlier paper we validated HPV DNA detection from self-collected vaginal swabs to physician-collected cervical swabs showing very good agreement between vaginal and cervical DNA detection 31.

Similar to other studies, we found younger age, higher number of recent and lifetime sex partners to be significant risk factors for new HPV infection 9;19. Younger age reflects onset of sexual activity as well as limited acquired immunity. The association of recent numbers of sexual partners with incident detection of HR-HPV suggests that part of the new infections are due to sexual behavior, however, the association of higher numbers of lifetime sexual partners with incident infection suggests that part of the new infections may be due to reactivated past infections. Married women had lower risk of new HPV infection compared to single women and women with high perception of their partner's AIDS risk were more likely to be at risk of new HPV infection. This may be a marker of the participant or her partner's sexual behaviors that were not directly measured or were misreported.

HIV-positive women were twice as likely to have a new HR-HPV infection in accord with published studies from US and Europe 3;40. With the exception of HPV31 and 33, the incident rate ratios for the other 11 HR-HPVs ranged from 1.5 to 6 times higher among HIV-positives compared to HIV-negatives (HPV 52 and 58, respectively). The incidence rate ratio for HPV16 was 2.7 among HIV-positive compared to HIV-negative women, similar to findings by Strickler 38 suggesting that HPV16 may be weakly associated with immune status in HIV-positive women compared to other types, and be better at evading the immune system, which can lead to higher persistence and its stronger association with cervical cancer.

HPV 31, 35, and 16 had the lowest clearance rates as reported in other studies 24;28. Similar to other studies 3;37;39, we observed lower HPV clearance rates among HIV-positive women compared to HIV-negative women. We found HPV viral burden to be associated with lower clearance, and this was highly significant among HIV-positive women. This may be an indication of the damage by HIV to the immune system and its inability to perform normally. Furthermore, higher HPV viral load is also associated with worse cytopathology, and hence could be an indication of higher grade cervical lesions among HIV-positive women. However, while we did not have pathology on all women, among those with colposcopy (and biopsy if it was indicated), we observed more lesions among HIV-positives than negatives. Additionally we found that age affected HPV clearance: women over 30 were less likely to clear an infection compared with women younger than 30 years, consistent with findings of other studies 3;17;19. We also found that women with more lifetime sex partners were less likely to clear their HPV infection. A similar finding was observed by Shew 36 among adolescents. This is suggestive of multiple past exposures, or reactivated infections acquired earlier, which may be less prone to clearance.

Interpretations of our results should take into account some limitations. Our application of the HC2 assay to all samples, followed by genotyping of all HC2-positive and 10% randomly selected HC2-negatives, assumed that HC2 detected all 13 HPV types in its probe with reasonable accuracy. We found 8% HC2-negative samples were PCR-positive, which could have resulted in an underestimation of the true incidence and clearance of HR-HPV. Differential virus quantity used in HC2 and line-blot assays, or variations in the laboratory techniques could be possible explanation for the discordant results between HC2 and line-blot assay. To minimize differences due to laboratory practices, and ensure quality control, one person (MS) performed all laboratory assays, and negative controls cell lines were included for DNA isolation and positive and negative controls were included in the PCR and genotyping procedures. Reasons for differences between HC2 and line-blot warrant further investigation.

Further, all factors found to be associated with HPV infection in other studies were not measured in this study. We could not assess the effect of CD4 cell counts and HIV viral load on incidence and clearance of HPV. Additionally because no women were using oral contraceptives or smoking cigarettes in this analysis, we could not assess their effects on incidence or clearance. Specific to the incidence and clearance analysis, some women may have acquired or lost their infection in between study visits which could lead to underestimation of incidence or overestimation of duration of infection. With regard to the latter, our objective was not to report on the duration of infection, but rather to characterize women who cleared their infection.

Because the epidemiology of HPV as measured by incidence and clearance in this representative rural Ugandan population was similar to studies which relied on cervical sampling, recruitment and retention of women for natural history studies of HPV may be increased by self-collection as an alternate to clinician-collected cervical specimens. In settings where obtaining the necessary data for the natural history of HPV poses a challenge for researchers, self-collection can provide a reliable method for obtaining samples and may be adopted in trials to increase compliance and reduce costs associated with conducting pelvic exams. Moreover, determining the effectiveness of vaccines in resource poor and HIV endemic countries is dependent on knowledge of natural history and epidemiology of HPV and can provide an important tool for future research or vaccine evaluation.


Sources of Support: We thank the Roche Diagnostics for providing the reagents and line blots for the genotyping assay, and Digene Corporation for providing the HC2 probe B kits at reduced costs. Mahboobeh Safaeian received the Fogarty HIV Associated Malignancies, New and Minority Investigator Award, Fogarty AIDS Training and Research Program, the Johns Hopkins University. She was also supported by the STI Training Grant NIH/NIAID T32AI50056.


Presented at 23rd International Papillomavirus Conference, Prague, Czech Republic, September 2006.

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