Superior Analytical Specificity of APTIMA mRNA HPV Testing over DNA Assays in a Resource-Limited South African Setting

Cervical cancer remains a leading cause of cancer-related morbidity and mortality among women in sub-Saharan Africa, where screening access is limited. It is mainly caused by persistent high-risk human papillomavirus (HR-HPV) infection, making HPV testing in screening programs imperative. The widely used DNA-based assays cannot distinguish transient from active infections, thus reducing specificity and risking overtreatment. In contrast, mRNA-based assays like APTIMA® detect E6/E7 transcripts, markers of active, likely persistent infections and improve clinical relevance. This cross-sectional study compared mRNA and DNA assay performance and characterized circulating HPV genotypes in a South African population to inform screening approaches in resource-limited settings. 527 cervical samples collected from women at a South African tertiary hospital were tested for HPV infections using two DNA assays (Abbott RealTime High-Risk HPV, Seegene Allplex™ II HPV28) and one mRNA assay (APTIMA® HPV). APTIMA® had the highest specificity (86.2%) and sensitivity (89.9%), outperforming Seegene (81.6%, 82.3%) and demonstrating stronger agreement with Abbott (Cohen’s Kappa = 0.80 vs. 0.70). ROC analysis confirmed APTIMA’s improved discrimination (AUC 0.8804 vs. 0.8681). Although Seegene detected more infections, many were likely transient and clinically insignificant. Findings support mRNA-based testing to better target high-risk women and reduce unnecessary interventions in resource-limited, high-burden settings.