Genetic Diversity of Human Papillomavirus and Comparative Analysis of Conventional and Molecular Screening Methods for Cervical Precancer among Women in Nakuru County Referral and Teaching Hospital, Kenya

Abstract

Background: Cervical cancer remains a consequential global public health challenge, mainly driven by persistent human papillomavirus (HPV) infection. In low-resource contexts such as Nakuru County, Kenya, incidence and mortality rates are high, with conventional screening methods such as visual inspection with acetic acid (VIA) and Lugol's iodine (VILI) restricted by variable sensitivity and specificity. Molecular HPV testing delivers superior accuracy but requires further evaluation in such contexts. This study examined HPV genetic diversity and compared the accuracy of conventional (VIA/VILI) and molecular HPV screening methods among women aged 25–55 at Nakuru County Hospital. It focused on HPV prevalence, test sensitivity and specificity, and factors affecting diagnostic differences, aiming to improve cervical precancer detection. Methodology: A prospective cross-sectional laboratory-based study was conducted at the Nakuru County Teaching and Referral Hospital between July and September 2024. A total of 123 women aged 25–55 years presenting for cervical cancer screening were recruited. Cervical specimens were collected following VIA and VILI procedures and subsequently subjected to HPV DNA testing. Nucleic acids were extracted and analyzed using the GeneXpert molecular platform to detect and identify high-risk HPV genotypes. Laboratory workflow included specimen collection, preservation, nucleic acid extraction, molecular amplification, and automated interpretation of results. Genotypic distribution, detection accuracy, and strain-specific profiles were assessed. Data on demographic and clinical characteristics and HPV test outcomes were recorded. Analytical performance parameters, including sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV), were computed. Comparative diagnostic performance was evaluated using the McNemar test, and multivariate logistic regression was performed to identify factors associated with diagnostic accuracy. Ethical approval was obtained from the Institutional Research Ethics Committee (IREC) of the University of Eastern Africa, Baraton (Approval No. UEAB/ISREC/02/2024, issued June 20, 2024). Regulatory clearance was also granted by the National Commission for Science, Technology, and Innovation (NACOSTI License No. NACOSTI/P/24/337222) and the Nakuru County Department of Health. All participants provided written informed consent, participation was voluntary, and confidentiality and anonymity were strictly maintained throughout the study. Results: HPV positivity was 24%, with predominant high-risk genotypes 16, 18, and 45. The Shannon-Weaver diversity index highlighted moderate genetic diversity Index (H′) of 1.513. VIA sensitivity stood at 60.5% and specificity 94.1%; VILI sensitivity was 68.2% and specificity 96.4%, using HPV testing as the gold standard. Ages 36-45 years and history of sexually transmitted infections (STIs) were significantly associated with HPV positivity (p < 0.05). The null hypothesis of diagnostic homogeneity was rejected, a confirmation of significant variability. Conclusions: Molecular HPV testing outperforms conventional methods in sensitivity and reliability for detecting high-risk HPV in low-resource settings. Recommendations: Need to integrate molecular diagnostics into national cervical cancer programs, expand HPV vaccination, and enhance community awareness. Future research ought to focus on cost-effective implementation and longitudinal studies on HPV persistence.