cervical tissue biopsy raw sequence reads
The prevalence of invasive cervical cancer (ICC) is high in Nigeria, with over 12,000 new cases responsible for over 8,000 deaths of women annually. Measuring HPV prevalence has generated inconsistent findings, due to variations in population demographics across regions and differences in diagnostic methods. We examined the distribution and prevalence of HPV genotypes among HIV-positive and HIV-negative women with and without ICC in Nigeria. We utilized baseline data and DNA samples from cervical tissue obtained from a prospective cohort study between March 2018 and September 2022. High-throughput next-generation amplicon sequencing of the HPV L-1 gene was used to identify and classify HPV genotypes. Logistic regression models estimated associations between HIV and HPV astatus, adjusting for other variables of interest. Among 286 women tested for HPV, X were HIV negative with ICC; Y were HIV positive with ICC; and Z were HIV positive without ICC. The prevalence of HR-HPV was 77.6% among HIV-positive women with ICC compared to 60.0% among HIV-negative women with ICC (p < 0.001). HIV-positive women more frequently had multiple HPV infections at 8.2%, compared to 1.4% among HIV-negative women with ICC and 2.1% HIV negative women without ICC (p < 0.001). HPV16 or HPV18 accounted for 65.1% (95% CI: 56.4, 72.9) of all HPV. The commonest HR-HPV detected included HPV16 (45.8%), HPV18 (19.4%), HPV45 (9.3%), and HPV35 (6.2%). In multivariable models, adjusting for age, BMI, education, parity, and study site, compared to HIV negative women, HIV-positive women more frequently had HR-HPV (odds ratio (OR) 3.26, 95% CI: 1.44, 7.35; p = 0.004) and any HPV infection (OR=3.87, 95% CI: 2.71, 5.04; p < 0.001). HIV-positive women had the highest prevalence of HR-HPV and were associated with increased odds of testing positive for HPV infection, highlighting the importance of understanding how long-term HIV infection may promote cervical cancer development.